An Introduction to Microbiomes

1. Apprill, A. (2017). Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean. Frontiers in Marine Science, 4, 222. https://doi.org/10.3389/fmars.2017.00222
2. Arif, I., Batool, M., & Schenk, P. M. (2020). Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience. Trends in Biotechnology, 38(12), 1385–1396. https://doi.org/10.1016/j.tibtech.2020.04.015
3. Backhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12:611–22. https://doi.org/10.1016/j.chom.2012.10.012
4. Baedke, J., Fábregas-Tejeda, A., & Nieves Delgado, A. (2020). The holobiont concept before Margulis. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 334(3), 149–155. https://doi.org/10.1002/jez.b.22931
5. Bashiardes S, Zilberman-Schapira G, Elinav E. Use of Metatranscriptomics in Microbiome Research. Bioinformatics and Biology Insights. January 2016. doi:10.4137/BBI.S34610
6. Berg, G., Rybakova, D., Fischer, D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020). https://doi.org/10.1186/s40168-020-00875-0
7. Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. (2017) Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol 15(3): e2001793. https://doi.org/10.1371/journal.pbio.2001793
8. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. Gut Microbiota’s Effect on Mental Health: The Gut-Brain Axis. Clinics and Practice. 2017; 7(4):131-136. https://doi.org/10.4081/cp.2017.987
9. Cryan, J. F., O’Riordan, K. J., Cowan, C. S. M., Sandhu, K. v, Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. v, Guzzetta, K. E., Jaggar, M., Long-Smith, C. M., Lyte, J. M., Martin, J. A., Molinero-Perez, A., Moloney, G., Morelli, E., Morillas, E., … Dinan, T. G. (2019). The Microbiota-Gut-Brain Axis. Physiological Reviews, 99(4), 1877–2013. https://doi.org/10.1152/physrev.00018.2018
10. Diakite, A., Dubourg, G., Dione, N. et al. Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep 10, 9674 (2020). https://doi.org/10.1038/s41598-020-66738-8
11. Elhady, A., Adss, S., Hallmann, J., & Heuer, H. (2018). Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes. Frontiers in Microbiology, 9, 1133. https://www.frontiersin.org/article/10.3389/fmicb.2018.01133
12. Daliri, E. B., Wei, S., Oh, D. H., & Lee, B. H. (2017). The human microbiome and metabolomics: Current concepts and applications. Critical reviews in food science and nutrition, 57(16), 3565–3576. https://doi.org/10.1080/10408398.2016.1220913
13. Foster, J. A., Rinaman, L., & Cryan, J. F. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress, 7, 124–136. https://doi.org/https://doi.org/10.1016/j.ynstr.2017.03.001
14. Garrett W. S. (2015). Cancer and the microbiota. Science (New York, N.Y.), 348(6230), 80–86. https://doi.org/10.1126/science.aaa4972
15. Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. v, & Knight, R. (2018). Current understanding of the human microbiome. Nature Medicine, 24(4), 392–400. https://doi.org/10.1038/nm.4517
16. Grice, E., Segre, J. The skin microbiome. Nat Rev Microbiol 9, 244–253 (2011). https://doi.org/10.1038/nrmicro2537
17. Hannula, S., Morriën, E., de Hollander, M. et al. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 11, 2294–2304 (2017). https://doi.org/10.1038/ismej.2017.90
18. Hernández-Álvarez, C., García-Oliva, F., Cruz-Ortega, R., Romero, M. F., Barajas, H. R., Piñero, D., & Alcaraz, L. D. (2022). Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. Science of The Total Environment, 805, 150136. https://doi.org/https://doi.org/10.1016/j.scitotenv.2021.150136
19. Hirt, H. (2020). Healthy soils for healthy plants for healthy humans. EMBO Reports, 21(8), e51069. https://doi.org/https://doi.org/10.15252/embr.202051069
20. Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., Patterson, P. H., & Mazmanian, S. K. (2013). Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell, 155(7), 1451–1463. https://doi.org/10.1016/j.cell.2013.11.024
21. Lin, H., He, Q. Y., Shi, L., Sleeman, M., Baker, M. S., & Nice, E. C. (2019). Proteomics and the microbiome: pitfalls and potential. Expert review of proteomics, 16(6), 501–511. https://doi.org/10.1080/14789450.2018.1523724
22. Human Microbiome Project / Program Initiatives. The NIH Common Fund. Retrieved 9 September 2021. https://commonfund.nih.gov/hmp/initiatives
23. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, et al. Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214. https://doi.org/10.1038/nature11234
24. Integrative HMP (iHMP) Research Network Consortium (2014). The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell host & microbe, 16(3), 276–289. https://doi.org/10.1016/j.chom.2014.08.014
25. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7;21(29):8787-803. doi: 10.3748/wjg.v21.i29.8787. PMID: 26269668; PMCID: PMC4528021. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528021/
26. Jansson, J. K., & Hofmockel, K. S. (2018). The soil microbiome—from metagenomics to metaphenomics. Current Opinion in Microbiology, 43, 162–168. https://doi.org/10.1016/j.mib.2018.01.013
27. Jiang, D., Armour, C. R., Hu, C., Mei, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019). Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in genetics, 10, 995. https://doi.org/10.3389/fgene.2019.00995
28. Lederberg J, Mccray AT. `Ome Sweet `Omics–A genealogical treasury of words. The Scientist. 2001;15(7):8–8. https://lhncbc.nlm.nih.gov/LHC-publications/pubs/OmeSweetOmicsAGenealogicalTreasuryofWords.html
29. Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, et al. (2013) Probiotic Bacteria Induce a ‘Glow of Health’. PLoS ONE 8(1): e53867. https://doi.org/10.1371/journal.pone.0053867
30. Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med 8, 51 (2016). https://doi.org/10.1186/s13073-016-0307-y
31. Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3, 31. https://doi.org/10.1186/s40168-015-0094-5
32. Margulis L. Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. In: Cambridge MA MLFR, editor. Symbiogenesis and Symbionticism: MIT Press; 1991. p. 1–14.
33. NIH Human Microbiome Project – About the Human Microbiome. https://hmpdacc.org/ihmp/overview/. Retrieved 9 September 2021.
34. O’Neill, C.A., Monteleone, G., McLaughlin, J.T. and Paus, R. (2016), The gut-skin axis in health and disease: A paradigm with therapeutic implications. BioEssays, 38: 1167-1176. https://doi.org/10.1002/bies.201600008
35. Petersen, C., & Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cellular microbiology, 16(7), 1024–1033. https://doi.org/10.1111/cmi.12308
36. Pratama, A. A., & van Elsas, J. D. (2018). The ‘Neglected’ Soil Virome – Potential Role and Impact. Trends in Microbiology, 26(8), 649–662. https://doi.org/https://doi.org/10.1016/j.tim.2017.12.004
37. Rosenberg, E. and Zilber-Rosenberg, I. (2011), Symbiosis and development: The hologenome concept. Birth Defects Research Part C: Embryo Today: Reviews, 93: 56-66. https://doi.org/10.1002/bdrc.20196
38. Saleem, M., Hu, J., & Jousset, A. (2019). More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. Annual Review of Ecology, Evolution, and Systematics, 50(1), 145–168. https://doi.org/10.1146/annurev-ecolsys-110617-062605
39. Salem I, Ramser A, Isham N and Ghannoum MA (2018) The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Front. Microbiol. 9:1459. doi: 10.3389/fmicb.2018.01459
40. Sender R, Fuchs S, Milo R (2016) Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 14(8): e1002533. https://doi.org/10.1371/journal.pbio.1002533
41. Simon, JC., Marchesi, J.R., Mougel, C. et al. Host-microbiota interactions: from holobiont theory to analysis. Microbiome 7, 5 (2019). https://doi.org/10.1186/s40168-019-0619-4
42. The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature 569, 641–648 (2019). https://doi.org/10.1038/s41586-019-1238-8
43. Trompette, A., Gollwitzer, E. S., Yadava, K., Sichelstiel, A. K., Sprenger, N., Ngom-Bru, C., Blanchard, C., Junt, T., Nicod, L. P., Harris, N. L., & Marsland, B. J. (2014). Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nature medicine, 20(2), 159–166. https://doi.org/10.1038/nm.3444
44. Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project. Nature 449, 804–810 (2007). https://doi.org/10.1038/nature06244
45. Whipps J, Lewis K, Cooke R. Mycoparasitism and plant disease control. In: Burge M, editor. Fungi Biol Control Syst. Manchester University Press; 1988. p. 161-187.
46. Zhong, W., Yian, G., Ville-Petri, F., A, K. G., Yangchun, X., Qirong, S., & Alexandre, J. (2021). Initial soil microbiome composition and functioning predetermine future plant health. Science Advances, 5(9), eaaw0759. https://doi.org/10.1126/sciadv.aaw0759

Analyzing Microbiomes

1. Allaband, C., McDonald, D., Vázquez-Baeza, Y., Minich, J. J., Tripathi, A., Brenner, D. A., Loomba, R., Smarr, L., Sandborn, W. J., Schnabl, B., Dorrestein, P., Zarrinpar, A., & Knight, R. (2019). Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clinical Gastroenterology and Hepatology, 17(2), 218–230. https://doi.org/https://doi.org/10.1016/j.cgh.2018.09.017
2. Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016). Use of Metatranscriptomics in Microbiome Research. Bioinformatics and Biology Insights, 10, BBI.S34610. https://doi.org/10.4137/BBI.S34610
3. Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. v, Jarmusch, A. K., & Dorrestein, P. C. (2021). Mass spectrometry-based metabolomics in microbiome investigations. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-021-00621-9
4. Bharti, R., & Grimm, D. G. (2021). Current challenges and best-practice protocols for microbiome analysis. Briefings in Bioinformatics, 22(1), 178–193. https://doi.org/10.1093/bib/bbz155
5. Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., Gordon, J. I., & Knight, R. (2011). Moving pictures of the human microbiome. Genome Biology, 12(5), R50. https://doi.org/10.1186/gb-2011-12-5-r50
6. Chen, I.-M. A., Chu, K., Palaniappan, K., Ratner, A., Huang, J., Huntemann, M., Hajek, P., Ritter, S., Varghese, N., Seshadri, R., Roux, S., Woyke, T., Eloe-Fadrosh, E. A., Ivanova, N. N., & Kyrpides, N. C. (2021). The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Research, 49(D1), D751–D763. https://doi.org/10.1093/nar/gkaa939
7. Chong, J., Liu, P., Zhou, G., & Xia, J. (2020). Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nature Protocols, 15(3), 799–821. https://doi.org/10.1038/s41596-019-0264-1
8. Costello, E. K., L, L. C., Micah, H., Noah, F., I, G. J., & Rob, K. (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time. Science, 326(5960), 1694–1697. https://doi.org/10.1126/science.1177486
9. de Cárcer, D. A., Cuív, P. Ó., Wang, T., Kang, S., Worthley, D., Whitehall, V., Gordon, I., McSweeney, C., Leggett, B., & Morrison, M. (2011). Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon. The ISME Journal, 5(5), 801–809. https://doi.org/10.1038/ismej.2010.177
10. Dhariwal, A., Chong, J., Habib, S., King, I. L., Agellon, L. B., & Xia, J. (2017). MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Research, 45(W1), W180–W188. https://doi.org/10.1093/nar/gkx295
11. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005). Diversity of the Human Intestinal Microbial Flora. Science, 308(5728), 1635–1638. https://doi.org/10.1126/science.1110591
12. Findley, K., & Grice, E. A. (2014). The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease. PLOS Pathogens, 10(11), e1004436-. https://doi.org/10.1371/journal.ppat.1004436
13. Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., & Huttenhower, C. (2014). Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences, 111(22), E2329. https://doi.org/10.1073/pnas.1319284111
14. Giannoukos, G., Ciulla, D. M., Huang, K., Haas, B. J., Izard, J., Levin, J. Z., Livny, J., Earl, A. M., Gevers, D., Ward, D. v, Nusbaum, C., Birren, B. W., & Gnirke, A. (2012). Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biology, 13(3), r23. https://doi.org/10.1186/gb-2012-13-3-r23
15. Gloor, G. B., Wu, J. R., Pawlowsky-Glahn, V., & Egozcue, J. J. (2016). It’s all relative: analyzing microbiome data as compositions. Annals of Epidemiology, 26(5), 322–329. https://doi.org/10.1016/j.annepidem.2016.03.003
16. Gonzalez, A., Navas-Molina, J. A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A. D., Orchanian, S. B., Sanders, J. G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C. J., Wang, M., Rideout, J. R., Bolyen, E., … Knight, R. (2018). Qiita: rapid, web-enabled microbiome meta-analysis. Nature Methods, 15(10), 796–798. https://doi.org/10.1038/s41592-018-0141-9
17. Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez-Hernández, N., Pérez-Cobas, A. E., Latorre, A., & Moya, A. (2011). Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota. PLOS ONE, 6(3), e17447-. https://doi.org/10.1371/journal.pone.0017447
18. Iorio, A., Biazzo, M., Gardini, S., Muda, A. O., Perno, C. F., Dallapiccola, B., & Putignani, L. (2022). Cross-correlation of virome–bacteriome–host–metabolome to study respiratory health. Trends in Microbiology, 30(1), 34–46. https://doi.org/10.1016/j.tim.2021.04.011
19. Jiang, D., Armour, C. R., Hu, C., Mei, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019). Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in Genetics, 10. https://www.frontiersin.org/article/10.3389/fgene.2019.00995
20. Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J.-F., Koonin, E. v, la Scola, B., & Raoult, D. (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18(12), 1185–1193. https://doi.org/https://doi.org/10.1111/1469-0691.12023
21. Lee-Sarwar KA, Lasky-Su J, Kelly RS, Litonjua AA, Weiss ST. Metabolome–Microbiome Crosstalk and Human Disease. Metabolites. 2020; 10(5):181. https://doi.org/10.3390/metabo10050181
22. Markowitz, V. M., Ivanova, N. N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.-M. A., Grechkin, Y., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Hugenholtz, P., & Kyrpides, N. C. (2008). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research, 36(suppl_1), D534–D538. https://doi.org/10.1093/nar/gkm869
23. McDonald, D., Embriette, H., W, D. J., T, M. J., Antonio, G., Gail, A., A, A. A., Bahar, B., Caitriona, B., Yingfeng, C., Lindsay, D. G., C, D. P., R, D. R., K, F. A., James, G., A, G. J., Grant, G., L, G. J., Philip, H., … Beau, G. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. MSystems, 3(3), e00031-18. https://doi.org/10.1128/mSystems.00031-18
24. Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A., & Finn, R. D. (2020). MGnify: the microbiome analysis resource in 2020. Nucleic Acids Research, 48(D1), D570–D578. https://doi.org/10.1093/nar/gkz1035
25. Nkrumah-Elie, Y., Elie, M., & Reisdorph, N. (2018). Chapter 14 – Systems Biology Approaches to Asthma Management. In S. J. Szefler, F. Holguin, & M. E. Wechsler (Eds.), Personalizing Asthma Management for the Clinician (pp. 151–160). Elsevier. https://doi.org/10.1016/B978-0-323-48552-4.00014-7
26. Rivera-Pinto, J., Egozcue, J. J., Pawlowsky-Glahn, V., Paredes, R., Noguera-Julian, M., Calle, M. L., & Catherine, L. (2022). Balances: a New Perspective for Microbiome Analysis. MSystems, 3(4), e00053-18. https://doi.org/10.1128/mSystems.00053-18
27. Sajulga, R., Easterly, C., Riffle, M., Mesuere, B., Muth, T., Mehta, S., Kumar, P., Johnson, J., Gruening, B. A., Schiebenhoefer, H., Kolmeder, C. A., Fuchs, S., Nunn, B. L., Rudney, J., Griffin, T. J., & Jagtap, P. D. (2020). Survey of metaproteomics software tools for functional microbiome analysis. PLOS ONE, 15(11), e0241503-. https://doi.org/10.1371/journal.pone.0241503
28. Sarhan, M. S., Hamza, M. A., Youssef, H. H., Patz, S., Becker, M., ElSawey, H., Nemr, R., Daanaa, H.-S. A., Mourad, E. F., Morsi, A. T., Abdelfadeel, M. R., Abbas, M. T., Fayez, M., Ruppel, S., & Hegazi, N. A. (2019). Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review. Journal of Advanced Research, 19, 15–27. https://doi.org/https://doi.org/10.1016/j.jare.2019.04.002
29. Schiebenhoefer, H., van den Bossche, T., Fuchs, S., Renard, B. Y., Muth, T., & Martens, L. (2019). Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Review of Proteomics, 16(5), 375–390. https://doi.org/10.1080/14789450.2019.1609944
30. Seng, P., Drancourt, M., Gouriet, F., la Scola, B., Fournier, P.-E., Rolain, J. M., & Raoult, D. (2009). Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry. Clinical Infectious Diseases, 49(4), 543–551. https://doi.org/10.1086/600885
31. Shakya, M., Lo, C.-C., & Chain, P. S. G. (2019). Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics, 10. https://www.frontiersin.org/article/10.3389/fgene.2019.00904
32. Wang, M., Carver, J. J., Phelan, V. v, Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. v, Meehan, M. J., Liu, W.-T., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., … Bandeira, N. (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828–837. https://doi.org/10.1038/nbt.3597
33. Watrous, J., Roach, P., Alexandrov, T., Heath, B. S., Yang, J. Y., Kersten, R. D., van der Voort, M., Pogliano, K., Gross, H., Raaijmakers, J. M., Moore, B. S., Laskin, J., Bandeira, N., & Dorrestein, P. C. (2012). Mass spectral molecular networking of living microbial colonies. Proceedings of the National Academy of Sciences, 109(26), E1743. https://doi.org/10.1073/pnas.120368910

Human Health and Disease

1. Dąbrowska, K., & Witkiewicz, W. (2016). Correlations of Host Genetics and Gut Microbiome Composition. Frontiers in Microbiology, 7, 1357. https://www.frontiersin.org/article/10.3389/fmicb.2016.01357
2. Kates, A. E., Jarrett, O., Skarlupka, J. H., Sethi, A., Duster, M., Watson, L., Suen, G., Poulsen, K., & Safdar, N. (2020). Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota. Frontiers in Cellular and Infection Microbiology, 10, 73. https://www.frontiersin.org/article/10.3389/fcimb.2020.00073
3. Kiecolt-Glaser, J. K., Wilson, S. J., & Madison, A. (2019). Marriage and Gut (Microbiome) Feelings: Tracing Novel Dyadic Pathways to Accelerated Aging. Psychosomatic Medicine, 81(8), 704–710. https://doi.org/10.1097/PSY.0000000000000647
4. Knights, D., Lassen, K. G., & Xavier, R. J. (2013). Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut, 62(10), 1505. https://doi.org/10.1136/gutjnl-2012-303954
5. Kurilshikov, A., Wijmenga, C., Fu, J., & Zhernakova, A. (2017). Host Genetics and Gut Microbiome: Challenges and Perspectives. Trends in Immunology, 38(9), 633–647. https://doi.org/https://doi.org/10.1016/j.it.2017.06.003
6. Martinez J., Showering, A., Oke, C., Jones, R. T., & Logan, J. G. (2020) Differential attraction in mosquito–human interactions and implications for disease control. Phil. Trans. R. Soc. B. Biol. Sci, 376(1818), 20190811. https://doi.org/10.1098/rstb.2019.0811
7. Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., Shilo, S., Lador, D., Vila, A. V., Zmora, N., Pevsner-Fischer, M., Israeli, D., Kosower, N., Malka, G., Wolf, B. C., … Segal, E. (2018). Environment dominates over host genetics in shaping human gut microbiota. Nature, 555(7695), 210–215. https://doi.org/10.1038/nature25973
8. Si, J., Lee, S., Park, J. M., Sung, J., & Ko, G. (2015). Genetic associations and shared environmental effects on the skin microbiome of Korean twins. BMC Genomics, 16(1), 992. https://doi.org/10.1186/s12864-015-2131-y
9. Silverman, G. J., Azzouz, D. F., & Alekseyenko, A. v. (2019). Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? Current Opinion in Immunology, 61, 80–85. https://doi.org/10.1016/j.coi.2019.08.007
10. Tabrett, A., & Horton, M. W. (2020). The influence of host genetics on the microbiome. F1000Research, 9, F1000 Faculty Rev-84. https://doi.org/10.12688/f1000research.20835.1
11. Woo, T. E., & Sibley, C. D. (2020). The emerging utility of the cutaneous microbiome in the treatment of acne and atopic dermatitis. Journal of the American Academy of Dermatology, 82(1), 222–228. https://doi.org/10.1016/j.jaad.2019.08.078

The Gut Microbiome

1. Abulizi, N., Quin, C., Brown, K., Chan, Y. K., Gill, S. K., & Gibson, D. L. (2019). Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids. Nutrients, 11(2). https://doi.org/10.3390/nu11020418
2. Arbuckle, M. R., McClain, M. T., Rubertone, M. v, Scofield, R. H., Dennis, G. J., James, J. A., & Harley, J. B. (2003). Development of Autoantibodies before the Clinical Onset of Systemic Lupus Erythematosus. New England Journal of Medicine, 349(16), 1526–1533. https://doi.org/10.1056/NEJMoa021933
3. Baker, S. S., Faden, H., Sayej, W., Patel, R., & Baker, R. D. (2010). Increasing Incidence of Community-Associated Atypical Clostridium difficile Disease in Children. Clinical Pediatrics, 49(7), 644–647. https://doi.org/10.1177/0009922809360927
4. Becattini, S., Taur, Y., & Pamer, E. G. (2016). Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends in Molecular Medicine, 22(6), 458–478. https://doi.org/10.1016/j.molmed.2016.04.003
5. Benson L, Song X, Campos J, Singh N. Changing epidemiology of Clostridium difficile-associated disease in children. Infect Control Hosp Epidemiol. 2007 Nov;28(11):1233-5. doi: 10.1086/520732. Epub 2007 Aug 27. PMID: 17926272.
6. Boulangé, C. L., Neves, A. L., Chilloux, J., Nicholson, J. K., & Dumas, M.-E. (2016). Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Medicine, 8(1), 42. https://doi.org/10.1186/s13073-016-0303-2
7. Camacho-Ortiz, A., Gutiérrez-Delgado, E. M., Garcia-Mazcorro, J. F., Mendoza-Olazarán, S., Martínez-Meléndez, A., Palau-Davila, L., Baines, S. D., Maldonado-Garza, H., & Garza-González, E. (2017). Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome. PLOS ONE, 12(12), e0189768-. https://doi.org/10.1371/journal.pone.0189768
8. Cammarota, G., Masucci, L., Ianiro, G., Bibbò, S., Dinoi, G., Costamagna, G., Sanguinetti, M., & Gasbarrini, A. (2015). Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection. Alimentary Pharmacology & Therapeutics, 41(9), 835–843. https://doi.org/10.1111/apt.13144
9. Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., Waget, A., Delmée, E., Cousin, B., Sulpice, T., Chamontin, B., Ferrières, J., Tanti, J.-F., Gibson, G. R., Casteilla, L., … Burcelin, R. (2007). Metabolic Endotoxemia Initiates Obesity and Insulin Resistance. Diabetes, 56(7), 1761. https://doi.org/10.2337/db06-1491
10. Clooney, A. G., Sutton, T. D. S., Shkoporov, A. N., Holohan, R. K., Daly, K. M., O’Regan, O., Ryan, F. J., Draper, L. A., Plevy, S. E., Ross, R. P., & Hill, C. (2019). Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease. Cell Host & Microbe, 26(6), 764-778.e5. https://doi.org/10.1016/j.chom.2019.10.009
11. Costello, M.-E., Ciccia, F., Willner, D., Warrington, N., Robinson, P. C., Gardiner, B., Marshall, M., Kenna, T. J., Triolo, G., & Brown, M. A. (2015). Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis. Arthritis & Rheumatology, 67(3), 686–691. https://doi.org/https://doi.org/10.1002/art.38967
12. Davenport, E. R., Mizrahi-Man, O., Michelini, K., Barreiro, L. B., Ober, C., & Gilad, Y. (2014). Seasonal Variation in Human Gut Microbiome Composition. PLOS ONE, 9(3), e90731-. https://doi.org/10.1371/journal.pone.0090731
13. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. v, Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559–563. https://doi.org/10.1038/nature12820
14. de Bandt, J.-P., Waligora-Dupriet, A.-J., & Butel, M.-J. (2011). Intestinal microbiota in inflammation and insulin resistance: relevance to humans. Current Opinion in Clinical Nutrition & Metabolic Care, 14(4). https://journals.lww.com/co-clinicalnutrition/Fulltext/2011/07000/Intestinal_microbiota_in_inflammation_and_insulin.5.aspx
15. DeFilipp, Z., Bloom, P. P., Torres Soto, M., Mansour, M. K., Sater, M. R. A., Huntley, M. H., Turbett, S., Chung, R. T., Chen, Y.-B., & Hohmann, E. L. (2019). Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant. New England Journal of Medicine, 381(21), 2043–2050. https://doi.org/10.1056/NEJMoa1910437
16. Everard, A., & Cani, P. D. (2013). Diabetes, obesity and gut microbiota. Best Practice & Research Clinical Gastroenterology, 27(1), 73–83. https://doi.org/10.1016/j.bpg.2013.03.007
17. Forbes, J. D., Bernstein, C. N., Tremlett, H., van Domselaar, G., & Knox, N. C. (2019). A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease? Frontiers in Microbiology, 9, 3249. https://www.frontiersin.org/article/10.3389/fmicb.2018.03249
18. Fujimoto, K., Kimura, Y., Allegretti, J. R., Yamamoto, M., Zhang, Y., Katayama, K., Tremmel, G., Kawaguchi, Y., Shimohigoshi, M., Hayashi, T., Uematsu, M., Yamaguchi, K., Furukawa, Y., Akiyama, Y., Yamaguchi, R., Crowe, S. E., Ernst, P. B., Miyano, S., Kiyono, H., … Uematsu, S. (2021). Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation. Gastroenterology, 160(6), 2089-2102.e12. https://doi.org/10.1053/j.gastro.2021.02.013
19. Gaulke, C. A., & Sharpton, T. J. (2018). The influence of ethnicity and geography on human gut microbiome composition. Nature Medicine, 24(10), 1495–1496. https://doi.org/10.1038/s41591-018-0210-8
20. George, R. H., Symonds, J. M., Dimock, F., Brown, J. D., Arabi, Y., Shinagawa, N., Keighley, M. R., Alexander-Williams, J., & Burdon, D. W. (1978). Identification of Clostridium difficile as a cause of pseudomembranous colitis. British Medical Journal, 1(6114), 695. https://doi.org/10.1136/bmj.1.6114.695
21. Giongo, A., Gano, K. A., Crabb, D. B., Mukherjee, N., Novelo, L. L., Casella, G., Drew, J. C., Ilonen, J., Knip, M., Hyöty, H., Veijola, R., Simell, T., Simell, O., Neu, J., Wasserfall, C. H., Schatz, D., Atkinson, M. A., & Triplett, E. W. (2011). Toward defining the autoimmune microbiome for type 1 diabetes. The ISME Journal, 5(1), 82–91. https://doi.org/10.1038/ismej.2010.92
22. Gu, Y., Zhou, G., Qin, X., Huang, S., Wang, B., & Cao, H. (2019). The Potential Role of Gut Mycobiome in Irritable Bowel Syndrome. Frontiers in Microbiology, 10, 1894. https://www.frontiersin.org/article/10.3389/fmicb.2019.01894
23. Halfvarson, J., Brislawn, C. J., Lamendella, R., Vázquez-Baeza, Y., Walters, W. A., Bramer, L. M., D’Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., McClure, E. E., Dunklebarger, M. F., Knight, R., & Jansson, J. K. (2017). Dynamics of the human gut microbiome in inflammatory bowel disease. Nature Microbiology, 2(5), 17004. https://doi.org/10.1038/nmicrobiol.2017.4
24. He, M., Miyajima, F., Roberts, P., Ellison, L., Pickard, D. J., Martin, M. J., Connor, T. R., Harris, S. R., Fairley, D., Bamford, K. B., D’Arc, S., Brazier, J., Brown, D., Coia, J. E., Douce, G., Gerding, D., Kim, H. J., Koh, T. H., Kato, H., … Lawley, T. D. (2013). Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nature Genetics, 45(1), 109–113. https://doi.org/10.1038/ng.2478
25. Hensgens, M. P. M., Keessen, E. C., Squire, M. M., Riley, T. v, Koene, M. G. J., de Boer, E., Lipman, L. J. A., & Kuijper, E. J. (2012). Clostridium difficile infection in the community: a zoonotic disease? Clinical Microbiology and Infection, 18(7), 635–645. https://doi.org/10.1111/j.1469-0691.2012.03853.x
26. Hoarau, G., Mukherjee, P. K., Gower-Rousseau, C., Hager, C., Chandra, J., Retuerto, M. A., Neut, C., Vermeire, S., Clemente, J., Colombel, J. F., Fujioka, H., Poulain, D., Sendid, B., Ghannoum, M. A., & A, B. R. (2021). Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. MBio, 7(5), e01250-16. https://doi.org/10.1128/mBio.01250-16
27. Jackson, M. A., Verdi, S., Maxan, M.-E., Shin, C. M., Zierer, J., Bowyer, R. C. E., Martin, T., Williams, F. M. K., Menni, C., Bell, J. T., Spector, T. D., & Steves, C. J. (2018). Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nature Communications, 9(1), 2655. https://doi.org/10.1038/s41467-018-05184-7
28. Jin, D., Wu, S., Zhang, Y., Lu, R., Xia, Y., Dong, H., & Sun, J. (2015). Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome. Clinical Therapeutics, 37(5), 996-1009.e7. https://doi.org/10.1016/j.clinthera.2015.04.004
29. Johanesen, P. A., Mackin, K. E., Hutton, M. L., Awad, M. M., Larcombe, S., Amy, J. M., & Lyras, D. (2015). Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance. Genes, 6(4), 1347–1360. https://doi.org/10.3390/genes6041347
30. Johnson, K. V.-A. (2020). Gut microbiome composition and diversity are related to human personality traits. Human Microbiome Journal, 15, 100069. https://doi.org/10.1016/j.humic.2019.100069
31. Kho, Z. Y., & Lal, S. K. (2018). The Human Gut Microbiome – A Potential Controller of Wellness and Disease. Frontiers in Microbiology, 9, 1835. https://www.frontiersin.org/article/10.3389/fmicb.2018.01835
32. Kim, S. K., Guevarra, R. B., Kim, Y. T., Kwon, J., Kim, H., Cho, J. H., Kim, H. B., & Lee, J. H. (2019). Role of Probiotics in Human Gut Microbiome-Associated Diseases. Journal of Microbiology and Biotechnology, 29(9), 1335–1340. https://doi.org/10.4014/jmb.1906.06064
33. Larsen, N., Vogensen, F. K., van den Berg, F. W. J., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010). Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults. PLOS ONE, 5(2), e9085-. https://doi.org/10.1371/journal.pone.0009085
34. Leber, A., Viladomiu, M., Hontecillas, R., Abedi, V., Philipson, C., Hoops, S., Howard, B., & Bassaganya-Riera, J. (2015). Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLOS ONE, 10(7), e0134849-. https://doi.org/10.1371/journal.pone.0134849
35. Lee, Y. K., Menezes, J. S., Umesaki, Y., & Mazmanian, S. K. (2011). Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proceedings of the National Academy of Sciences, 108(Supplement 1), 4615. https://doi.org/10.1073/pnas.1000082107
36. Magne, F., Gotteland, M., Gauthier, L., Zazueta, A., Pesoa, S., Navarrete, P., & Balamurugan, R. (2020). The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? Nutrients, 12(5). https://doi.org/10.3390/nu12051474
37. Martinez-Gili, L., McDonald, J. a K., Liu, Z., Kao, D., Allegretti, J. R., Monaghan, T. M., Barker, G. F., Miguéns Blanco, J., Williams, H. R. T., Holmes, E., Thursz, M. R., Marchesi, J. R., & Mullish, B. H. (2020). Understanding the mechanisms of efficacy of fecal microbiota transplant in treating recurrent Clostridioides difficile infection and beyond: the contribution of gut microbial-derived metabolites. Gut Microbes, 12(1), 1810531. https://doi.org/10.1080/19490976.2020.1810531
38. Mattila, E., Uusitalo–Seppälä, R., Wuorela, M., Lehtola, L., Nurmi, H., Ristikankare, M., Moilanen, V., Salminen, K., Seppälä, M., Mattila, P. S., Anttila, V., & Arkkila, P. (2012). Fecal Transplantation, Through Colonoscopy, Is Effective Therapy for Recurrent Clostridium difficile Infection. Gastroenterology, 142(3), 490–496. https://doi.org/https://doi.org/10.1053/j.gastro.2011.11.037
39. McDermott, A. J., & Huffnagle, G. B. (2014). The microbiome and regulation of mucosal immunity. Immunology, 142(1), 24–31. https://doi.org/https://doi.org/10.1111/imm.12231
40. McQuade, J. L., Ologun, G. O., Arora, R., & Wargo, J. A. (2020). Gut Microbiome Modulation Via Fecal Microbiota Transplant to Augment Immunotherapy in Patients with Melanoma or Other Cancers. Current Oncology Reports, 22(7), 74. https://doi.org/10.1007/s11912-020-00913-y
41. Mikuls, T. R., Thiele, G. M., Deane, K. D., Payne, J. B., O’Dell, J. R., Yu, F., Sayles, H., Weisman, M. H., Gregersen, P. K., Buckner, J. H., Keating, R. M., Derber, L. A., Robinson, W. H., Holers, V. M., & Norris, J. M. (2012). Porphyromonas gingivalis and disease-related autoantibodies in individuals at increased risk of rheumatoid arthritis. Arthritis & Rheumatism, 64(11), 3522–3530. https://doi.org/https://doi.org/10.1002/art.34595
42. Monaco, C. L., Gootenberg, D. B., Zhao, G., Handley, S. A., Ghebremichael, M. S., Lim, E. S., Lankowski, A., Baldridge, M. T., Wilen, C. B., Flagg, M., Norman, J. M., Keller, B. C., Luévano, J. M., Wang, D., Boum, Y., Martin, J. N., Hunt, P. W., Bangsberg, D. R., Siedner, M. J., … Virgin, H. W. (2016). Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host & Microbe, 19(3), 311–322. https://doi.org/https://doi.org/10.1016/j.chom.2016.02.011
43. Musso, G., Gambino, R., & Cassader, M. (2011). Interactions Between Gut Microbiota and Host Metabolism Predisposing to Obesity and Diabetes. Annual Review of Medicine, 62(1), 361–380. https://doi.org/10.1146/annurev-med-012510-175505
44. Nagpal, R., & Yadav, H. (2017). Bacterial Translocation from the Gut to the Distant Organs: An Overview. Annals of Nutrition and Metabolism, 71(suppl 1)(Suppl. 1), 11–16. https://doi.org/10.1159/000479918
45. Nagpal, R., Newman, T. M., Wang, S., Jain, S., Lovato, J. F., & Yadav, H. (2018). Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. Journal of Diabetes Research, 2018, 3462092. https://doi.org/10.1155/2018/3462092
46. Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., Stappenbeck, T. S., McGovern, D. P. B., Keshavarzian, A., Mutlu, E. A., Sauk, J., Gevers, D., Xavier, R. J., Wang, D., Parkes, M., & Virgin, H. W. (2015). Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell, 160(3), 447–460. https://doi.org/https://doi.org/10.1016/j.cell.2015.01.002
47. Ouwehand, A. C., Kirjavainen, P. v, Grönlund, M.-M., Isolauri, E., & Salminen, S. J. (1999). Adhesion of probiotic micro-organisms to intestinal mucus. International Dairy Journal, 9(9), 623–630. https://doi.org/10.1016/S0958-6946(99)00132-6
48. Qin, X., Gu, Y., Liu, T., Wang, C., Zhong, W., Wang, B., & Cao, H. (2021). Gut mycobiome: A promising target for colorectal cancer. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1875(1), 188489. https://doi.org/10.1016/j.bbcan.2020.188489
49. Reyes, A., Blanton, L. v, Cao, S., Zhao, G., Manary, M., Trehan, I., Smith, M. I., Wang, D., Virgin, H. W., Rohwer, F., & Gordon, J. I. (2015). Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proceedings of the National Academy of Sciences, 112(38), 11941. https://doi.org/10.1073/pnas.1514285112
50. Rogers, M. A. M., & Aronoff, D. M. (2016). The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection, 22(2), 178.e1-178.e9. https://doi.org/10.1016/j.cmi.2015.10.003
51. Rouphael, N. G., O’Donnell, J. A., Bhatnagar, J., Lewis, F., Polgreen, P. M., Beekmann, S., Guarner, J., Killgore, G. E., Coffman, B., Campbell, J., Zaki, S. R., & McDonald, L. C. (2008). Clostridium difficile–associated diarrhea: an emerging threat to pregnant women. American Journal of Obstetrics and Gynecology, 198(6), 635.e1-635.e6. https://doi.org/10.1016/j.ajog.2008.01.062
52. Shi, N., Li, N., Duan, X., & Niu, H. (2017). Interaction between the gut microbiome and mucosal immune system. Military Medical Research, 4(1), 14. https://doi.org/10.1186/s40779-017-0122-9
53. Shkoporov, A. N., & Hill, C. (2019). Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome. Cell Host & Microbe, 25(2), 195–209. https://doi.org/10.1016/j.chom.2019.01.017
54. Sohail, M. U., Althani, A., Anwar, H., Rizzi, R., & Marei, H. E. (2017). Role of the Gastrointestinal Tract Microbiome in the Pathophysiology of Diabetes Mellitus. Journal of Diabetes Research, 2017, 9631435. https://doi.org/10.1155/2017/9631435
55. Stewart, D. B., Wright, J., Maria, F., McLimans, C. J., Vasily, T., Isabella, A., Owen, B., Hoi-Tong, W., Jeff, B., Rebecca, D., Regina, L., & Rosa, K.-B. (2021). Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. MSphere, 4(4), e00454-19. https://doi.org/10.1128/mSphere.00454-19
56. Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008). Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome. Cell Host & Microbe, 3(4), 213–223. https://doi.org/10.1016/j.chom.2008.02.015
57. Xu, F., Fu, Y., Sun, T., Jiang, Z., Miao, Z., Shuai, M., Gou, W., Ling, C., Yang, J., Wang, J., Chen, Y., & Zheng, J.-S. (2020). The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. Microbiome, 8(1), 145. https://doi.org/10.1186/s40168-020-00923-9
58. Xu, Z., & Knight, R. (2015). Dietary effects on human gut microbiome diversity. British Journal of Nutrition, 113(S1), S1–S5. https://doi.org/DOI: 10.1017/S0007114514004127
59. Yan, A., Butcher, J., Mack, D., & Stintzi, A. (2020). Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface. Frontiers in Cellular and Infection Microbiology, 10, 593. https://www.frontiersin.org/article/10.3389/fcimb.2020.582187
60. Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–227. https://doi.org/10.1038/nature11053
61. Zhang, F., Zuo, T., Yeoh, Y. K., Cheng, F. W. T., Liu, Q., Tang, W., Cheung, K. C. Y., Yang, K., Cheung, C. P., Mo, C. C., Hui, M., Chan, F. K. L., Li, C.-K., Chan, P. K. S., & Ng, S. C. (2021). Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nature Communications, 12(1), 65. https://doi.org/10.1038/s41467-020-20240-x
62. Zou, Y., Ju, X., Chen, W., Yuan, J., Wang, Z., Aluko, R. E., & He, R. (2020). Rice bran attenuated obesity via alleviating dyslipidemia, browning of white adipocytes and modulating gut microbiota in high-fat diet-induced obese mice. Food & Function, 11(3), 2406–2417. https://doi.org/10.1039/C9FO01524H

The Oral Microbiome

1. Aas, J. A., Paster, B. J., Stokes, L. N., Ingar, O., & Dewhirst, F. E. (2005). Defining the Normal Bacterial Flora of the Oral Cavity. Journal of Clinical Microbiology, 43(11), 5721–5732. https://doi.org/10.1128/JCM.43.11.5721-5732.2005
2. Abnet, C. C., Qiao, Y.-L., Dawsey, S. M., Dong, Z.-W., Taylor, P. R., & Mark, S. D. (2005). Tooth loss is associated with increased risk of total death and death from upper gastrointestinal cancer, heart disease, and stroke in a Chinese population-based cohort. International Journal of Epidemiology, 34(2), 467–474. https://doi.org/10.1093/ije/dyh375
3. Acs, G., Shulman, R., Ng, M. W., & Chussid, S. (1999). The effect of dental rehabilitation on the body weight of children with early childhood caries. Pediatric dentistry, 21(2), 109–113.
4. Al-hebshi, N. N., Alharbi, F. A., Mahri, M., & Chen, T. (2017). Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis. Genes, 8(4), 106. https://doi.org/10.3390/genes8040106
5. Al-hebshi, N. N., Nasher, A. T., Maryoud, M. Y., Homeida, H. E., Chen, T., Idris, A. M., & Johnson, N. W. (2017). Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma. Scientific Reports, 7(1), 1834. https://doi.org/10.1038/s41598-017-02079-3
6. Amerongen, A. V. N., & Veerman, E. C. I. (2002). Saliva – the defender of the oral cavity. Oral Diseases, 8(1), 12–22. https://doi.org/10.1034/j.1601-0825.2002.1o816.x
7. Avila, M., Ojcius, D. M., & Yilmaz, Ö. (2009). The Oral Microbiota: Living with a Permanent Guest. DNA and Cell Biology, 28(8), 405–411. https://doi.org/10.1089/dna.2009.0874
8. Bakhti, S. Z., & Latifi-Navid, S. (2021). Oral microbiota and Helicobacter pylori in gastric carcinogenesis: what do we know and where next? BMC Microbiology, 21(1), 71. https://doi.org/10.1186/s12866-021-02130-4
9. Benabdelkader, S., Andreani, J., Gillet, A., Terrer, E., Pignoly, M., Chaudet, H., Aboudharam, G., & la Scola, B. (2019). Specific clones of Trichomonas tenax are associated with periodontitis. PLOS ONE, 14(3), e0213338-. https://doi.org/10.1371/journal.pone.0213338
10. Blostein, F., Foote, S., Salzman, E., McNeil, D. W., Marazita, M. L., Martin, E. T., & Foxman, B. (2021). Associations Between Salivary Bacteriome Diversity and Salivary Human Herpesvirus Detection in Early Childhood: A Prospective Cohort Study. Journal of the Pediatric Infectious Diseases Society, 10(8), 856–863. https://doi.org/10.1093/jpids/piab044
11. Chalabi, M., Moghim, S., Mogharehabed, A., Najafi, F., & Rezaie, F. (2008). EBV and CMV in chronic periodontitis: a prevalence study. Archives of Virology, 153(10), 1917. https://doi.org/10.1007/s00705-008-0186-7
12. Chhour, K. L., Nadkarni, M. A., Byun, R., Martin, F. E., Jacques, N. A., & Hunter, N. (2005). Molecular Analysis of Microbial Diversity in Advanced Caries. Journal of Clinical Microbiology, 43(2), 843–849. https://doi.org/10.1128/JCM.43.2.843-849.2005
13. Chrysanthakopoulos, N. A., & Chrysanthakopoulos, P. A. (2016). Association between indices of clinically-defined periodontitis and self-reported history of systemic medical conditions. Journal of Investigative and Clinical Dentistry, 7(1), 27–36. https://doi.org/10.1111/jicd.12119
14. Corby, P. M., Lyons-Weiler, J., Bretz, W. A., Hart, T. C., Aas, J. A., Boumenna, T., Goss, J., Corby, A. L., Junior, H. M., Weyant, R. J., & Paster, B. J. (2005). Microbial Risk Indicators of Early Childhood Caries. Journal of Clinical Microbiology, 43(11), 5753–5759. https://doi.org/10.1128/JCM.43.11.5753-5759.2005
15. Costalonga, M., & Herzberg, M. C. (2014). The oral microbiome and the immunobiology of periodontal disease and caries. Immunology Letters, 162(2, Part A), 22–38. https://doi.org/10.1016/j.imlet.2014.08.017
16. Cross, B. W., & Ruhl, S. (2018). Glycan recognition at the saliva – oral microbiome interface. Cellular Immunology, 333, 19–33. https://doi.org/10.1016/j.cellimm.2018.08.008
17. Cui, J., Cui, H., Yang, M., Du, S., Li, J., Li, Y., Liu, L., Zhang, X., & Li, S. (2019). Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade. Protein & Cell, 10(7), 496–509. https://doi.org/10.1007/s13238-018-0596-6
18. Davenport, E. R. (2017). Tooth Be Told, Genetics Influences Oral Microbiome. Cell Host & Microbe, 22(3), 251–253. https://doi.org/https://doi.org/10.1...om.2017.08.018
19. Dewhirst, F. E., Tuste, C., Jacques, Paster, B. J., Tanner, A. C. R., Wen-Han, Y., Abirami, L., & Wade, W. G. (2010). The Human Oral Microbiome. Journal of Bacteriology, 192(19), 5002–5017. https://doi.org/10.1128/JB.00542-10
20. Duran-Pinedo, A. E., & Frias-Lopez, J. (2015). Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes and Infection, 17(7), 505–516. https://doi.org/10.1016/j.micinf.2015.03.014
21. Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014). Oligotyping analysis of the human oral microbiome. Proceedings of the National Academy of Sciences, 111(28), E2875. https://doi.org/10.1073/pnas.1409644111
22. Filoche, S., Wong, L., & Sissons, C. H. (2009). Oral Biofilms: Emerging Concepts in Microbial Ecology. Journal of Dental Research, 89(1), 8–18. https://doi.org/10.1177/0022034509351812
23. Fitzpatrick, S. G., & Katz, J. (2010). The association between periodontal disease and cancer: A review of the literature. Journal of Dentistry, 38(2), 83–95. https://doi.org/10.1016/j.jdent.2009.10.007
24. Flemmig, T. F., & Beikler, T. (2011). Control of oral biofilms. Periodontology 2000, 55(1), 9–15. https://doi.org/10.1111/j.1600-0757.2010.00383.x
25. Fukui, Y., Aoki, K., Ishii, Y., & Tateda, K. (2018). The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection. BMC Microbiology, 18(1), 127. https://doi.org/10.1186/s12866-018-1274-9
26. Gao, Z., Kang, Y., Yu, J., & Ren, L. (2014). Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections. Genomics, Proteomics & Bioinformatics, 12(3), 144–150. https://doi.org/10.1016/j.gpb.2014.06.001
27. Ghannoum, M. A., Jurevic, R. J., Mukherjee, P. K., Cui, F., Sikaroodi, M., Naqvi, A., & Gillevet, P. M. (2010). Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals. PLOS Pathogens, 6(1), e1000713-. https://doi.org/10.1371/journal.ppat.1000713
28. Gopinath, D., Wie, C. C., Banerjee, M., Thangavelu, L., Kumar R, P., Nallaswamy, D., Botelho, M. G., & Johnson, N. W. (2021). Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users. Clinical Oral Investigations. https://doi.org/10.1007/s00784-021-04137-7
29. Grassl, N., Kulak, N. A., Pichler, G., Geyer, P. E., Jung, J., Schubert, S., Sinitcyn, P., Cox, J., & Mann, M. (2016). Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Medicine, 8(1), 44. https://doi.org/10.1186/s13073-016-0293-0
30. Griffen, A. L., Beall, C. J., Campbell, J. H., Firestone, N. D., Kumar, P. S., Yang, Z. K., Podar, M., & Leys, E. J. (2012). Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. The ISME Journal, 6(6), 1176–1185. https://doi.org/10.1038/ismej.2011.191
31. Gross, E. L., Leys, E. J., Gasparovich, E. R., Firestone, N. D., Swartzbaum, J. A., Janies, D. A., Asnani, K., & Griffen, A. L. (2010). Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth. Journal of Clinical Microbiology, 48(11), 4121–4128. https://doi.org/10.1128/JCM.01232-10
32. Hajishengallis, G., & Lamont, R. J. (2012). Beyond the red complex and into more complexity: the polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology. Molecular Oral Microbiology, 27(6), 409–419. https://doi.org/10.1111/j.2041-1014.2012.00663.x
33. Han, S., Chen, Y., Hu, J., & Ji, Z. (2014). Tongue images and tongue coating microbiome in patients with colorectal cancer. Microbial Pathogenesis, 77, 1–6. https://doi.org/10.1016/j.micpath.2014.10.003
34. Haubek, D. (2010). The highly leukotoxic JP2 clone of Aggregatibacter actinomycetemcomitans: Evolutionary aspects, epidemiology and etiological role in aggressive periodontitis. APMIS, 118.
35. Hong, B. Y., Hoare, A., Cardenas, A., Dupuy, A. K., Choquette, L., Salner, A. L., Schauer, P. K., Hegde, U., Peterson, D. E., Dongari-Bagtzoglou, A., Strausbaugh, L. D., & Diaz, P. I. (2020). The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes. Journal of Dental Research, 99(6), 730–738. https://doi.org/10.1177/0022034520915879
36. Horz, H.-P., & Conrads, G. (2007). Diagnosis and anti-infective therapy of periodontitis. Expert Review of Anti-Infective Therapy, 5(4), 703–715. https://doi.org/10.1586/14787210.5.4.703
37. Ioannidou, E., & Swede, H. (2011). Disparities in Periodontitis Prevalence among Chronic Kidney Disease Patients. Journal of Dental Research, 90(6), 730–734. https://doi.org/10.1177/0022034511402209
38. Jeffcoat, M. K., Jeffcoat, R. L., Gladowski, P. A., Bramson, J. B., & Blum, J. J. (2014). Impact of Periodontal Therapy on General Health: Evidence from Insurance Data for Five Systemic Conditions. American Journal of Preventive Medicine, 47(2), 166–174. https://doi.org/10.1016/j.amepre.2014.04.001
39. Jiang, B., Liang, X., Chen, Y., Ma, T., Liu, L., Li, J., Jiang, R., Chen, T., Zhang, X., & Li, S. (2012). Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports, 2(1), 936. https://doi.org/10.1038/srep00936
40. Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., & Whitely, M. (2014). Metatranscriptomics of the Human Oral Microbiome during Health and Disease. MBio, 5(2), e01012-14. https://doi.org/10.1128/mBio.01012-14
41. Kamio, N., Imai, K., Shimizu, K., Cueno, M. E., Tamura, M., Saito, Y., & Ochiai, K. (2015). Neuraminidase-producing oral mitis group streptococci potentially contribute to influenza viral infection and reduction in antiviral efficacy of zanamivir. Cellular and Molecular Life Sciences, 72(2), 357–366. https://doi.org/10.1007/s00018-014-1669-1
42. Kolenbrander, P. E., Palmer, R. J., Jr, Rickard, A. H., Jakubovics, N. S., Chalmers, N. I., & Diaz, P. I. (2006). Bacterial interactions and successions during plaque development. Periodontology 2000, 42, 47–79. https://doi.org/10.1111/j.1600-0757.2006.00187.x
43. Koo, H., & Bowen, W. H. (2014). Candida albicans and Streptococcus mutans: a potential synergistic alliance to cause virulent tooth decay in children. Future Microbiology, 9(12), 1295–1297. https://doi.org/10.2217/fmb.14.92
44. Kori, J. A., Saleem, F., Ullah, S., & Azim, M. K. (2020). Characterization of Oral bacteriome dysbiosis in type 2 diabetic patients. MedRxiv, 2020.04.09.20052613. https://doi.org/10.1101/2020.04.09.20052613
45. Kumaraswamy, K. L., & Vidya, M. (2011). Human papilloma virus and oral infections: An update. Journal of Cancer Research and Therapeutics, 7(2), 120-127. https://doi.org/10.4103/0973-1482.82915
46. Kurkivuori, J., Salaspuro, V., Kaihovaara, P., Kari, K., Rautemaa, R., Grönroos, L., Meurman, J. H., & Salaspuro, M. (2007). Acetaldehyde production from ethanol by oral streptococci. Oral Oncology, 43(2), 181–186. https://doi.org/10.1016/j.oraloncology.2006.02.005
47. Lepp, P. W., Brinig, M. M., Ouverney, C. C., Palm, K., Armitage, G. C., & Relman, D. A. (2004). Methanogenic Archaea and human periodontal disease. Proceedings of the National Academy of Sciences of the United States of America, 101(16), 6176. https://doi.org/10.1073/pnas.0308766101
48. Li, Y., Wang, K., Zhang, B., Tu, Q., Yao, Y., Cui, B., Ren, B., He, J., Shen, X., van Nostrand, J. D., Zhou, J., Shi, W., Xiao, L., Lu, C., & Zhou, X. (2019). Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus. International Journal of Oral Science, 11(2), 13. https://doi.org/10.1038/s41368-019-0045-2
49. Lim, Y., Totsika, M., Morrison, M., & Punyadeera, C. (2017). The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols. Scientific Reports, 7(1), 8523. https://doi.org/10.1038/s41598-017-07885-3
50. Lin, M., Li, X., Wang, J., Cheng, C., Zhang, T., Han, X., Song, Y., Wang, Z., & Wang, S. (2020). Saliva Microbiome Changes in Patients With Periodontitis With and Without Chronic Obstructive Pulmonary Disease. Frontiers in Cellular and Infection Microbiology, 10, 124. https://www.frontiersin.org/article/10.3389/fcimb.2020.00124
51. Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Li, L., Chen, H., & Xiang, C. (2010). Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing. Microbial Ecology, 60(3), 677–690. https://doi.org/10.1007/s00248-010-9712-8
52. Listgarten, M. A. (1986). Pathogenesis of periodontitis. Journal of Clinical Periodontology, 13(5), 418–425. https://doi.org/10.1111/j.1600-051X.1986.tb01485.x
53. Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., Stine, O. C., Hasturk, H., Kasif, S., Segrè, D., Pop, M., & Amar, S. (2012). Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease. PLOS ONE, 7(6), e37919-. https://doi.org/10.1371/journal.pone.0037919
54. Loesche, W. J., & Grenier, E. (1976). Detection of Streptococcus mutans in plaque samples by the direct fluorescent antibody test. Journal of dental research, 55, A87–A93. https://doi.org/10.1177/002203457605500127011
55. Low, W., Tan, S., & Schwartz, S. (1999). The effect of severe caries on the quality of life in young children. Pediatric Dentistry, 21(6), 325–326. http://europepmc.org/abstract/MED/10509332
56. Lu, H., Ren, Z., Li, A., Li, J., Xu, S., Zhang, H., Jiang, J., Yang, J., Luo, Q., Zhou, K., Zheng, S., & Li, L. (2019). Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls. Journal of Oral Microbiology, 11(1), 1563409. https://doi.org/10.1080/20002297.2018.1563409
57. Mager, D. L., Haffajee, A. D., Devlin, P. M., Norris, C. M., Posner, M. R., & Goodson, J. M. (2005). The salivary microbiota as a diagnostic indicator of oral cancer: A descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. Journal of Translational Medicine, 3(1), 27. https://doi.org/10.1186/1479-5876-3-27
58. Mandel, I. D. (1987). The Functions of Saliva. Journal of Dental Research, 66(1_suppl), 623–627. https://doi.org/10.1177/00220345870660S103
59. Marsh, P. D., Do, T., Beighton, D., & Devine, D. A. (2016). Influence of saliva on the oral microbiota. Periodontology 2000, 70(1), 80–92. https://doi.org/10.1111/prd.12098
60. Martínez, A., Kuraji, R., & Kapila, Y. L. (2021). The human oral virome: Shedding light on the dark matter. Periodontology 2000, 87(1), 282–298. https://doi.org/10.1111/prd.12396
61. Matarazzo, F., Ribeiro, A. C., Feres, M., Faveri, M., & Mayer, M. P. A. (2011). Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects. Journal of Clinical Periodontology, 38(7), 621–627. https://doi.org/10.1111/j.1600-051X.2011.01734.x
62. McIlvanna, E., Linden, G. J., Craig, S. G., Lundy, F. T., & James, J. A. (2021). Fusobacterium nucleatum and oral cancer: a critical review. BMC Cancer, 21(1), 1212. https://doi.org/10.1186/s12885-021-08903-4
63. Michaud, D. S., Fu, Z., Shi, J., & Chung, M. (2017). Periodontal Disease, Tooth Loss, and Cancer Risk. Epidemiologic Reviews, 39(1), 49–58. https://doi.org/10.1093/epirev/mxx006
64. Miller E. H., Annavajhala, M. K., Chong, A. M., Park, H., Nobel, Y. R., Soroush, A., Blackett, J. W., Krigel, A., Phipps, M. M., Freedberg, D. E., Zucker, J., Sano, E. D., Uhlemann, E. C., & Abrams, J. A.(2021). Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19. Microbiology Spectrum, 9(2), e00055-21. https://doi.org/10.1128/Spectrum.00055-21
65. Mohammed, M. M. A., al Kawas, S., & Al-Qadhi, G. (2021). Tongue-coating microbiome as a cancer predictor: A scoping review. Archives of Oral Biology, 132, 105271. https://doi.org/10.1016/j.archoralbio.2021.105271
66. Mukherjee, P. K., Wang, H., Retuerto, M., Zhang, H., Burkey, B., Ghannoum, M. A., & Eng, C. (2017). Bacteriome and mycobiome associations in oral tongue cancer. Oncotarget, 8(57), 97273–97289. https://doi.org/10.18632/oncotarget.21921
67. Munson, M. A., Banerjee, A., Watson, T. F., & Wade, W. G. (2004). Molecular Analysis of the Microflora Associated with Dental Caries. Journal of Clinical Microbiology, 42(7), 3023–3029. https://doi.org/10.1128/JCM.42.7.3023-3029.2004
68. Ng, E., Tay, J. R. H., Balan, P., Ong, M. M. A., Bostanci, N., Belibasakis, G. N., & Seneviratne, C. J. (2021). Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis. Journal of Periodontal Research, 56(2), 205–218. https://doi.org/10.1111/jre.12811
69. Parahitiyawa, N. B., Scully, C., Leung, W. K., Yam, W. C., Jin, L. J., & Samaranayake, L. P. (2010). Exploring the oral bacterial flora: current status and future directions. Oral Diseases, 16(2), 136–145. https://doi.org/10.1111/j.1601-0825.2009.01607.x
70. Peters, B. A., Wu, J., Pei, Z., Yang, L., Purdue, M. P., Freedman, N. D., Jacobs, E. J., Gapstur, S. M., Hayes, R. B., & Ahn, J. (2017). Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers. Cancer Research, 77(23), 6777. https://doi.org/10.1158/0008-5472.CAN-17-1296
71. Peterson, S. N., Snesrud, E., Liu, J., Ong, A. C., Kilian, M., Schork, N. J., & Bretz, W. (2013). The Dental Plaque Microbiome in Health and Disease. PLOS ONE, 8(3), e58487-. https://doi.org/10.1371/journal.pone.0058487
72. Pihlstrom, B. L., Michalowicz, B. S., & Johnson, N. W. (2005). Periodontal diseases. The Lancet, 366(9499), 1809–1820. https://doi.org/10.1016/S0140-6736(05)67728-8
73. Pushalkar, S., Ji, X., Li, Y., Estilo, C., Yegnanarayana, R., Singh, B., Li, X., & Saxena, D. (2012). Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiology, 12(1), 144. https://doi.org/10.1186/1471-2180-12-144
74. Rôças, I. N., Siqueira, J. F., Jr, Santos, K. R., & Coelho, A. M. (2001). “Red complex” (Bacteroides forsythus, Porphyromonas gingivalis, and Treponema denticola) in endodontic infections: a molecular approach. Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics, 91(4), 468–471. https://doi.org/10.1067/moe.2001.114379
75. Sajid, M., Srivastava, S., Joshi, L., & Bharadwaj, M. (2021). Impact of smokeless tobacco-associated bacteriome in oral carcinogenesis. Anaerobe, 70, 102400. https://doi.org/10.1016/j.anaerobe.2021.102400
76. Sampaio-Maia, B., Caldas, I. M., Pereira, M. L., Pérez-Mongiovi, D., & Araujo, R. (2016). Chapter Four – The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases. In S. Sariaslani & G. Michael Gadd (Eds.), Advances in Applied Microbiology (Vol. 97, pp. 171–210). Academic Press. https://doi.org/10.1016/bs.aambs.2016.08.002
77. Sato, N., Kakuta, M., Hasegawa, T., Yamaguchi, R., Uchino, E., Kobayashi, W., Sawada, K., Tamura, Y., Tokuda, I., Murashita, K., Nakaji, S., Imoto, S., Yanagita, M., & Okuno, Y. (2020). Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers. Npj Biofilms and Microbiomes, 6(1), 11. https://doi.org/10.1038/s41522-020-0121-6
78. Sato, Y., Yamagishi, J., Yamashita, R., Shinozaki, N., Ye, B., Yamada, T., Yamamoto, M., Nagasaki, M., & Tsuboi, A. (2015). Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLOS ONE, 10(6), e0131607-. https://doi.org/10.1371/journal.pone.0131607
79. Scannapieco, F. A. (1994). Saliva-Bacterium Interactions in Oral Microbial Ecology. Critical Reviews in Oral Biology & Medicine, 5(3), 203–248. https://doi.org/10.1177/10454411940050030201
80. Scher, J. U., Bretz, W. A., & Abramson, S. B. (2014). Periodontal disease and subgingival microbiota as contributors for rheumatoid arthritis pathogenesis: modifiable risk factors? Current Opinion in Rheumatology, 26(4), 424–429. https://doi.org/10.1097/BOR.0000000000000076
81. Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012). Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology, 13(6), R42. https://doi.org/10.1186/gb-2012-13-6-r42
82. Selwitz, R. H., Ismail, A. I., & Pitts, N. B. (2007). Dental caries. The Lancet, 369(9555), 51–59. https://doi.org/10.1016/S0140-6736(07)60031-2
83. Seymour, G. J., Ford, P. J., Cullinan, M. P., Leishman, S., & Yamazaki, K. (2007). Relationship between periodontal infections and systemic disease. Clinical Microbiology and Infection, 13(s4), 3–10. https://doi.org/10.1111/j.1469-0691.2007.01798.x
84. Shi, B., Chang, M., Martin, J., Mitreva, M., Lux, R., Klokkevold, P., Sodergren, E., Weinstock, G. M., Haake, S. K., & Li, H. (2021). Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis. MBio, 6(1), e01926-14. https://doi.org/10.1128/mBio.01926-14
85. Socransky, S. S., & Haffajee, A. D. (2005). Periodontal microbial ecology. Periodontology 2000, 38(1), 135–187. https://doi.org/10.1111/j.1600-0757.2005.00107.x
86. Socransky, S. S., Haffajee, A. D., Cugini, M. A., Smith, C., & Kent Jr., R. L. (1998). Microbial complexes in subgingival plaque. Journal of Clinical Periodontology, 25(2), 134–144. https://doi.org/10.1111/j.1600-051X.1998.tb02419.x
87. Springer, S. A., & Gagneux, P. (2013). Glycan Evolution in Response to Collaboration, Conflict, and Constraint *. Journal of Biological Chemistry, 288(10), 6904–6911. https://doi.org/10.1074/jbc.R112.424523
88. Takahashi, N., Washio, J., & Mayanagi, G. (2010). Metabolomics of Supragingival Plaque and Oral Bacteria. Journal of Dental Research, 89(12), 1383–1388. https://doi.org/10.1177/0022034510377792
89. Teles, R. P., Gursky, L. C., Faveri, M., Rosa, E. A., Teles, F. R. F., Feres, M., Socransky, S. S., & Haffajee, A. D. (2010). Relationships between subgingival microbiota and GCF biomarkers in generalized aggressive periodontitis. Journal of Clinical Periodontology, 37(4), 313–323. https://doi.org/10.1111/j.1600-051X.2010.01534.x
90. Tribble, G. D., Angelov, N., Weltman, R., Wang, B.-Y., Eswaran, S. v, Gay, I. C., Parthasarathy, K., Dao, D.-H. v, Richardson, K. N., Ismail, N. M., Sharina, I. G., Hyde, E. R., Ajami, N. J., Petrosino, J. F., & Bryan, N. S. (2019). Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. Frontiers in Cellular and Infection Microbiology, 9, 39. https://www.frontiersin.org/article/10.3389/fcimb.2019.00039
91. van der Meulen, T. A., Harmsen, H. J. M., Bootsma, H., Liefers, S. C., Vich Vila, A., Zhernakova, A., Fu, J., Wijmenga, C., Spijkervet, F. K. L., Kroese, F. G. M., & Vissink, A. (2018). Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients. Rheumatology, 57(12), 2225–2234. https://doi.org/10.1093/rheumatology/key215
92. Van Essche, M., Quirynen, M., Sliepen, I., Loozen, G., Boon, N., van Eldere, J., & Teughels, W. (2011). Killing of anaerobic pathogens by predatory bacteria. Molecular Oral Microbiology, 26(1), 52–61. https://doi.org/10.1111/j.2041-1014.2010.00595.x
93. Vartoukian, S. R., Palmer, R. M., & Wade, W. G. (2009). Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease. Applied and Environmental Microbiology, 75(11), 3777–3786. https://doi.org/10.1128/AEM.02763-08
94. Wade, W. G. (2013). The oral microbiome in health and disease. Pharmacological Research, 69(1), 137–143. https://doi.org/10.1016/j.phrs.2012.11.006
95. Wang, L., Ganly, I. (2014). The oral microbiome and oral cancer. Clinics in Laboratory Medicine, 34, 711–719. https://doi.org/10.1016/j.cll.2014.08.004
96. Wang, T.-F., Jen, I.-A., Chou, C., & Lei, Y.-P. (2014). Effects of periodontal therapy on metabolic control in patients with type 2 diabetes mellitus and periodontal disease: a meta-analysis. Medicine, 93(28), e292–e292. https://doi.org/10.1097/MD.0000000000000292
97. Wantland, W. W., Wantland, E. M., Remo, J. W., & Winquist, D. L. (1958). Studies on Human Mouth Protozoa. Journal of Dental Research, 37(5), 949–950. https://doi.org/10.1177/00220345580370052601
98. Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., & Borisy, G. G. (2014). Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Frontiers in Microbiology, 5, 568. https://www.frontiersin.org/article/10.3389/fmicb.2014.00568
99. Wilbert, S. A., Mark Welch, J. L., & Borisy, G. G. (2020). Spatial Ecology of the Human Tongue Dorsum Microbiome. Cell Reports, 30(12), 4003-4015.e3. https://doi.org/10.1016/j.celrep.2020.02.097
100. Willis, J. R., & Gabaldón, T. (2020). The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems. Microorganisms, 8(2). https://doi.org/10.3390/microorganisms8020308
101. Xiao, J., Grier, A., Faustoferri, R. C., Alzoubi, S., Gill, A. L., Feng, C., Liu, Y., Quivey, R. G., Kopycka-Kedzierawski, D. T., Koo, H., & Gill, S. R. (2018). Association between Oral Candida and Bacteriome in Children with Severe ECC. Journal of Dental Research, 97(13), 1468–1476. https://doi.org/10.1177/0022034518790941
102. Zarco, M. F., Vess, T. J., & Ginsburg, G. S. (2012). The oral microbiome in health and disease and the potential impact on personalized dental medicine. Oral Diseases, 18(2), 109–120. https://doi.org/10.1111/j.1601-0825.2011.01851.x
103. Zhou, X., Han, J., Liu, Z., Song, Y., Wang, Z., & Sun, Z. (2014). Effects of periodontal treatment on lung function and exacerbation frequency in patients with chronic obstructive pulmonary disease and chronic periodontitis: A 2-year pilot randomized controlled trial. Journal of Clinical Periodontology, 41(6), 564–572. https://doi.org/https://doi.org/10.1111/jcpe.12247
104. Zuo, Y., Whitbeck, J. C., Haila, G. J., Hakim, A. A., Rothlauf, P. W., Eisenberg, R. J., Cohen, G. H., & Krummenacher, C. (2019). Saliva enhances infection of gingival fibroblasts by herpes simplex virus 1. PLOS ONE, 14(10), e0223299-. https://doi.org/10.1371/journal.pone.0223299

The Skin Microbiome

1. Bek-Thomsen, M., Lomholt, H. B., & Kilian, M. (2008). Acne is Not Associated with Yet-Uncultured Bacteria. Journal of Clinical Microbiology, 46(10), 3355–3360. https://doi.org/10.1128/JCM.00799-08
2. Belkaid, Y., & Harrison, O. J. (2017). Homeostatic Immunity and the Microbiota. Immunity, 46(4), 562–576. https://doi.org/10.1016/j.immuni.2017.04.008
3. Bierber, T. (2008). Mechanisms of disease: atopic dermatitis. N Engl J Med, 358, 358-1483.
4. Blicharz, L., Rudnicka, L., & Samochocki, Z. (2019). Staphylococcus aureus: an underestimated factor in the pathogenesis of atopic dermatitis? Postepy Dermatologii i Alergologii, 36(1), 11–17. https://doi.org/10.5114/ada.2019.82821
5. Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nature Reviews Microbiology, 16(3), 143–155. https://doi.org/10.1038/nrmicro.2017.157
6. Capone, K. A., Dowd, S. E., Stamatas, G. N., & Nikolovski, J. (2011). Diversity of the Human Skin Microbiome Early in Life. Journal of Investigative Dermatology, 131(10), 2026–2032. https://doi.org/10.1038/jid.2011.168
7. Casas, C., Paul, C., Lahfa, M., Livideanu, B., Lejeune, O., Alvarez-Georges, S., Saint-Martory, C., Degouy, A., Mengeaud, V., Ginisty, H., Durbise, E., Schmitt, A. M., & Redoulès, D. (2012). Quantification of Demodex folliculorum by PCR in rosacea and its relationship to skin innate immune activation. Experimental Dermatology, 21(12), 906–910. https://doi.org/10.1111/exd.12030
8. Cogen, A. L., Yamasaki, K., Sanchez, K. M., Dorschner, R. A., Lai, Y., MacLeod, D. T., Torpey, J. W., Otto, M., Nizet, V., Kim, J. E., & Gallo, R. L. (2010). Selective Antimicrobial Action Is Provided by Phenol-Soluble Modulins Derived from Staphylococcus epidermidis, a Normal Resident of the Skin. Journal of Investigative Dermatology, 130(1), 192–200. https://doi.org/10.1038/jid.2009.243
9. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971. https://doi.org/10.1073/pnas.1002601107
10. Dreno, B., Martin, R., Moyal, D., Henley, J. B., Khammari, A., & Seité, S. (2017). Skin microbiome and acne vulgaris: Staphylococcus, a new actor in acne. Experimental Dermatology, 26(9), 798–803. https://doi.org/10.1111/exd.13296
11. Fahlén, A., Engstrand, L., Baker, B. S., Powles, A., & Fry, L. (2012). Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Archives of Dermatological Research, 304(1), 15–22. https://doi.org/10.1007/s00403-011-1189-x
12. Findley, K., & Grice, E. A. (2014). The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease. PLOS Pathogens, 10(11), e1004436-. https://doi.org/10.1371/journal.ppat.1004436
13. Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., Schoenfeld, D., Nomicos, E., Park, M., Becker, J., Benjamin, B., Blakesley, R., Bouffard, G., Brooks, S., Coleman, H., Dekhtyar, M., Gregory, M., Guan, X., Gupta, J., … Program, N. I. H. I. S. C. C. S. (2013). Topographic diversity of fungal and bacterial communities in human skin. Nature, 498(7454), 367–370. https://doi.org/10.1038/nature12171
14. Fitz-Gibbon, S., Tomida, S., Chiu, B.-H., Nguyen, L., Du, C., Liu, M., Elashoff, D., Erfe, M. C., Loncaric, A., Kim, J., Modlin, R. L., Miller, J. F., Sodergren, E., Craft, N., Weinstock, G. M., & Li, H. (2013). Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. Journal of Investigative Dermatology, 133(9), 2152–2160. https://doi.org/10.1038/jid.2013.21
15. Forton, F. M. N. (2012). Papulopustular rosacea, skin immunity and Demodex: pityriasis folliculorum as a missing link. Journal of the European Academy of Dermatology and Venereology, 26(1), 19–28. https://doi.org/10.1111/j.1468-3083.2011.04310.x
16. Forton, F., & Seys, B. (1993). Density of Demodex folliculorum in rosacea: a case-control study using standardized skin-surface biopsy. British Journal of Dermatology, 128(6), 650–659. https://doi.org/10.1111/j.1365-2133.1993.tb00261.x
17. Gao, Z., Tseng, C., Strober, B. E., Pei, Z., & Blaser, M. J. (2008). Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions. PLOS ONE, 3(7), e2719-. https://doi.org/10.1371/journal.pone.0002719
18. Gardiner M, Vicaretti M, Sparks J, Bansal S, Bush S, Liu M, Darling A, Harry E, Burke CM. (2017). A longitudinal study of the diabetic skin and wound microbiome. PeerJ 5:e3543 https://doi.org/10.7717/peerj.3543
19. Georgala, S., Katoulis, A. C., Kylafis, G. D., Koumantaki-Mathioudaki, E., Georgala, C., & Aroni, K. (2001). Increased density of Demodex folliculorum and evidence of delayed hypersensitivity reaction in subjects with papulopustular rosacea. Journal of the European Academy of Dermatology and Venereology, 15(5), 441–444. https://doi.org/10.1046/j.1468-3083.2001.00331.x
20. Grice, E. A., & Segre, J. A. (2011). The skin microbiome. Nature Reviews Microbiology, 9(4), 244–253. https://doi.org/10.1038/nrmicro2537
21. Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Nisc Comparative Sequencing Program, Bouffard, G. G., Blakesley, R. W., Muray, P. R., Green, E. D., Turner, M. L., & Segre, J. A. (2009). Topographical and Temporal Diversity of the Human Skin Microbiome. Science, 324(5931), 1190–1192. https://doi.org/10.1126/science.1171700
22. Iwase, T., Uehara, Y., Shinji, H., Tajima, A., Seo, H., Takada, K., Agata, T., & Mizunoe, Y. (2010). Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 465(7296), 346–349. https://doi.org/10.1038/nature09074
23. Kalan, L. R., Meisel, J. S., Loesche, M. A., Horwinski, J., Soaita, I., Chen, X., Uberoi, A., Gardner, S. E., & Grice, E. A. (2019). Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy. Cell Host & Microbe, 25(5), 641-655.e5. https://doi.org/10.1016/j.chom.2019.03.006
24. Kennedy, E. A., Connolly, J., Hourihane, J. O., Fallon, P. G., McLean, W. H. I., Murray, D., Jo, J.-H., Segre, J. A., Kong, H. H., & Irvine, A. D. (2017). Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year. Journal of Allergy and Clinical Immunology, 139(1), 166–172. https://doi.org/10.1016/j.jaci.2016.07.029
25. Koller, B., Müller-Wiefel, A. S., Rupec, R., Korting, H. C., & Ruzicka, T. (2011). Chitin Modulates Innate Immune Responses of Keratinocytes. PLOS ONE, 6(2), e16594-. https://doi.org/10.1371/journal.pone.0016594
26. Kong, H. H. (2011). Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends in Molecular Medicine, 17(6), 320–328. https://doi.org/10.1016/j.molmed.2011.01.013
27. Kong, H. H., Oh, J., Deming, C., Conlan, S., Grice, E. A., Beatson, M. A., Nomicos, E., Polley, E. C., Komarow, H. D., Program, N. C. S., Murray, P. R., Turner, M. L., & Segre, J. A. (2012). Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Research, 22(5), 850–859. http://genome.cshlp.org/content/22/5/850.abstract
28. Kuhbacher, A., Burger-Kentischer, A., & Rupp, S. (2017). Interaction of Candida species with the skin. Microorganisms. 5(2), 32. https://doi.org/10.3390/microorganisms5020032
29. Lacey, N., Delaney, S., Kavanagh, K., & Powell, F. C. (2007). Mite-related bacterial antigens stimulate inflammatory cells in rosacea. British Journal of Dermatology, 157(3), 474–481. https://doi.org/10.1111/j.1365-2133.2007.08028.x
30. Lacey, N., Kavanagh, K., & Tseng, S. C. G. (2009). Under the lash: Demodex mites in human diseases. The Biochemist, 31(4), 20–24. https://doi.org/10.1042/BIO03104020
31. Lacey, N., Ní Raghallaigh, S., & Powell, F. C. (2011). Demodex mites – commensals, parasites or mutualistic organisms? Dermatology, 222(2), 128-30. doi:http://dx.doi.org/10.1159/000323009
32. McKelvey, K., Xue, M., Whitmont, K., Shen, K., Cooper, A., & Jackson, C. (2012). Potential anti-inflammatory treatments for chronic wounds. Wound Practice & Research: Journal of the Australian Wound Management Association, 20(2), 86–89. https://search.informit.org/doi/10.3316/informit.656354654775105
33. Naik, S., Bouladoux, N., Linehan, J. L., Han, S.-J., Harrison, O. J., Wilhelm, C., Conlan, S., Himmelfarb, S., Byrd, A. L., Deming, C., Quinones, M., Brenchley, J. M., Kong, H. H., Tussiwand, R., Murphy, K. M., Merad, M., Segre, J. A., & Belkaid, Y. (2015). Commensal–dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 520(7545), 104–108. https://doi.org/10.1038/nature14052
34. Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., Spencer, S., Hall, J. A., Dzutsev, A., Kong, H., Campbell, D. J., Trinchieri, G., Segre, J. A., & Belkaid, Y. (2012). Compartmentalized control of skin immunity by resident commensals. Science (New York, N.Y.), 337(6098), 1115–1119. https://doi.org/10.1126/science.1225152
35. Nakamura, Y., Oscherwitz, J., Cease, K. B., Chan, S. M., Muñoz-Planillo, R., Hasegawa, M., Villaruz, A. E., Cheung, G. Y. C., McGavin, M. J., Travers, J. B., Otto, M., Inohara, N., & Núñez, G. (2013). Staphylococcus δ-toxin induces allergic skin disease by activating mast cells. Nature, 503(7476), 397–401. https://doi.org/10.1038/nature12655
36. Nakatsuji, T., Chen, T. H., Two, A. M., Chun, K. A., Narala, S., Geha, R. S., Hata, T. R., & Gallo, R. L. (2016). Staphylococcus aureus Exploits Epidermal Barrier Defects in Atopic Dermatitis to Trigger Cytokine Expression. Journal of Investigative Dermatology, 136(11), 2192–2200. https://doi.org/10.1016/j.jid.2016.05.127
37. Niebuhr, M., Gathmann, M., Scharonow, H., Mamerow, D., Mommert, S., Balaji, H., & Werfel, T. (2011). Staphylococcal Alpha-Toxin Is a Strong Inducer of Interleukin-17 in Humans. Infection and Immunity, 79(4), 1615–1622. https://doi.org/10.1128/IAI.00958-10
38. Norlind, R. (1955). Significance of infections in origin of psoriasis. Acta Rheumatol Scand, 1, 135-44.
39. Oh, J., Byrd, A. L., Park, M., Kong, H. H., & Segre, J. A. (2016). Temporal Stability of the Human Skin Microbiome. Cell, 165(4), 854–866. https://doi.org/10.1016/j.cell.2016.04.008
40. Oh, J., Freeman, A. F., Program, N. C. S., Park, M., Sokolic, R., Candotti, F., Holland, S. M., Segre, J. A., & Kong, H. H. (2013). The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Research, 23(12), 2103–2114. http://genome.cshlp.org/content/23/12/2103.abstract
41. Otto, M. (2009). Staphylococcus epidermidis — the “accidental” pathogen. Nature Reviews Microbiology, 7(8), 555–567. https://doi.org/10.1038/nrmicro2182
42. Otto, M. (2012). Molecular basis of Staphylococcus epidermidis infections. Seminars in Immunopathology, 34(2), 201–214. https://doi.org/10.1007/s00281-011-0296-2
43. Owen, C. M., Chalmers, R., O’Sullivan, T., & Griffiths, C. E.M. (2000) Antistreptococcal interventions for guttate and chronic plaque psoriasis. Cochrane Database of Systematic Reviews, 2. Art. No.: CD001976. DOI: 10.1002/14651858.CD001976.
44. PrabhuDas, M., Adkins, B., Gans, H., King, C., Levy, O., Ramilo, O., & Siegrist, C.-A. (2011). Challenges in infant immunity: implications for responses to infection and vaccines. Nature Immunology, 12(3), 189–194. https://doi.org/10.1038/ni0311-189
45. Price, L. B., Liu, C. M., Melendez, J. H., Frankel, Y. M., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C., Keim, P. S., Lazarus, G. S., & Zenilman, J. M. (2009). Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota. PLOS ONE, 4(7), e6462-. https://doi.org/10.1371/journal.pone.0006462
46. Schommer, N. N., & Gallo, R. L. (2013). Structure and function of the human skin microbiome. Trends in Microbiology, 21(12), 660–668. https://doi.org/10.1016/j.tim.2013.10.001
47. Statnikov, A., Alekseyenko, A. v, Li, Z., Henaff, M., Perez-Perez, G. I., Blaser, M. J., & Aliferis, C. F. (2013). Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison. Scientific Reports, 3(1), 2620. https://doi.org/10.1038/srep02620
48. Verbanic, S., Shen, Y., Lee, J., Deacon, J. M., & Chen, I. A. (2020). Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds. Npj Biofilms and Microbiomes, 6(1), 21. https://doi.org/10.1038/s41522-020-0130-5
49. Weyrich, L. S., Dixit, S., Farrer, A. G., Cooper, A. J., & Cooper, A. J. (2015). The skin microbiome: Associations between altered microbial communities and disease. Australasian Journal of Dermatology, 56(4), 268–274. https://doi.org/10.1111/ajd.12253
50. Williams, M. R., & Gallo, R. L. (2015). The Role of the Skin Microbiome in Atopic Dermatitis. Current Allergy and Asthma Reports, 15(11), 65. https://doi.org/10.1007/s11882-015-0567-4
51. Wolcott, R., Costerton, J. W., Raoult, D., & Cutler, S. J. (2013). The polymicrobial nature of biofilm infection. Clinical Microbiology and Infection, 19(2), 107–112. https://doi.org/10.1111/j.1469-0691.2012.04001.x

The Respiratory Microbiome

1. Abreu, N. A., Nagalingam, N. A., Song, Y., Roediger, F. C., Pletcher, S. D., Goldberg, A. N., & Lynch, S. V. (2012). Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis. Science Translational Medicine, 4(151), 151ra124-151ra124. https://doi.org/10.1126/scitranslmed.3003783
2. Beck, J. M., Schloss, P. D., Venkataraman, A., Twigg, H., Jablonski, K. A., Bushman, F. D., Campbell, T. B., Charlson, E. S., Collman, R. G., Crothers, K., Curtis, J. L., Drews, K. L., Flores, S. C., Fontenot, A. P., Foulkes, M. A., Frank, I., Ghedin, E., Huang, L., Lynch, S. v, … Young, V. B. (2015). Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. American Journal of Respiratory and Critical Care Medicine, 192(11), 1335–1344. https://doi.org/10.1164/rccm.201501-0128OC
3. Biesbroek, G., Tsivtsivadze, E., Sanders, E. A. M., Montijn, R., Veenhoven, R. H., Keijser, B. J. F., & Bogaert, D. (2014). Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children. American Journal of Respiratory and Critical Care Medicine, 190(11), 1283–1292. https://doi.org/10.1164/rccm.201407-1240OC
4. Bosch, A. A. T. M., Levin, E., van Houten, M. A., Hasrat, R., Kalkman, G., Biesbroek, G., de Steenhuijsen Piters, W. A. A., de Groot, P.-K. C. M., Pernet, P., Keijser, B. J. F., Sanders, E. A. M., & Bogaert, D. (2016). Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery. EBioMedicine, 9, 336–345. https://doi.org/10.1016/j.ebiom.2016.05.031
5. Bousbia, S., Papazian, L., Saux, P., Forel, J. M., Auffray, J.-P., Martin, C., Raoult, D., & la Scola, B. (2012). Repertoire of Intensive Care Unit Pneumonia Microbiota. PLOS ONE, 7(2), e32486-. https://doi.org/10.1371/journal.pone.0032486
6. Carmody, L. A., Zhao, J., Schloss, P. D., Petrosino, J. F., Murray, S., Young, V. B., Li, J. Z., & LiPuma, J. J. (2013). Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation. Annals of the American Thoracic Society, 10(3), 179–187. https://doi.org/10.1513/AnnalsATS.201211-107OC
7. Chalmers, J. D., Taylor, J. K., Mandal, P., Choudhury, G., Singanayagam, A., Akram, A. R., & Hill, A. T. (2011). Validation of the Infectious Diseases Society of America/American Thoratic Society Minor Criteria for Intensive Care Unit Admission in Community-Acquired Pneumonia Patients Without Major Criteria or Contraindications to Intensive Care Unit Care. Clinical Infectious Diseases, 53(6), 503–511. https://doi.org/10.1093/cid/cir463
8. Charlson, E. S., Diamond, J. M., Bittinger, K., Fitzgerald, A. S., Yadav, A., Haas, A. R., Bushman, F. D., & Collman, R. G. (2012). Lung-enriched Organisms and Aberrant Bacterial and Fungal Respiratory Microbiota after Lung Transplant. American Journal of Respiratory and Critical Care Medicine, 186(6), 536–545. https://doi.org/10.1164/rccm.201204-0693OC
9. Cui, L., Morris, A., Huang, L., Beck, J. M., Twigg, H. L., von Mutius, E., & Ghedin, E. (2014). The Microbiome and the Lung. Annals of the American Thoracic Society, 11(Supplement 4), S227–S232. https://doi.org/10.1513/AnnalsATS.201402-052PL
10. de Steenhuijsen Piters, W. A. A., Huijskens, E. G. W., Wyllie, A. L., Biesbroek, G., van den Bergh, M. R., Veenhoven, R. H., Wang, X., Trzciński, K., Bonten, M. J., Rossen, J. W. A., Sanders, E. A. M., & Bogaert, D. (2016). Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. The ISME Journal, 10(1), 97–108. https://doi.org/10.1038/ismej.2015.99
11. Denning, D. W., Pashley, C., Hartl, D., Wardlaw, A., Godet, C., del Giacco, S., Delhaes, L., & Sergejeva, S. (2014). Fungal allergy in asthma–state of the art and research needs. Clinical and Translational Allergy, 4(1), 14. https://doi.org/10.1186/2045-7022-4-14
12. Dickson, R. P., & Huffnagle, G. B. (2015). The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease. PLOS Pathogens, 11(7), e1004923-. https://doi.org/10.1371/journal.ppat.1004923
13. Dickson, R. P., Martinez, F. J., & Huffnagle, G. B. (2014). The role of the microbiome in exacerbations of chronic lung diseases. The Lancet, 384(9944), 691–702. https://doi.org/10.1016/S0140-6736(14)61136-3
14. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971. https://doi.org/10.1073/pnas.1002601107
15. Durack, J., Boushey, H. A., & Lynch, S. v. (2016). Airway Microbiota and the Implications of Dysbiosis in Asthma. Current Allergy and Asthma Reports, 16(8), 52. https://doi.org/10.1007/s11882-016-0631-8
16. Fall, T., Lundholm, C., Örtqvist, A. K., Fall, K., Fang, F., Hedhammar, Å., Kämpe, O., Ingelsson, E., & Almqvist, C. (2015). Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma. JAMA Pediatrics, 169(11), e153219–e153219. https://doi.org/10.1001/jamapediatrics.2015.3219
17. File, T. M. (2003). Community-acquired pneumonia. The Lancet, 362(9400), 1991–2001. https://doi.org/10.1016/S0140-6736(03)15021-0
18. Fujimura, K. E., Johnson, C. C., Ownby, D. R., Cox, M. J., Brodie, E. L., Havstad, S. L., Zoratti, E. M., Woodcroft, K. J., Bobbitt, K. R., Wegienka, G., Boushey, H. A., & Lynch, S. v. (2010). Man’s best friend? The effect of pet ownership on house dust microbial communities. The Journal of Allergy and Clinical Immunology, 126(2), 410-412.e4123. https://doi.org/10.1016/j.jaci.2010.05.042
19. Fukata, M., & Arditi, M. (2013). The role of pattern recognition receptors in intestinal inflammation. Mucosal Immunology, 6(3), 451–463. https://doi.org/10.1038/mi.2013.13
20. Hakansson, A. P., Orihuela, C. J., & Bogaert, D. (2018). Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection. Physiological Reviews, 98(2), 781–811. https://doi.org/10.1152/physrev.00040.2016
21. Hamilos, D. L. (2019). Biofilm Formations in Pediatric Respiratory Tract Infection. Current Infectious Disease Reports, 21(2), 6. https://doi.org/10.1007/s11908-019-0658-9
22. Hanada, S., Pirzadeh, M., Carver, K. Y., & Deng, J. C. (2018). Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Frontiers in Immunology, 9, 2640. https://www.frontiersin.org/article/10.3389/fimmu.2018.02640
23. Hilty, M., Burke, C., Pedro, H., Cardenas, P., Bush, A., Bossley, C., Davies, J., Ervine, A., Poulter, L., Pachter, L., Moffatt, M. F., & Cookson, W. O. C. (2010). Disordered Microbial Communities in Asthmatic Airways. PLOS ONE, 5(1), e8578-. https://doi.org/10.1371/journal.pone.0008578
24. Høiby, N., Ciofu, O., & Bjarnsholt, T. (2010). Pseudomonas aeruginosa biofilms in cystic fibrosis. Future Microbiology, 5(11), 1663–1674. https://doi.org/10.2217/fmb.10.125
25. Huang, Y. J., & Boushey, H. A. (2015). The microbiome in asthma. Journal of Allergy and Clinical Immunology, 135(1), 25–30. https://doi.org/10.1016/j.jaci.2014.11.011
26. Huang, Y. J., Sethi, S., Murphy, T., Nariya, S., Boushey, H. A., & Lynch, S. V. (2014). Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. Journal of clinical microbiology, 52(8), 2813–2823. https://doi.org/10.1128/JCM.00035-14
27. Iwai, S., Huang, D., Fong, S., Jarlsberg, L. G., Worodria, W., Yoo, S., Cattamanchi, A., Davis, J. L., Kaswabuli, S., Segal, M., Huang, L., & Lynch, S. v. (2014). The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients. PLOS ONE, 9(4), e95726-. https://doi.org/10.1371/journal.pone.0095726
28. Jain, S., Self, W. H., Wunderink, R. G., Fakhran, S., Balk, R., Bramley, A. M., Reed, C., Grijalva, C. G., Anderson, E. J., Courtney, D. M., Chappell, J. D., Qi, C., Hart, E. M., Carroll, F., Trabue, C., Donnelly, H. K., Williams, D. J., Zhu, Y., Arnold, S. R., … Finelli, L. (2015). Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults. New England Journal of Medicine, 373(5), 415–427. https://doi.org/10.1056/NEJMoa1500245
29. Keogh, R. H., & Stanojevic, S. (2018). A guide to interpreting estimated median age of survival in cystic fibrosis patient registry reports. Journal of Cystic Fibrosis, 17(2), 213–217. https://doi.org/10.1016/j.jcf.2017.11.014
30. Khalkhali, H. R., Oshnouei, S., Salarilak, S., Rahimi Rad, M., Karamyar, M., & Khashabi, J. (2014). Effects of antibiotic consumption on children 2-8 years of age developing asthma. Epidemiology and Health, 36, e2014006–e2014006. https://doi.org/10.4178/epih/e2014006
31. Krone, C. L., Biesbroek, G., Trzciński, K., Sanders, E. A. M., & Bogaert, D. (2014). Respiratory microbiota dynamics following Streptococcus pneumoniae acquisition in young and elderly mice. Infection and Immunity, 82(4), 1725–1731. https://doi.org/10.1128/iai.01290-13
32. Mallia, P., Message, S. D., Gielen, V., Contoli, M., Gray, K., Kebadze, T., Aniscenko, J., Laza-Stanca, V., Edwards, M. R., Slater, L., Papi, A., Stanciu, L. A., Kon, O. M., Johnson, M., & Johnston, S. L. (2011). Experimental Rhinovirus Infection as a Human Model of Chronic Obstructive Pulmonary Disease Exacerbation. American Journal of Respiratory and Critical Care Medicine, 183(6), 734–742. https://doi.org/10.1164/rccm.201006-0833OC
33. Mika, M., Mack, I., Korten, I., Qi, W., Aebi, S., Frey, U., Latzin, P., & Hilty, M. (2015). Dynamics of the nasal microbiota in infancy: A prospective cohort study. Journal of Allergy and Clinical Immunology, 135(4), 905-912.e11. https://doi.org/10.1016/j.jaci.2014.12.1909
34. Millares, L., Ferrari, R., Gallego, M., Garcia-Nuñez, M., Pérez-Brocal, V., Espasa, M., Pomares, X., Monton, C., Moya, A., & Monsó, E. (2014). Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. European Journal of Clinical Microbiology & Infectious Diseases, 33(7), 1101–1111. https://doi.org/10.1007/s10096-013-2044-0
35. Nguyen, L. D. N., Deschaght, P., Merlin, S., Loywick, A., Audebert, C., van Daele, S., Viscogliosi, E., Vaneechoutte, M., & Delhaes, L. (2016). Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation. PLOS ONE, 11(12), e0168860-. https://doi.org/10.1371/journal.pone.0168860
36. Nguyen, L. D. N., Viscogliosi, E., & Delhaes, L. (2015). The lung mycobiome: an emerging field of the human respiratory microbiome. Frontiers in Microbiology, 6, 89. https://www.frontiersin.org/article/10.3389/fmicb.2015.00089
37. Ober, C., & Yao, T.-C. (2011). The genetics of asthma and allergic disease: a 21st century perspective. Immunological Reviews, 242(1), 10–30. https://doi.org/10.1111/j.1600-065X.2011.01029.x
38. Orazi, G., & O’Toole, G. A. (2021). Pseudomonas aeruginosa Alters Staphylococcus aureus Sensitivity to Vancomycin in a Biofilm Model of Cystic Fibrosis Infection. MBio, 8(4), e00873-17. https://doi.org/10.1128/mBio.00873-17
39. Ownby, D. R., Johnson, C. C., & Peterson, E. L. (2002). Exposure to Dogs and Cats in the First Year of Life and Risk of Allergic Sensitization at 6 to 7 Years of Age. JAMA, 288(8), 963–972. https://doi.org/10.1001/jama.288.8.963
40. Pashley, C. H., Fairs, A., Free, R. C., & Wardlaw, A. J. (2012). DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology. Fungal Biology, 116(2), 214–224. https://doi.org/10.1016/j.funbio.2011.11.004
41. Pettigrew, M. M., Tanner, W., & Harris, A. D. (2021). The Lung Microbiome and Pneumonia. The Journal of Infectious Diseases, 223(Supplement_3), S241–S245. https://doi.org/10.1093/infdis/jiaa702
42. Popgeorgiev, N., Temmam, S., Raoult, D., & Desnues, C. (2013). Describing the Silent Human Virome with an Emphasis on Giant Viruses. Intervirology, 56(6), 395–412. https://doi.org/10.1159/000354561
43. Prescott, S. L. (2013). Early-life environmental determinants of allergic diseases and the wider pandemic of inflammatory noncommunicable diseases. Journal of Allergy and Clinical Immunology, 131(1), 23–30. https://doi.org/https://doi.org/10.1016/j.jaci.2012.11.019
44. Price, K. E., Hampton, T. H., Gifford, A. H., Dolben, E. L., Hogan, D. A., Morrison, H. G., Sogin, M. L., & O’Toole, G. A. (2013). Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome, 1(1), 27. https://doi.org/10.1186/2049-2618-1-27
45. Ramos-Sevillano, E., Wade, W. G., Mann, A., Gilbert, A., Lambkin-Williams, R., Killingley, B., Nguyen-Van-Tam, J. S., & Tang, C. M. (2019). The Effect of Influenza Virus on the Human Oropharyngeal Microbiome. Clinical Infectious Diseases, 68(12), 1993–2002. https://doi.org/10.1093/cid/ciy821
46. Rohde, G., Wiethege, A., Borg, I., Kauth, M., Bauer, T. T., Gillissen, A., Bufe, A., & Schultze-Werninghaus, G. (2003). Respiratory viruses in exacerbations of chronic obstructive pulmonary disease requiring hospitalisation: a case-control study. Thorax, 58(1), 37. https://doi.org/10.1136/thorax.58.1.37
47. SEEMUNGAL, T., HARPER-OWEN, R., BHOWMIK, A., MORIC, I., SANDERSON, G., MESSAGE, S., MacCALLUM, P., MEADE, T. W., JEFFRIES, D. J., JOHNSTON, S. L., & WEDZICHA, J. A. (2001). Respiratory Viruses, Symptoms, and Inflammatory Markers in Acute Exacerbations and Stable Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 164(9), 1618–1623. https://doi.org/10.1164/ajrccm.164.9.2105011
48. Shilts, M. H., Rosas-Salazar, C., Tovchigrechko, A., Larkin, E. K., Torralba, M., Akopov, A., Halpin, R., Peebles, R. S., Moore, M. L., Anderson, L. J., Nelson, K. E., Hartert, T. v, & Das, S. R. (2016). Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery. Microbial Ecology, 71(1), 233–242. https://doi.org/10.1007/s00248-015-0663-y
49. Stearns, J. C., Davidson, C. J., McKeon, S., Whelan, F. J., Fontes, M. E., Schryvers, A. B., Bowdish, D. M. E., Kellner, J. D., & Surette, M. G. (2015). Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. The ISME Journal, 9(5), 1246–1259. https://doi.org/10.1038/ismej.2014.250
50. Sze, M. A., Dimitriu, P. A., Suzuki, M., McDonough, J. E., Campbell, J. D., Brothers, J. F., Erb-Downward, J. R., Huffnagle, G. B., Hayashi, S., Elliott, W. M., Cooper, J., Sin, D. D., Lenburg, M. E., Spira, A., Mohn, W. W., & Hogg, J. C. (2015). Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 192(4), 438–445. https://doi.org/10.1164/rccm.201502-0223OC
51. Teo, S. M., Mok, D., Pham, K., Kusel, M., Serralha, M., Troy, N., Holt, B. J., Hales, B. J., Walker, M. L., Hollams, E., Bochkov, Y. A., Grindle, K., Johnston, S. L., Gern, J. E., Sly, P. D., Holt, P. G., Holt, K. E., & Inouye, M. (2015). The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development. Cell Host & Microbe, 17(5), 704–715. https://doi.org/https://doi.org/10.1016/j.chom.2015.03.008
52. Teo, S. M., Mok, D., Pham, K., Kusel, M., Serralha, M., Troy, N., Holt, B. J., Hales, B. J., Walker, M. L., Hollams, E., Bochkov, Y. A., Grindle, K., Johnston, S. L., Gern, J. E., Sly, P. D., Holt, P. G., Holt, K. E., & Inouye, M. (2015). The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development. Cell Host & Microbe, 17(5), 704–715. https://doi.org/10.1016/j.chom.2015.03.008
53. Underhill, D. M., & Iliev, I. D. (2014). The mycobiota: interactions between commensal fungi and the host immune system. Nature Reviews Immunology, 14(6), 405–416. https://doi.org/10.1038/nri3684
54. Unger, S. A., & Bogaert, D. (2017). The respiratory microbiome and respiratory infections. Journal of Infection, 74, S84–S88. https://doi.org/10.1016/S0163-4453(17)30196-2
55. Urb, M., Snarr, B. D., Wojewodka, G., Lehoux, M., Lee, M. J., Ralph, B., Divangahi, M., King, I. L., McGovern, T. K., Martin, J. G., Fraser, R., Radzioch, D., & Sheppard, D. C. (2015). Evolution of the Immune Response to Chronic Airway Colonization with Aspergillus fumigatus Hyphae. Infection and immunity, 83(9), 3590–3600. https://doi.org/10.1128/IAI.00359-15
56. Valley, T. S., Sjoding, M. W., Ryan, A. M., Iwashyna, T. J., & Cooke, C. R. (2015). Association of Intensive Care Unit Admission With Mortality Among Older Patients With Pneumonia. JAMA, 314(12), 1272–1279. https://doi.org/10.1001/jama.2015.11068
57. van Woerden, H. C., Gregory, C., Brown, R., Marchesi, J. R., Hoogendoorn, B., & Matthews, I. P. (2013). Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infectious Diseases, 13(1), 69. https://doi.org/10.1186/1471-2334-13-69
58. Wang, Z., Bafadhel, M., Haldar, K., Spivak, A., Mayhew, D., Miller, B. E., Tal-Singer, R., Johnston, S. L., Ramsheh, M. Y., Barer, M. R., Brightling, C. E., & Brown, J. R. (2016). Lung microbiome dynamics in COPD exacerbations. European Respiratory Journal, 47(4), 1082. https://doi.org/10.1183/13993003.01406-2015
59. Wardlaw, T., Salama, P., Johansson, E. W., & Mason, E. (2006). Pneumonia: the leading killer of children. The Lancet, 368(9541), 1048–1050. https://doi.org/10.1016/S0140-6736(06)69334-3
60. Watson, R. L., de Koff, E. M., & Bogaert, D. (2019). Characterising the respiratory microbiome. European Respiratory Journal, 53(2), 1801711. https://doi.org/10.1183/13993003.01711-2018
61. Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D., & Rohwer, F. (2009). Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals. PLOS ONE, 4(10), e7370-. https://doi.org/10.1371/journal.pone.0007370
62. Zaura, E., Nicu, E. A., Krom, B. P., & Keijser, B. J. F. (2014). Acquiring and maintaining a normal oral microbiome: current perspective. Frontiers in Cellular and Infection Microbiology, 4, 85. https://www.frontiersin.org/article/10.3389/fcimb.2014.00085
63. Zhao, J., Schloss, P. D., Kalikin, L. M., Carmody, L. A., Foster, B. K., Petrosino, J. F., Cavalcoli, J. D., VanDevanter, D. R., Murray, S., Li, J. Z., Young, V. B., & LiPuma, J. J. (2012). Decade-long bacterial community dynamics in cystic fibrosis airways. Proceedings of the National Academy of Sciences, 109(15), 5809. https://doi.org/10.1073/pnas.1120577109
64. Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., & Cao, B. (2020). Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet, 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3

The Vaginal Microbiome

1. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Science Translational Medicine, 6(237), 237ra65-237ra65. https://doi.org/10.1126/scitranslmed.3008599
2. Aagaard, K., Riehle, K., Ma, J., Segata, N., Mistretta, T.-A., Coarfa, C., Raza, S., Rosenbaum, S., van den Veyver, I., Milosavljevic, A., Gevers, D., Huttenhower, C., Petrosino, J., & Versalovic, J. (2012). A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. PLOS ONE, 7(6), e36466-. https://doi.org/10.1371/journal.pone.0036466
3. Abou Chacra, L., & Fenollar, F. (2021). Exploring the global vaginal microbiome and its impact on human health. Microbial Pathogenesis, 160, 105172. https://doi.org/10.1016/j.micpath.2021.105172
4. Albert, A. Y. K., Chaban, B., Wagner, E. C., Schellenberg, J. J., Links, M. G., van Schalkwyk, J., Reid, G., Hemmingsen, S. M., Hill, J. E., Money, D., & Group, V. R. (2015). A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types. PLOS ONE, 10(8), e0135620-. https://doi.org/10.1371/journal.pone.0135620
5. Allonsius, C. N., Vandenheuvel, D., Oerlemans, E. F. M., Petrova, M. I., Donders, G. G. G., Cos, P., Delputte, P., & Lebeer, S. (2019). Inhibition of Candida albicans morphogenesis by chitinase from Lactobacillus rhamnosus GG. Scientific Reports, 9(1), 2900. https://doi.org/10.1038/s41598-019-39625-0
6. Amabebe, E., & Anumba, D. O. C. (2018). The Vaginal Microenvironment: The Physiologic Role of Lactobacilli. Frontiers in Medicine, 5, 181. https://doi.org/10.3389/fmed.2018.00181
7. Amsel, R., Totten, P. A., Spiegel, C. A., Chen, K. C. S., Eschenbach, D., & Holmes, K. K. (1983). Nonspecific vaginitis: Diagnostic criteria and microbial and epidemiologic associations. The American Journal of Medicine, 74(1), 14–22. https://doi.org/10.1016/0002-9343(83)91112-9
8. Anahtar, M. N., Byrne, E. H., Doherty, K. E., Bowman, B. A., Yamamoto, H. S., Soumillon, M., Padavattan, N., Ismail, N., Moodley, A., Sabatini, M. E., Ghebremichael, M. S., Nusbaum, C., Huttenhower, C., Virgin, H. W., Ndung’u, T., Dong, K. L., Walker, B. D., Fichorova, R. N., & Kwon, D. S. (2015). Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract. Immunity, 42(5), 965–976. https://doi.org/10.1016/j.immuni.2015.04.019
9. Auriemma, R. S., Scairati, R., del Vecchio, G., Liccardi, A., Verde, N., Pirchio, R., Pivonello, R., Ercolini, D., & Colao, A. (2021). The Vaginal Microbiome: A Long Urogenital Colonization Throughout Woman Life. Frontiers in Cellular and Infection Microbiology, 11, 613. https://www.frontiersin.org/article/10.3389/fcimb.2021.686167
10. AVONTS, D., SERCU, M., HEYERICK, P., VANDERMEEREN, I., MEHEUS, A., & PIOT, P. (1990). Incidence of Uncomplicated Genital Infections in Women Using Oral Contraception or an Intrauterine Device: A Prospective Study. Sexually Transmitted Diseases, 17(1), 23–29. http://www.jstor.org/stable/44971143
11. Belay, N., Mukhopadhyay, B., E, C. de M., Galask, R., & Daniels, L. (1990). Methanogenic bacteria in human vaginal samples. Journal of Clinical Microbiology, 28(7), 1666–1668. https://doi.org/10.1128/jcm.28.7.1666-1668.1990
12. Boskey, E. R., Cone, R. A., Whaley, K. J., & Moench, T. R. (2001). Origins of vaginal acidity: high d/l lactate ratio is consistent with bacteria being the primary source. Human Reproduction, 16(9), 1809–1813. https://doi.org/10.1093/humrep/16.9.1809
13. Bradford, L. L., & Ravel, J. (2017). The vaginal mycobiome: A contemporary perspective on fungi in women’s health and diseases. Virulence, 8(3), 342–351. https://doi.org/10.1080/21505594.2016.1237332
14. Bradshaw, C. S., & Sobel, J. D. (2016). Current Treatment of Bacterial Vaginosis—Limitations and Need for Innovation. The Journal of Infectious Diseases, 214(suppl_1), S14–S20. https://doi.org/10.1093/infdis/jiw159
15. Brotman, R. M., Klebanoff, M. A., Nansel, T. R., Yu, K. F., Andrews, W. W., Zhang, J., & Schwebke, J. R. (2010). Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection. The Journal of infectious diseases, 202(12), 1907–1915. https://doi.org/10.1086/657320
16. Calzolari, E., Masciangelo, R., Milite, V., & Verteramo, R. (2000). Bacterial vaginosis and contraceptive methods. International Journal of Gynecology & Obstetrics, 70(3), 341–346. https://doi.org/https://doi.org/10.1016/S0020-7292(00)00217-4
17. Ceccarani, C., Foschi, C., Parolin, C., D’Antuono, A., Gaspari, V., Consolandi, C., Laghi, L., Camboni, T., Vitali, B., Severgnini, M., & Marangoni, A. (2019). Diversity of vaginal microbiome and metabolome during genital infections. Scientific Reports, 9(1), 14095. https://doi.org/10.1038/s41598-019-50410-x
18. Chee, W. J. Y., Chew, S. Y., & Than, L. T. L. (2020). Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health. Microbial Cell Factories, 19(1), 203. https://doi.org/10.1186/s12934-020-01464-4
19. Cherpes, T. L., Meyn, L. A., Krohn, M. A., Lurie, J. G., & Hillier, S. L. (2003). Association between acquisition of herpes simplex virus type 2 in women and bacterial vaginosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 37(3), 319–325. https://doi.org/10.1086/375819
20. Chew, S. Y., & Than, L. T. L. (2016). Vulvovaginal candidosis: contemporary challenges and the future of prophylactic and therapeutic approaches. Mycoses, 59(5), 262–273. https://doi.org/https://doi.org/10.1111/myc.12455
21. Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017). Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nature Medicine, 23(3), 314–326. https://doi.org/10.1038/nm.4272
22. Collado, M. C., Rautava, S., Aakko, J., Isolauri, E., & Salminen, S. (2016). Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Scientific Reports, 6(1), 23129. https://doi.org/10.1038/srep23129
23. de Seta, F., Campisciano, G., Zanotta, N., Ricci, G., & Comar, M. (2019). The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis. Frontiers in Microbiology, 10, 2451. https://www.frontiersin.org/article/10.3389/fmicb.2019.02451
24. de Seta, F., Lonnee-Hoffmann, R., Campisciano, G., Comar, M., Verstraelen, H., Vieira-Baptista, P., Ventolini, G., & Lev-Sagie, A. (2022). The Vaginal Microbiome: III. The Vaginal Microbiome in Various Urogenital Disorders. Journal of Lower Genital Tract Disease, 26(1). https://journals.lww.com/jlgtd/Fulltext/2022/01000/The_Vaginal_Microbiome__III__The_Vaginal.17.aspx
25. Diop, K., Dufour, J.-C., Levasseur, A., & Fenollar, F. (2019). Exhaustive repertoire of human vaginal microbiota. Human Microbiome Journal, 11, 100051. https://doi.org/10.1016/j.humic.2018.11.002
26. Donders, G. G. G., Bosmans, E., Dekeersmaecker, A., Vereecken, A., van Bulck, B., & Spitz, B. (2000). Pathogenesis of abnormal vaginal bacterial flora. American Journal of Obstetrics and Gynecology, 182(4), 872–878. https://doi.org/10.1016/S0002-9378(00)70338-3
27. Eriksen B. (1999). A randomized, open, parallel-group study on the preventive effect of an estradiol-releasing vaginal ring (Estring) on recurrent urinary tract infections in postmenopausal women. American journal of obstetrics and gynecology, 180(5), 1072–1079. https://doi.org/10.1016/s0002-9378(99)70597-1
28. Fan, W., Kan, H., Liu, H. Y., Wang, T. L., He, Y. N., Zhang, M., Li, Y. X., Li, Y. J., Meng, W., Li, Q., Hu, A. Q., & Zheng, Y. J. (2022). Association between Human Genetic Variants and the Vaginal Bacteriome of Pregnant Women. MSystems, 6(4), e00158-21. https://doi.org/10.1128/mSystems.00158-21
29. Farage, M. A., Miller, K. W., & Sobel, J. D. (2010). Dynamics of the Vaginal Ecosystem—Hormonal Influences. Infectious Diseases: Research and Treatment, 3, IDRT.S3903. https://doi.org/10.4137/IDRT.S3903
30. Feehily, C., Crosby, D., Walsh, C. J., Lawton, E. M., Higgins, S., McAuliffe, F. M., & Cotter, P. D. (2020). Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth. Npj Biofilms and Microbiomes, 6(1), 50. https://doi.org/10.1038/s41522-020-00162-8
31. Fettweis, J. M., Brooks, J. P., Serrano, M. G., Sheth, N. U., Girerd, P. H., Edwards, D. J., Strauss, J. F., Consortium, T. V. M., Jefferson, K. K., & Buck, G. A. (2014). Differences in vaginal microbiome in African American women versus women of European ancestry. Microbiology (Reading, England), 160(Pt 10), 2272–2282. https://doi.org/10.1099/mic.0.081034-0
32. Fettweis, J. M., Serrano, M. G., Brooks, J. P., Edwards, D. J., Girerd, P. H., Parikh, H. I., Huang, B., Arodz, T. J., Edupuganti, L., Glascock, A. L., Xu, J., Jimenez, N. R., Vivadelli, S. C., Fong, S. S., Sheth, N. U., Jean, S., Lee, V., Bokhari, Y. A., Lara, A. M., … Buck, G. A. (2019). The vaginal microbiome and preterm birth. Nature Medicine, 25(6), 1012–1021. https://doi.org/10.1038/s41591-019-0450-2
33. Foxman B. (2014). Urinary tract infection syndromes: occurrence, recurrence, bacteriology, risk factors, and disease burden. Infectious disease clinics of North America, 28(1), 1–13. https://doi.org/10.1016/j.idc.2013.09.003
34. France, M. T., Ma, B., Gajer, P., Brown, S., Humphrys, M. S., Holm, J. B., Waetjen, L. E., Brotman, R. M., & Ravel, J. (2020). VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome, 8(1), 166. https://doi.org/10.1186/s40168-020-00934-6
35. Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J., Schütte, U. M., Zhong, X., Koenig, S. S., Fu, L., Ma, Z. S., Zhou, X., Abdo, Z., Forney, L. J., & Ravel, J. (2012). Temporal dynamics of the human vaginal microbiota. Science translational medicine, 4(132), 132ra52. https://doi.org/10.1126/scitranslmed.3003605
36. Goldacre, M. J., Watt, B., Loudon, N., Milne, L. J., Loudon, J. D., & Vessey, M. P. (1979). Vaginal microbial flora in normal young women. British Medical Journal, 1(6176), 1450. https://doi.org/10.1136/bmj.1.6176.1450
37. Greenbaum, S., Greenbaum, G., Moran-Gilad, J., & Weintraub, A. Y. (2019). Ecological dynamics of the vaginal microbiome in relation to health and disease. American Journal of Obstetrics and Gynecology, 220(4), 324–335. https://doi.org/https://doi.org/10.1016/j.ajog.2018.11.1089
38. Gupta, P., Singh, M. P., & Goyal, K. (2020). Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity. Frontiers in Public Health, 8, 326. https://www.frontiersin.org/article/10.3389/fpubh.2020.00326
39. Gupta, S., Kakkar, V., & Bhushan, I. (2019). Crosstalk between Vaginal Microbiome and Female Health: A review. Microbial Pathogenesis, 136, 103696. https://doi.org/10.1016/j.micpath.2019.103696
40. Happel, A. U., Varsani, A., Balle, C., Passmore, J. A., & Jaspan, H. (2020). The Vaginal Virome-Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes?. Viruses, 12(8), 832. https://doi.org/10.3390/v12080832
41. Hemmerling, A., Harrison, W., Schroeder, A., Park, J., Korn, A., Shiboski, S., Foster-Rosales, A., & Cohen, C. R. (2010). Phase 2a Study Assessing Colonization Efficiency, Safety, and Acceptability of Lactobacillus crispatus CTV-05 in Women With Bacterial Vaginosis. Sexually Transmitted Diseases, 37(12). https://journals.lww.com/stdjournal/Fulltext/2010/12000/Phase_2a_Study_Assessing_Colonization_Efficiency,.3.aspx
42. Hillebrand, L., Harmanli, O. H., Whiteman, V., & Khandelwal, M. (2002). Urinary tract infections in pregnant women with bacterial vaginosis. American journal of obstetrics and gynecology, 186(5), 916–917. https://doi.org/10.1067/mob.2002.123987
43. Hooton, T. M. (2012). Uncomplicated Urinary Tract Infection. New England Journal of Medicine, 366(11), 1028–1037. https://doi.org/10.1056/NEJMcp1104429
44. Hyman, R. W., Fukushima, M., Jiang, H., Fung, E., Rand, L., Johnson, B., Vo, K. C., Caughey, A. B., Hilton, J. F., Davis, R. W., & Giudice, L. C. (2014). Diversity of the Vaginal Microbiome Correlates With Preterm Birth. Reproductive Sciences, 21(1), 32–40. https://doi.org/10.1177/1933719113488838
45. Jang, S. J., Lee, K., Kwon, B., You, H. J., & Ko, G. (2019). Vaginal lactobacilli inhibit growth and hyphae formation of Candida albicans. Scientific Reports, 9(1), 8121. https://doi.org/10.1038/s41598-019-44579-4
46. Kim, J.-M., & Park, Y. J. (2017). Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article. Jmm, 23(3), 139–145. https://doi.org/10.6118/jmm.2017.23.3.139
47. Kolter, J., & Henneke, P. (2017). Codevelopment of Microbiota and Innate Immunity and the Risk for Group B Streptococcal Disease. Frontiers in Immunology, 8, 1497. https://www.frontiersin.org/article/10.3389/fimmu.2017.01497
48. Lagenaur, L. A., Hemmerling, A., Chiu, C., Miller, S., Lee, P. P., Cohen, C. R., & Parks, T. P. (2021). Connecting the Dots: Translating the Vaginal Microbiome Into a Drug. The Journal of Infectious Diseases, 223(Supplement_3), S296–S306. https://doi.org/10.1093/infdis/jiaa676
49. Lai, S. K., Hida, K., Shukair, S., Wang, Y. Y., Figueiredo, A., Cone, R., Hope, T. J., & Hanes, J. (2009). Human immunodeficiency virus type 1 is trapped by acidic but not by neutralized human cervicovaginal mucus. Journal of virology, 83(21), 11196–11200. https://doi.org/10.1128/JVI.01899-08
50. Lee, J. B. L., & Neild, G. H. (2007). Urinary tract infection. Medicine, 35(8), 423–428. https://doi.org/10.1016/j.mpmed.2007.05.009
51. Lewis, A. L., & Gilbert, N. M. (2020). Roles of the vagina and the vaginal microbiota in urinary tract infection: evidence from clinical correlations and experimental models. GMS Infectious Diseases, 8, Doc02–Doc02. https://doi.org/10.3205/id000046
52. Liebenberg, L. J. P., Masson, L., Arnold, K. B., Mckinnon, L. R., Werner, L., Proctor, E., Archary, D., Mansoor, L. E., Lauffenburger, D. A., Abdool Karim, Q., Abdool Karim, S. S., & Passmore, J.-A. S. (2017). Genital-Systemic Chemokine Gradients and the Risk of HIV Acquisition in Women. Journal of Acquired Immune Deficiency Syndromes (1999), 74(3), 318–325. https://doi.org/10.1097/QAI.0000000000001218
53. Ma, B., Forney, L. J., & Ravel, J. (2012). Vaginal Microbiome: Rethinking Health and Disease. Annual Review of Microbiology, 66(1), 371–389. https://doi.org/10.1146/annurev-micro-092611-150157
54. Mancabelli, L., Tarracchini, C., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2021). Vaginotypes of the human vaginal microbiome. Environmental Microbiology, 23(3), 1780–1792. https://doi.org/https://doi.org/10.1111/1462-2920.15441
55. Margolis, E., & Fredricks, D. N. (2015). Chapter 83 – Bacterial Vaginosis-Associated Bacteria. In Y.-W. Tang, M. Sussman, D. Liu, I. Poxton, & J. Schwartzman (Eds.), Molecular Medical Microbiology (Second Edition) (pp. 1487–1496). Academic Press. https://doi.org/10.1016/B978-0-12-397169-2.00083-4
56. Marrazzo, J. M., Fiedler, T. L., Srinivasan, S., Thomas, K. K., Liu, C., Ko, D., Xie, H., Saracino, M., & Fredricks, D. N. (2012). Extravaginal Reservoirs of Vaginal Bacteria as Risk Factors for Incident Bacterial Vaginosis. The Journal of Infectious Diseases, 205(10), 1580–1588. https://doi.org/10.1093/infdis/jis242
57. Martin, D. H., & Marrazzo, J. M. (2016). The Vaginal Microbiome: Current Understanding and Future Directions. The Journal of Infectious Diseases, 214(suppl_1), S36–S41. https://doi.org/10.1093/infdis/jiw184
58. Martin, H. L., Richardson, B. A., Nyange, P. M., Lavreys, L., Hillier, S. L., Chohan, B., Mandaliya, K., Ndinya-Achola, J. O., Bwayo, J., & Kreiss, J. (1999). Vaginal lactobacilli, microbial flora, and risk of human immunodeficiency virus type 1 and sexually transmitted disease acquisition. The Journal of infectious diseases, 180(6), 1863–1868. https://doi.org/10.1086/315127
59. Miller, C. J., & Shattock, R. J. (2003). Target cells in vaginal HIV transmission. Microbes and Infection, 5(1), 59–67. https://doi.org/10.1016/S1286-4579(02)00056-4
60. Mitchell, H. (2004). Vaginal discharge—causes, diagnosis, and treatment. BMJ, 328(7451), 1306. https://doi.org/10.1136/bmj.328.7451.1306
61. Molenaar, M. C., Singer, M., & Ouburg, S. (2018). The two-sided role of the vaginal microbiome in Chlamydia trachomatis and Mycoplasma genitalium pathogenesis. Journal of reproductive immunology, 130, 11–17. https://doi.org/10.1016/j.jri.2018.08.006
62. Murphy, K., & Mitchell, C. M. (2016). The Interplay of Host Immunity, Environment and the Risk of Bacterial Vaginosis and Associated Reproductive Health Outcomes. The Journal of Infectious Diseases, 214(suppl_1), S29–S35. https://doi.org/10.1093/infdis/jiw140
63. Neggers, Y. H., Nansel, T. R., Andrews, W. W., Schwebke, J. R., Yu, K., Goldenberg, R. L., & Klebanoff, M. A. (2007). Dietary Intake of Selected Nutrients Affects Bacterial Vaginosis in Women. The Journal of Nutrition, 137(9), 2128–2133. https://doi.org/10.1093/jn/137.9.2128
64. Nicolle, L. E., Harding, G. K., Preiksaitis, J., & Ronald, A. R. (1982). The association of urinary tract infection with sexual intercourse. The Journal of infectious diseases, 146(5), 579–583. https://doi.org/10.1093/infdis/146.5.579
65. Nugent, R. P., Krohn, M. A., & Hillier, S. L. (1991). Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. Journal of Clinical Microbiology, 29(2), 297–301. https://doi.org/10.1128/jcm.29.2.297-301.1991
66. Oduyebo, O. O., Anorlu, R. I., & Ogunsola, F. T. (2009). The effects of antimicrobial therapy on bacterial vaginosis in non-pregnant women. The Cochrane database of systematic reviews, (3), CD006055. https://doi.org/10.1002/14651858.CD006055.pub2
67. Oerlemans, E. F. M., Bellen, G., Claes, I., Henkens, T., Allonsius, C. N., Wittouck, S., van den Broek, M. F. L., Wuyts, S., Kiekens, F., Donders, G. G. G., & Lebeer, S. (2020). Impact of a lactobacilli-containing gel on vulvovaginal candidosis and the vaginal microbiome. Scientific Reports, 10(1), 7976. https://doi.org/10.1038/s41598-020-64705-x
68. Onderdonk, A. B., Delaney, M. L., & Fichorova, R. N. (2016). The Human Microbiome during Bacterial Vaginosis. Clinical Microbiology Reviews, 29(2), 223–238. https://doi.org/10.1128/CMR.00075-15
69. Peipert, J. F., Lapane, K. L., Allsworth, J. E., Redding, C. A., Blume, J. D., & Stein, M. D. (2008). Bacterial vaginosis, race, and sexually transmitted infections: does race modify the association?. Sexually transmitted diseases, 35(4), 363–367. https://doi.org/10.1097/OLQ.0b013e31815e4179
70. Peters, B. M., Yano, J., Noverr, M. C., & Fidel Jr, P. L. (2014). Candida Vaginitis: When Opportunism Knocks, the Host Responds. PLOS Pathogens, 10(4), e1003965-. https://doi.org/10.1371/journal.ppat.1003965
71. Petrova, M. I., Imholz, N. C. E., Verhoeven, T. L. A., Balzarini, J., van Damme, E. J. M., Schols, D., Vanderleyden, J., & Lebeer, S. (2016). Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation. PLOS ONE, 11(8), e0161337-. https://doi.org/10.1371/journal.pone.0161337
72. Phares, C. R., Lynfield, R., Farley, M. M., Mohle-Boetani, J., Harrison, L. H., Petit, S., Craig, A. S., Schaffner, W., Zansky, S. M., Gershman, K., Stefonek, K. R., Albanese, B. A., Zell, E. R., Schuchat, A., & Schrag, S. J. (2008). Epidemiology of Invasive Group B Streptococcal Disease in the United States, 1999-2005. JAMA, 299(17), 2056–2065. https://doi.org/10.1001/jama.299.17.2056
73. Pino, A., Bartolo, E., Caggia, C., Cianci, A., & Randazzo, C. L. (2019). Detection of vaginal lactobacilli as probiotic candidates. Scientific Reports, 9(1), 3355. https://doi.org/10.1038/s41598-019-40304-3
74. Prais, D., Straussberg, R., Avitzur, Y., Nussinovitch, M., Harel, L., & Amir, J. (2003). Bacterial susceptibility to oral antibiotics in community acquired urinary tract infection. Archives of Disease in Childhood, 88(3), 215. https://doi.org/10.1136/adc.88.3.215
75. Prince, A. L., Chu, D. M., Seferovic, M. D., Antony, K. M., Ma, J., & Aagaard, K. M. (2015). The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome. Cold Spring Harbor Perspectives in Medicine, 5(6). https://doi.org/10.1101/cshperspect.a023051
76. Quin, C., Vollman, D. M., Ghosh, S., Haskey, N., Estaki, M., Pither, J., Barnett, J. A., Jay, M. N., Birnie, B. W., & Gibson, D. L. (2020). Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants. The ISME Journal, 14(8), 2090–2104. https://doi.org/10.1038/s41396-020-0672-9
77. Rautava, S., Luoto, R., Salminen, S., & Isolauri, E. (2012). Microbial contact during pregnancy, intestinal colonization and human disease. Nature Reviews Gastroenterology & Hepatology, 9(10), 565–576. https://doi.org/10.1038/nrgastro.2012.144
78. Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., Brotman, R. M., Davis, C. C., Ault, K., Peralta, L., & Forney, L. J. (2011). Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences, 108(Supplement 1), 4680. https://doi.org/10.1073/pnas.1002611107
79. Raz, R., & Stamm, W. E. (1993). A controlled trial of intravaginal estriol in postmenopausal women with recurrent urinary tract infections. The New England journal of medicine, 329(11), 753–756. https://doi.org/10.1056/NEJM199309093291102
80. Schwebke, J. R. (2000). Asymptomatic bacterial vaginosis: Response to therapy. American Journal of Obstetrics and Gynecology, 183(6), 1434–1439. https://doi.org/https://doi.org/10.1067/mob.2000.107735
81. Sewankambo, N., Gray, R. H., Wawer, M. J., Paxton, L., McNaim, D., Wabwire-Mangen, F., Serwadda, D., Li, C., Kiwanuka, N., Hillier, S. L., Rabe, L., Gaydos, C. A., Quinn, T. C., & Konde-Lule, J. (1997). HIV-1 infection associated with abnormal vaginal flora morphology and bacterial vaginosis. Lancet (London, England), 350(9077), 546–550. https://doi.org/10.1016/s0140-6736(97)01063-5
82. Sheerin, N. S. (2011). Urinary tract infection. Medicine, 39(7), 384–389. https://doi.org/10.1016/j.mpmed.2011.04.003
83. Siqueira, J. D., Curty, G., Xutao, D., Hofer, C. B., Machado, E. S., Seuánez, H. N., Soares, M. A., Delwart, & E., Soares, E. A. (2019). Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency. Viruses, 11(5):422. https://doi.org/10.3390/v11050422
84. Stapleton A. E. (2016). The Vaginal Microbiota and Urinary Tract Infection. Microbiology spectrum, 4(6), 10.1128/microbiolspec.UTI-0025-2016. https://doi.org/10.1128/microbiolspec.UTI-0025-2016
85. Stapleton, A. E., Au-Yeung, M., Hooton, T. M., Fredricks, D. N., Roberts, P. L., Czaja, C. A., Yarova-Yarovaya, Y., Fiedler, T., Cox, M., & Stamm, W. E. (2011). Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 52(10), 1212–1217. https://doi.org/10.1093/cid/cir183
86. Sumati, A. H., & Saritha, N. K. (2009). Association of urinary tract infection in women with bacterial vaginosis. Journal of global infectious diseases, 1(2), 151–152. https://doi.org/10.4103/0974-777X.56254
87. Swidsinski, A., Mendling, W., Loening-Baucke, V., Swidsinski, S., Dörffel, Y., Scholze, J., Lochs, H., & Verstraelen, H. (2008). An adherent Gardnerella vaginalis biofilm persists on the vaginal epithelium after standard therapy with oral metronidazole. American Journal of Obstetrics and Gynecology, 198(1), 97.e1-97.e6. https://doi.org/10.1016/j.ajog.2007.06.039
88. Ta, L. D. H., Chan, J. C. Y., Yap, G. C., Purbojati, R. W., Drautz-Moses, D. I., Koh, Y. M., Tay, C. J. X., Huang, C.-H., Kioh, D. Y. Q., Woon, J. Y., Tham, E. H., Loo, E. X. L., Shek, L. P. C., Karnani, N., Goh, A., van Bever, H. P. S., Teoh, O. H., Chan, Y. H., Lay, C., … Lee, B. W. (2020). A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema. Gut Microbes, 12(1), 1801964. https://doi.org/10.1080/19490976.2020.1801964
89. Tachedjian, G., Aldunate, M., Bradshaw, C. S., & Cone, R. A. (2017). The role of lactic acid production by probiotic Lactobacillus species in vaginal health. Research in Microbiology, 168(9), 782–792. https://doi.org/10.1016/j.resmic.2017.04.001
90. Taha, T. E., Hoover, D. R., Dallabetta, G. A., Kumwenda, N. I., Mtimavalye, L. A. R., Yang, L.-P., Liomba, G. N., Broadhead, R. L., Chiphangwi, J. D., & Miotti, P. G. (1998). Bacterial vaginosis and disturbances of vaginal flora: association with increased acquisition of HIV. AIDS, 12(13). https://journals.lww.com/aidsonline/...aginal.19.aspx
91. Tan, C. W., & Chlebicki, M. P. (2016). Urinary tract infections in adults. Singapore Medical Journal, 57(9), 485–490. https://doi.org/10.11622/smedj.2016153
92. Tazi, A., Plainvert, C., Anselem, O., Ballon, M., Marcou, V., Seco, A., el Alaoui, F., Joubrel, C., el Helali, N., Falloukh, E., Frigo, A., Raymond, J., Trieu-Cuot, P., Branger, C., le Monnier, A., Azria, E., Ancel, P.-Y., Jarreau, P. H., Mandelbrot, L., … Poyart, C. (2019). Risk Factors for Infant Colonization by Hypervirulent CC17 Group B Streptococcus: Toward the Understanding of Late-onset Disease. Clinical Infectious Diseases, 69(10), 1740–1748. https://doi.org/10.1093/cid/ciz033
93. Torcia, M. G. (2019). Interplay among Vaginal Microbiome, Immune Response and Sexually Transmitted Viral Infections. International Journal of Molecular Sciences, 20(2):266. https://doi.org/10.3390/ijms20020266
94. van de Wijgert, J., & Verwijs, M. C. (2020). Lactobacilli-containing vaginal probiotics to cure or prevent bacterial or fungal vaginal dysbiosis: a systematic review and recommendations for future trial designs. BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 287–299. https://doi.org/10.1111/1471-0528.15870
95. Verstraelen, H., Verhelst, R., Vaneechoutte, M., & Temmerman, M. (2010). The epidemiology of bacterial vaginosis in relation to sexual behaviour. BMC Infectious Diseases, 10(1), 81. https://doi.org/10.1186/1471-2334-10-81
96. Wiesenfeld, H. C., Hillier, S. L., Krohn, M. A., Landers, D. v, & Sweet, R. L. (2003). Bacterial Vaginosis Is a Strong Predictor of Neisseria gonorrhoeae and Chlamydia trachomatis Infection. Clinical Infectious Diseases, 36(5), 663–668. https://doi.org/10.1086/367658
97. Wylie, K. M., Wylie, T. N., Cahill, A. G., Macones, G. A., Tuuli, M. G., & Stout, M. J. (2018). The vaginal eukaryotic DNA virome and preterm birth. American Journal of Obstetrics and Gynecology, 219(2), 189.e1-189.e12. https://doi.org/10.1016/j.ajog.2018.04.048
98. Xu, J., Bian, G., Zheng, M., Lu, G., Chan, W.-Y., Li, W., Yang, K., Chen, Z.-J., & Du, Y. (2020). Fertility factors affect the vaginal microbiome in women of reproductive age. American Journal of Reproductive Immunology, 83(4), e13220. https://doi.org/10.1111/aji.13220
99. Zabor, E. C., Klebanoff, M., Yu, K., Zhang, J., Nansel, T., Andrews, W., Schwebke, J., & Jeffcoat, M. (2010). Association between periodontal disease, bacterial vaginosis, and sexual risk behaviours. Journal of Clinical Periodontology, 37(10), 888–893. https://doi.org/10.1111/j.1600-051X.2010.01593.x
100. Zaleznik, D. F., Rench, M. A., Hillier, S., Krohn, M. A., Platt, R., Lee, M.-L. T., Flores, A. E., Ferrieri, P., & Baker, C. J. (2000). Invasive Disease Due to Group B Streptococcus in Pregnant Women and Neonates from Diverse Population Groups. Clinical Infectious Diseases, 30(2), 276–281. https://doi.org/10.1086/313665
101. Zapata, H. J., & Quagliarello, V. J. (2015). The Microbiota and Microbiome in Aging: Potential Implications in Health and Age-Related Diseases. Journal of the American Geriatrics Society, 63(4), 776–781. https://doi.org/10.1111/jgs.13310
102. Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., & Martin, D. H. (2016). Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome, 4(1), 16. https://doi.org/10.1186/s40168-016-0161-6

Mental Health and Multi-Microbiome Interactions

1. Acharya, C., Sahingur, S. E., & Bajaj, J. S. (2017). Microbiota, cirrhosis, and the emerging oral-gut-liver axis. JCI Insight, 2(19), e94416. https://doi.org/10.1172/jci.insight.94416
2. Allali, I., Bakri, Y., Amzazi, S., & Ghazal, H. (2021). Gut-Lung Axis in COVID-19. Interdisciplinary Perspectives on Infectious Diseases, 2021, 6655380. https://doi.org/10.1155/2021/6655380
3. Alonso, R., Pisa, D., Fernández-Fernández, A. M., & Carrasco, L. (2018). Infection of Fungi and Bacteria in Brain Tissue From Elderly Persons and Patients With Alzheimer’s Disease. Frontiers in Aging Neuroscience, 10. https://www.frontiersin.org/article/10.3389/fnagi.2018.00159
4. Bäsler, K., Galliano, M.-F., Bergmann, S., Rohde, H., Wladykowski, E., Vidal-y-Sy, S., Guiraud, B., Houdek, P., Schüring, G., Volksdorf, T., Caruana, A., Bessou-Touya, S., Schneider, S. W., Duplan, H., & Brandner, J. M. (2017). Biphasic influence of Staphylococcus aureus on human epidermal tight junctions. Annals of the New York Academy of Sciences, 1405(1), 53–70. https://doi.org/https://doi.org/10.1111/nyas.13418
5. Bear T, Dalziel J, Coad J, Roy N, Butts C, & Gopal P. (2021). The Microbiome-Gut-Brain Axis and Resilience to Developing Anxiety or Depression under Stress. Microorganisms, 9(4):723. https://doi.org/10.3390/microorganisms9040723
6. Beri, K. (2018). Skin microbiome & host immunity: applications in regenerative cosmetics & transdermal drug delivery. Future Science OA, 4(6), FSO302. https://doi.org/10.4155/fsoa-2017-0117
7. Boix-Amorós, A., Collado, M. C., & Mira, A. (2016). Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation. Frontiers in microbiology, 7, 492. https://doi.org/10.3389/fmicb.2016.00492
8. Borre, Y. E., O’Keeffe, G. W., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2014). Microbiota and neurodevelopmental windows: implications for brain disorders. Trends in Molecular Medicine, 20(9), 509–518. https://doi.org/10.1016/j.molmed.2014.05.002
9. Branton, W. G., Ellestad, K. K., Maingat, F., Wheatley, B. M., Rud, E., Warren, R. L., Holt, R. A., Surette, M. G., & Power, C. (2013). Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status. PLOS ONE, 8(1), e54673-. https://doi.org/10.1371/journal.pone.0054673
10. Bruce-Keller, A. J., Salbaum, J. M., & Berthoud, H.-R. (2018). Harnessing Gut Microbes for Mental Health: Getting From Here to There. Biological Psychiatry, 83(3), 214–223. https://doi.org/10.1016/j.biopsych.2017.08.014
11. Bui, U. T., Finlayson, K., & Edwards, H. (2018). Risk factors for infection in patients with chronic leg ulcers: A survival analysis. International Journal of Clinical Practice, 72(12), e13263. https://doi.org/10.1111/ijcp.13263
12. Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Goldman, B. D., Ahn, M., Styner, M. A., Thompson, A. L., Geng, X., Gilmore, J. H., & Knickmeyer, R. C. (2018). Infant Gut Microbiome Associated With Cognitive Development. Biological Psychiatry, 83(2), 148–159. https://doi.org/10.1016/j.biopsych.2017.06.021
13. Civardi, E., Garofoli, F., Tzialla, C., Paolillo, P., Bollani, L., & Stronati, M. (2013). Microorganisms in human milk: lights and shadows. The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians, 26 Suppl 2, 30–34. https://doi.org/10.3109/14767058.2013.829693
14. Cowan, C. S. M., Hoban, A. E., Ventura-Silva, A. P., Dinan, T. G., Clarke, G., & Cryan, J. F. (2018). Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling. BioEssays, 40(1), 1700172. https://doi.org/https://doi.org/10.1...bies.201700172
15. Cryan, J. F., & Dinan, T. G. (2012). Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13(10), 701–712. https://doi.org/10.1038/nrn3346
16. Cryan, J. F., O’Riordan, K. J., Cowan, C. S. M., Sandhu, K. v, Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. v, Guzzetta, K. E., Jaggar, M., Long-Smith, C. M., Lyte, J. M., Martin, J. A., Molinero-Perez, A., Moloney, G., Morelli, E., Morillas, E., … Dinan, T. G. (2019). The Microbiota-Gut-Brain Axis. Physiological Reviews, 99(4), 1877–2013. https://doi.org/10.1152/physrev.00018.2018
17. Dash, S., Clarke, G., Berk, M., & Jacka, F. N. (2015). The gut microbiome and diet in psychiatry: focus on depression. Current Opinion in Psychiatry, 28(1). https://journals.lww.com/co-psychiatry/Fulltext/2015/01000/The_gut_microbiome_and_diet_in_psychiatry__focus.2.aspx
18. De Pessemier B, Grine L, Debaere M, Maes A, Paetzold B, Callewaert C. (2021). Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions. Microorganisms, 9(2):353. https://doi.org/10.3390/microorganisms9020353
19. Desbonnet, L., Clarke, G., Shanahan, F., Dinan, T. G., & Cryan, J. F. (2014). Microbiota is essential for social development in the mouse. Molecular Psychiatry, 19(2), 146–148. https://doi.org/10.1038/mp.2013.65
20. Diaz Heijtz, R. (2016). Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior. Seminars in Fetal and Neonatal Medicine, 21(6), 410–417. https://doi.org/10.1016/j.siny.2016.04.012
21. Dinan, T. G., & Cryan, J. F. (2017). Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration. The Journal of Physiology, 595(2), 489–503. https://doi.org/10.1113/JP273106
22. Dinan, T. G., Stanton, C., & Cryan, J. F. (2013). Psychobiotics: A Novel Class of Psychotropic. Biological Psychiatry, 74(10), 720–726. https://doi.org/10.1016/j.biopsych.2013.05.001
23. Dominy, S. S., Casey, L., Florian, E., Malgorzata, B., Agata, M., Andrei, K., Mai, N., Ursula, H., Debasish, R., Christina, G., J, H. L., Shirin, A.-K., Samer, K., Alexander, L., I, R. M., Barbara, P., Piotr, M., Annelie, H., Karina, A., … Jan, P. (2022). Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Science Advances, 5(1), eaau3333. https://doi.org/10.1126/sciadv.aau3333
24. Drago, L., Zuccotti, G. V., Romanò, C. L., Goswami, K., Villafañe, J. H., Mattina, R., & Parvizi, J. (2019). Oral–Gut Microbiota and Arthritis: Is There an Evidence-Based Axis? Journal of Clinical Medicine, 8(10):1753. https://doi.org/10.3390/jcm8101753
25. du Teil Espina, M., Gabarrini, G., Harmsen, H. J. M., Westra, J., van Winkelhoff, A. J., & van Dijl, J. M. (2019). Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis. FEMS Microbiology Reviews, 43(1), 1–18. https://doi.org/10.1093/femsre/fuy035
26. Enaud, R., Prevel, R., Ciarlo, E., Beaufils, F., Wieërs, G., Guery, B., & Delhaes, L. (2020). The Gut-Lung Axis in Health and Respiratory Diseases: A Place for Inter-Organ and Inter-Kingdom Crosstalks. Frontiers in Cellular and Infection Microbiology, 10. https://www.frontiersin.org/article/10.3389/fcimb.2020.00009
27. Frati F, Salvatori C, Incorvaia C, Bellucci A, Di Cara G, Marcucci F, & Esposito S. (2019). The Role of the Microbiome in Asthma: The Gut–Lung Axis. International Journal of Molecular Sciences, 20(1):123. https://doi.org/10.3390/ijms20010123
28. Gareau, M. G. (2016). Chapter Eleven – Cognitive Function and the Microbiome. In J. F. Cryan & G. Clarke (Eds.), International Review of Neurobiology (Vol. 131, pp. 227–246). Academic Press. https://doi.org/10.1016/bs.irn.2016.08.001
29. Green, J., Jester, R., McKinley, R., & Pooler, A. (2014). The impact of chronic venous leg ulcers: a systematic review. Journal of Wound Care, 23(12), 601–612. https://doi.org/10.12968/jowc.2014.23.12.601
30. Gupta, M. A., Jarosz, P., & Gupta, A. K. (2017). Posttraumatic stress disorder (PTSD) and the dermatology patient. Clinics in Dermatology, 35(3), 260–266. https://doi.org/10.1016/j.clindermatol.2017.01.005
31. Gur, T. L., Worly, B. L., & Bailey, M. T. (2015). Stress and the Commensal Microbiota: Importance in Parturition and Infant Neurodevelopment. Frontiers in Psychiatry, 6. https://www.frontiersin.org/article/10.3389/fpsyt.2015.00005
32. Hassan, Z., Mustafa, S., Rahim, R. A., & Isa, N. M. (2016). Anti-breast cancer effects of live, heat-killed and cytoplasmic fractions of Enterococcus faecalis and Staphylococcus hominis isolated from human breast milk. In vitro cellular & developmental biology. Animal, 52(3), 337–348. https://doi.org/10.1007/s11626-015-9978-8
33. He, Z., Cui, B.-T., Zhang, T., Li, P., Long, C.-Y., Ji, G.-Z., & Zhang, F.-M. (2017). Fecal microbiota transplantation cured epilepsy in a case with Crohn’s disease: The first report. World Journal of Gastroenterology, 23(19), 3565–3568. https://doi.org/10.3748/wjg.v23.i19.3565
34. Heikkilä, M. P., & Saris, P. E. (2003). Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. Journal of applied microbiology, 95(3), 471–478. https://doi.org/10.1046/j.1365-2672.2003.02002.x
35. Heneka, M. T., Kummer, M. P., & Latz, E. (2014). Innate immune activation in neurodegenerative disease. Nature Reviews Immunology, 14(7), 463–477. https://doi.org/10.1038/nri3705
36. Hoban, A. E., Stilling, R. M., Moloney, G., Shanahan, F., Dinan, T. G., Clarke, G., & Cryan, J. F. (2018). The microbiome regulates amygdala-dependent fear recall. Molecular Psychiatry, 23(5), 1134–1144. https://doi.org/10.1038/mp.2017.100
37. Ilievski, V., Zuchowska, P. K., Green, S. J., Toth, P. T., Ragozzino, M. E., Le, K., Aljewari, H. W., O’Brien-Simpson, N. M., Reynolds, E. C., & Watanabe, K. (2018). Chronic oral application of a periodontal pathogen results in brain inflammation, neurodegeneration and amyloid beta production in wild type mice. PLOS ONE, 13(10), e0204941-. https://doi.org/10.1371/journal.pone.0204941
38. Jung, C.-R., Lin, Y.-T., & Hwang, B.-F. (2015). Ozone, Particulate Matter, and Newly Diagnosed Alzheimer’s Disease: A Population-Based Cohort Study in Taiwan. Journal of Alzheimer’s Disease, 44, 573–584. https://doi.org/10.3233/JAD-140855
39. Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E. L., Roux, S., Sadowsky, M. J., Lipson, K. S., Sullivan, M. B., Caporaso, J. G., & Krajmalnik-Brown, R. (2017). Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome, 5(1), 10. https://doi.org/10.1186/s40168-016-0225-7
40. Kelly, J., Kennedy, P., Cryan, J., Dinan, T., Clarke, G., & Hyland, N. (2015). Breaking Down the Barriers: The Gut Microbiome, Intestinal Permeability and Stress-related Psychiatric Disorders. Frontiers in Cellular Neuroscience, 9. https://www.frontiersin.org/article/10.3389/fncel.2015.00392
41. Kesika, P., Suganthy, N., Sivamaruthi, B. S., & Chaiyasut, C. (2021). Role of gut-brain axis, gut microbial composition, and probiotic intervention in Alzheimer’s disease. Life Sciences, 264, 118627. https://doi.org/10.1016/j.lfs.2020.118627
42. Kirrane, E. F., Bowman, C., Davis, J. A., Hoppin, J. A., Blair, A., Chen, H., Patel, M. M., Sandler, D. P., Tanner, C. M., Vinikoor-Imler, L., Ward, M. H., Luben, T. J., & Kamel, F. (2015). Associations of Ozone and PM2.5 Concentrations With Parkinson’s Disease Among Participants in the Agricultural Health Study. Journal of Occupational and Environmental Medicine, 57(5), 509–517. https://doi.org/10.1097/JOM.0000000000000451
43. Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017). Our Gut Microbiome: The Evolving Inner Self. Cell, 171(7), 1481–1493. https://doi.org/10.1016/j.cell.2017.11.024
44. Lara-Villoslada, F., Olivares, M., Sierra, S., Rodríguez, J. M., Boza, J., & Xaus, J. (2007). Beneficial effects of probiotic bacteria isolated from breast milk. The British journal of nutrition, 98 Suppl 1, S96–S100. https://doi.org/10.1017/S0007114507832910
45. Leclercq, S., Cani, P. D., Neyrinck, A. M., Stärkel, P., Jamar, F., Mikolajczak, M., Delzenne, N. M., & de Timary, P. (2012). Role of intestinal permeability and inflammation in the biological and behavioral control of alcohol-dependent subjects. Brain, Behavior, and Immunity, 26(6), 911–918. https://doi.org/10.1016/j.bbi.2012.04.001
46. Li, M., van Esch, B. C. A. M., Wagenaar, G. T. M., Garssen, J., Folkerts, G., & Henricks, P. A. J. (2018). Pro- and anti-inflammatory effects of short chain fatty acids on immune and endothelial cells. European Journal of Pharmacology, 831, 52–59. https://doi.org/10.1016/j.ejphar.2018.05.003
47. Liang S, Wu X, Hu X, Wang T, & Jin F. (2018b). Recognizing Depression from the Microbiota–Gut–Brain Axis. International Journal of Molecular Sciences, 19(6):1592. https://doi.org/10.3390/ijms19061592
48. Liang, S., Wang, T., Hu, X., Luo, J., Li, W., Wu, X., Duan, Y., & Jin, F. (2015). Administration of Lactobacillus helveticus NS8 improves behavioral, cognitive, and biochemical aberrations caused by chronic restraint stress. Neuroscience, 310, 561–577. https://doi.org/10.1016/j.neuroscience.2015.09.033
49. Liang, S., Wu, X., & Jin, F. (2018). Gut-Brain Psychology: Rethinking Psychology From the Microbiota–Gut–Brain Axis. Frontiers in Integrative Neuroscience, 12. https://www.frontiersin.org/article/10.3389/fnint.2018.00033
50. Limon, J. J., Tang, J., Li, D., Wolf, A. J., Michelsen, K. S., Funari, V., Gargus, M., Nguyen, C., Sharma, P., Maymi, V. I., Iliev, I. D., Skalski, J. H., Brown, J., Landers, C., Borneman, J., Braun, J., Targan, S. R., McGovern, D. P. B., & Underhill, D. M. (2019). Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell Host & Microbe, 25(3), 377-388.e6. https://doi.org/10.1016/j.chom.2019.01.007
51. Link, C. D. (2021). Is There a Brain Microbiome? Neuroscience Insights, 16, 26331055211018708–26331055211018708. https://doi.org/10.1177/26331055211018709
52. Luczynski, P., McVey Neufeld, K.-A., Oriach, C. S., Clarke, G., Dinan, T. G., & Cryan, J. F. (2016). Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behavior. International Journal of Neuropsychopharmacology, 19(8), pyw020. https://doi.org/10.1093/ijnp/pyw020
53. Ma, Q., Xing, C., Long, W., Wang, H. Y., Liu, Q., & Wang, R.-F. (2019). Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis. Journal of Neuroinflammation, 16(1), 53. https://doi.org/10.1186/s12974-019-1434-3
54. Maitre Y, Micheneau P, Delpierre A, Mahalli R, Guerin M, Amador G, Denis F. (2020). Did the Brain and Oral Microbiota Talk to Each Other? A Review of the Literature. Journal of Clinical Medicine, 9(12):3876. https://doi.org/10.3390/jcm9123876
55. Manderino L, Carroll I, Azcarate-Peril MA, Rochette A, Heinberg L, Peat C, Steffen K, Mitchell J, Gunstad J. Preliminary Evidence for an Association Between the Composition of the Gut Microbiome and Cognitive Function in Neurologically Healthy Older Adults. J Int Neuropsychol Soc. 2017 Sep;23(8):700-705. doi: 10.1017/S1355617717000492. Epub 2017 Jun 23. PMID: 28641593; PMCID: PMC6111127.
56. Mika, A., Day, H. E. W., Martinez, A., Rumian, N. L., Greenwood, B. N., Chichlowski, M., Berg, B. M., & Fleshner, M. (2017). Early life diets with prebiotics and bioactive milk fractions attenuate the impact of stress on learned helplessness behaviours and alter gene expression within neural circuits important for stress resistance. European Journal of Neuroscience, 45(3), 342–357. https://doi.org/https://doi.org/10.1111/ejn.13444
57. Mika, A., Day, H. E. W., Martinez, A., Rumian, N. L., Greenwood, B. N., Chichlowski, M., Berg, B. M., & Fleshner, M. (2017). Early life diets with prebiotics and bioactive milk fractions attenuate the impact of stress on learned helplessness behaviours and alter gene expression within neural circuits important for stress resistance. European Journal of Neuroscience, 45(3), 342–357. https://doi.org/10.1111/ejn.13444
58. Mousavi, S. E., Delgado-Saborit, J. M., Adivi, A., Pauwels, S., & Godderis, L. (2021). Air pollution and endocrine disruptors induce human microbiome imbalances: A systematic review of recent evidence and possible biological mechanisms. Science of The Total Environment, 151654. https://doi.org/10.1016/j.scitotenv.2021.151654
59. Mumaw, C. L., Levesque, S., McGraw, C., Robertson, S., Lucas, S., Stafflinger, J. E., Campen, M. J., Hall, P., Norenberg, J. P., Anderson, T., Lund, A. K., McDonald, J. D., Ottens, A. K., & Block, M. L. (2016). Microglial priming through the lung—brain axis: the role of air pollution-induced circulating factors. The FASEB Journal, 30(5), 1880–1891. https://doi.org/10.1096/fj.201500047
60. Mussap, M., Noto, A., & Fanos, V. (2016). Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites. Expert Review of Molecular Diagnostics, 16(8), 869–881. https://doi.org/10.1080/14737159.2016.1202765
61. Narengaowa, Kong, W., Lan, F., Awan, U. F., Qing, H., & Ni, J. (2021). The Oral-Gut-Brain AXIS: The Influence of Microbes in Alzheimer’s Disease. Frontiers in Cellular Neuroscience, 15. https://www.frontiersin.org/article/10.3389/fncel.2021.633735
62. Nishida, A. H., & Ochman, H. (2018). Rates of gut microbiome divergence in mammals. Molecular Ecology, 27(8), 1884–1897. https://doi.org/10.1111/mec.14473
63. Nyangahu, D. D., & Jaspan, H. B. (2019). Influence of maternal microbiota during pregnancy on infant immunity. Clinical & Experimental Immunology, 198(1), 47–56. https://doi.org/10.1111/cei.13331
64. O’Mahony, S. M., Clarke, G., Dinan, T. G., & Cryan, J. F. (2017). Early-life adversity and brain development: Is the microbiome a missing piece of the puzzle? Neuroscience, 342, 37–54. https://doi.org/10.1016/j.neuroscience.2015.09.068
65. O’Neill, C. A., Monteleone, G., McLaughlin, J. T., & Paus, R. (2016). The gut-skin axis in health and disease: A paradigm with therapeutic implications. BioEssays, 38(11), 1167–1176. https://doi.org/10.1002/bies.201600008
66. Ojo-Okunola, A., Claassen-Weitz, S., Mwaikono, K. S., Gardner-Lubbe, S., Stein, D. J., Zar, H. J., Nicol, M. P., & du Toit, E. (2019) Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women. Nutrients, 11(6):1390. https://doi.org/10.3390/nu11061390
67. Ojo-Okunola, A., Nicol, M., & Du Toit, E. (2018). Human Breast Milk Bacteriome in Health and Disease. Nutrients, 10(11):1643. https://doi.org/10.3390/nu10111643
68. Olivares, M., Díaz-Ropero, M. P., Martín, R., Rodríguez, J. M., & Xaus, J. (2006). Antimicrobial potential of four Lactobacillus strains isolated from breast milk. Journal of applied microbiology, 101(1), 72–79. https://doi.org/10.1111/j.1365-2672.2006.02981.x
69. Olsen, I. (2008). Update on bacteraemia related to dental procedures. Transfusion and Apheresis Science, 39(2), 173–178. https://doi.org/10.1016/j.transci.2008.06.008
70. Olsen, I., & Hicks, S. D. (2020). Oral microbiota and autism spectrum disorder (ASD). Journal of Oral Microbiology, 12(1), 1702806. https://doi.org/10.1080/20002297.2019.1702806
71. Olsen, I., & Singhrao, S. K. (2015). Can oral infection be a risk factor for Alzheimer’s disease? Journal of Oral Microbiology, 7(1), 29143. https://doi.org/10.3402/jom.v7.29143
72. Park S-Y, Hwang B-O, Lim M, Ok S-H, Lee S-K, Chun K-S, Park K-K, Hu Y, Chung W-Y, Song N-Y. (2021). Oral–Gut Microbiome Axis in Gastrointestinal Disease and Cancer. Cancers, 13(9):2124. https://doi.org/10.3390/cancers13092124
73. Pedras, S., Carvalho, R., & Pereira, M. G. (2016). Predictors of quality of life in patients with diabetic foot ulcer: The role of anxiety, depression, and functionality. Journal of Health Psychology, 23(11), 1488–1498. https://doi.org/10.1177/1359105316656769
74. Penders, J., Thijs, C., van den Brandt, P. A., Kummeling, I., Snijders, B., Stelma, F., Adams, H., van Ree, R., & Stobberingh, E. E. (2007). Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut, 56(5), 661. https://doi.org/10.1136/gut.2006.100164
75. Pirbaglou, M., Katz, J., de Souza, R. J., Stearns, J. C., Motamed, M., & Ritvo, P. (2016). Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials. Nutrition Research, 36(9), 889–898. https://doi.org/10.1016/j.nutres.2016.06.009
76. Potgieter, M., Bester, J., Kell, D. B., & Pretorius, E. (2015). The dormant blood microbiome in chronic, inflammatory diseases. FEMS Microbiology Reviews, 39(4), 567–591. https://doi.org/10.1093/femsre/fuv013
77. Power, M. C., Weisskopf, M. G., Alexeeff, S. E., Coull, B. A., Spiro, A., & Swartz, J. (2011). Traffic-Related Air Pollution and Cognitive Function in a Cohort of Older Men. Environmental Health Perspectives, 119(5), 682–687. https://doi.org/10.1289/ehp.1002767
78. Ranjan, R., Abhinay, A., & Mishra, M. (2018). Can oral microbial infections be a risk factor for neurodegeneration? A review of the literature. Neurol India, 66:344-51
79. Renner R, Erfurt-Berge C. (2017). Depression and quality of life in patients with chronic wounds: ways to measure their influence and their effect on daily life. Chronic Wound Care Management and Research, 4:143-151 https://doi.org/10.2147/CWCMR.S124917
80. Roberts, A. L., Kristen, L., Hart, J. E., Francine, L., Just, A. C., Bobb, J. F., Koenen, K. C., Alberto, A., & Weisskopf, M. G. (2013). Perinatal Air Pollutant Exposures and Autism Spectrum Disorder in the Children of Nurses’ Health Study II Participants. Environmental Health Perspectives, 121(8), 978–984. https://doi.org/10.1289/ehp.1206187
81. Rook, G. A. W., & Lowry, C. A. (2008). The hygiene hypothesis and psychiatric disorders. Trends in Immunology, 29(4), 150–158. https://doi.org/10.1016/j.it.2008.01.002
82. Roy, S., Elgharably, H., Sinha, M., Ganesh, K., Chaney, S., Mann, E., Miller, C., Khanna, S., Bergdall, V. K., Powell, H. M., Cook, C. H., Gordillo, G. M., Wozniak, D. J., & Sen, C. K. (2014). Mixed-species biofilm compromises wound healing by disrupting epidermal barrier function. The Journal of Pathology, 233(4), 331–343. https://doi.org/10.1002/path.4360
83. Salem, I., Ramser, A., Isham, N., & Ghannoum, M. A. (2018). The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Frontiers in Microbiology, 9. https://www.frontiersin.org/article/10.3389/fmicb.2018.01459
84. Salliss, M. E., Farland, L. v, Mahnert, N. D., & Herbst-Kralovetz, M. M. (2022). The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain. Human Reproduction Update, 28(1), 92–131. https://doi.org/10.1093/humupd/dmab035
85. Sampson, T. R., & Mazmanian, S. K. (2015). Control of Brain Development, Function, and Behavior by the Microbiome. Cell Host & Microbe, 17(5), 565–576. https://doi.org/10.1016/j.chom.2015.04.011
86. Sencio, V., Barthelemy, A., Tavares, L. P., Machado, M. G., Soulard, D., Cuinat, C., Queiroz-Junior, C. M., Noordine, M.-L., Salomé-Desnoulez, S., Deryuter, L., Foligné, B., Wahl, C., Frisch, B., Vieira, A. T., Paget, C., Milligan, G., Ulven, T., Wolowczuk, I., Faveeuw, C., … Trottein, F. (2020). Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal Superinfection through Altered Short-Chain Fatty Acid Production. Cell Reports, 30(9), 2934-2947.e6. https://doi.org/10.1016/j.celrep.2020.02.013
87. Sharon, G., Sampson, T. R., Geschwind, D. H., & Mazmanian, S. K. (2016). The Central Nervous System and the Gut Microbiome. Cell, 167(4), 915–932. https://doi.org/10.1016/j.cell.2016.10.027
88. Sinha, S., Lin, G., & Ferenczi, K. (2021). The skin microbiome and the gut-skin axis. Clinics in Dermatology, 39(5), 829–839. https://doi.org/10.1016/j.clindermatol.2021.08.021
89. Slyepchenko, A., Maes, M., Jacka, F. N., Köhler, C. A., Barichello, T., McIntyre, R. S., Berk, M., Grande, I., Foster, J. A., Vieta, E., & Carvalho, A. F. (2017). Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities. Psychotherapy and Psychosomatics, 86(1), 31–46. https://doi.org/10.1159/000448957
90. Slykerman, R. F., Thompson, J., Waldie, K. E., Murphy, R., Wall, C., & Mitchell, E. A. (2017). Antibiotics in the first year of life and subsequent neurocognitive outcomes. Acta Paediatrica, 106(1), 87–94. https://doi.org/10.1111/apa.13613
91. Smythies, L. E., & Smythies, J. R. (2014). Microbiota, the immune system, black moods and the brain—melancholia updated. Frontiers in Human Neuroscience, 8. https://www.frontiersin.org/article/10.3389/fnhum.2014.00720
92. Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ (Clinical Research Ed.), 299(6710), 1259–1260. https://doi.org/10.1136/bmj.299.6710.1259
93. Stumpf, R. M., Wilson, B. A., Rivera, A., Yildirim, S., Yeoman, C. J., Polk, J. D., White, B. A., & Leigh, S. R. (2013). The primate vaginal microbiome: Comparative context and implications for human health and disease. American Journal of Physical Anthropology, 152(S57), 119–134. https://doi.org/10.1002/ajpa.22395
94. Taghinezhad-S, S., Keyvani, H., Bermúdez-Humarán, L. G., Donders, G. G. G., Fu, X., & Mohseni, A. H. (2021). Twenty years of research on HPV vaccines based on genetically modified lactic acid bacteria: an overview on the gut-vagina axis. Cellular and Molecular Life Sciences, 78(4), 1191–1206. https://doi.org/10.1007/s00018-020-03652-2
95. Vaughan, A., Frazer, Z. A., Hansbro, P. M., & Yang, I. A. (2019). COPD and the gut-lung axis: the therapeutic potential of fibre. Journal of Thoracic Disease, 11(Suppl 17), S2173–S2180. https://doi.org/10.21037/jtd.2019.10.40
96. Volk, H. E., Lurmann, F., Penfold, B., Hertz-Picciotto, I., & McConnell, R. (2013). Traffic-Related Air Pollution, Particulate Matter, and Autism. JAMA Psychiatry, 70(1), 71–77. https://doi.org/10.1001/jamapsychiatry.2013.266
97. Vuong, H. E., Yano, J. M., Fung, T. C., & Hsiao, E. Y. (2017). The Microbiome and Host Behavior. Annual Review of Neuroscience, 40(1), 21–49. https://doi.org/10.1146/annurev-neuro-072116-031347
98. Walker, R. W., Clemente, J. C., Peter, I., & Loos, R. J. F. (2017). The prenatal gut microbiome: are we colonized with bacteria in utero? Pediatric Obesity, 12(S1), 3–17. https://doi.org/10.1111/ijpo.12217
99. Walker, W. A., & Iyengar, R. S. (2015). Breast milk, microbiota, and intestinal immune homeostasis. Pediatric research, 77(1-2), 220–228. https://doi.org/10.1038/pr.2014.160
100. Wang, H., Liang, S., Wang, M., Gao, J., Sun, C., Wang, J., Xia, W., Wu, S., Sumner, S. J., Zhang, F., Sun, C., & Wu, L. (2016). Potential serum biomarkers from a metabolomics study of autism. Journal of Psychiatry & Neuroscience : JPN, 41(1), 27–37. https://doi.org/10.1503/jpn.140009
101. Wang, T., Sha, L., Li, Y., Zhu, L., Wang, Z., Li, K., Lu, H., Bao, T., Guo, L., Zhang, X., & Wang, H. (2020). Dietary α-Linolenic Acid-Rich Flaxseed Oil Exerts Beneficial Effects on Polycystic Ovary Syndrome Through Sex Steroid Hormones—Microbiota—Inflammation Axis in Rats. Frontiers in Endocrinology, 11. https://www.frontiersin.org/article/10.3389/fendo.2020.00284
102. Wang, W., Lv, S., Zhou, Y., Fu, J., Li, C., & Liu, P. (2011). Tumor necrosis factor-α affects blood–brain barrier permeability in acetaminophen-induced acute liver failure. European Journal of Gastroenterology & Hepatology, 23(7). https://journals.lww.com/eurojgh/Fulltext/2011/07000/Tumor_necrosis_factor___affects_blood_brain.2.aspx
103. Watson, R. L., de Koff, E. M., & Bogaert, D. (2019). Characterising the respiratory microbiome. European Respiratory Journal, 53(2), 1801711. https://doi.org/10.1183/13993003.01711-2018
104. Wellenius, G. A., Boyle, L. D., Coull, B. A., Milberg, W. P., Gryparis, A., Schwartz, J., Mittleman, M. A., & Lipsitz, L. A. (2012). Residential Proximity to Nearest Major Roadway and Cognitive Function in Community-Dwelling Seniors: Results from the MOBILIZE Boston Study. Journal of the American Geriatrics Society, 60(11), 2075–2080. https://doi.org/https://doi.org/10.1111/j.1532-5415.2012.04195.x
105. Whiteside, S. A., McGinniss, J. E., & Collman, R. G. (2021). The lung microbiome: progress and promise. The Journal of Clinical Investigation, 131(15). https://doi.org/10.1172/jci150473
106. Yang, Y., Tian, J., & Yang, B. (2018). Targeting gut microbiome: A novel and potential therapy for autism. Life Sciences, 194, 111–119. https://doi.org/10.1016/j.lfs.2017.12.027
107. Zhan, X., Stamova, B., Jin, L.-W., DeCarli, C., Phinney, B., & Sharp, F. R. (2016). Gram-negative bacterial molecules associate with Alzheimer disease pathology. Neurology, 87(22), 2324. https://doi.org/10.1212/WNL.0000000000003391
108. Zhang, J., Sadowska, G. B., Chen, X., Park, S. Y., Kim, J.-E., Bodge, C. A., Cummings, E., Lim, Y.-P., Makeyev, O., Besio, W. G., Gaitanis, J., Banks, W. A., & Stonestreet, B. S. (2015). Anti-IL-6 neutralizing antibody modulates blood-brain barrier function in the ovine fetus. The FASEB Journal, 29(5), 1739–1753.https://doi.org/10.1096/fj.14-258822

Environmental Nutrient Cycling and Human Health

1. Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., Sunagawa, S., Hingamp, P., Ogata, H., Lima-Mendez, G., Roux, S., González, J. M., Arrieta, J. M., Alam, I. S., Kamau, A., Bowler, C., Raes, J., Pesant, S., Bork, P., … Gasol, J. M. (2019). Metabolic Architecture of the Deep Ocean Microbiome. http://hdl.handle.net/10754/656339
2. Albright, M. B. N., Johansen, R., Thompson, J., Lopez, D., Gallegos-Graves, L. v, Kroeger, M. E., Runde, A., Mueller, R. C., Washburne, A., Munsky, B., Yoshida, T., & Dunbar, J. (2020). Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.542220
3. Amado, A. M., & Roland, F. (2017). Editorial: Microbial Role in the Carbon Cycle in Tropical Inland Aquatic Ecosystems. Frontiers in Microbiology, 8. https://www.frontiersin.org/article/10.3389/fmicb.2017.00020
4. Ávila, M. P., Oliveira-Junior, E. S., Reis, M. P., Hester, E. R., Diamantino, C., Veraart, A. J., Lamers, L. P. M., Kosten, S., & Nascimento, A. M. A. (2019). The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling. Microbial Ecology, 78(3), 575–588. https://doi.org/10.1007/s00248-019-01331-9
5. Feng, J., Wang, C., Lei, J., Yang, Y., Yan, Q., Zhou, X., Tao, X., Ning, D., Yuan, M. M., Qin, Y., Shi, Z. J., Guo, X., He, Z., van Nostrand, J. D., Wu, L., Bracho-Garillo, R. G., Penton, C. R., Cole, J. R., Konstantinidis, K. T., … Zhou, J. (2020). Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome, 8(1), 3. https://doi.org/10.1186/s40168-019-0778-3
6. Hamilton, T. L., Peters, J. W., Skidmore, M. L., & Boyd, E. S. (2013). Molecular evidence for an active endogenous microbiome beneath glacial ice. The ISME Journal, 7(7), 1402–1412. https://doi.org/10.1038/ismej.2013.31
7. Hough, M., McClure, A., Bolduc, B., Dorrepaal, E., Saleska, S., Klepac-Ceraj, V., & Rich, V. (2020). Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.00796
8. März, C., Butler, P. G., Carter, G. D. O., & Verhagen, I. T. E. (2021). Editorial: The Marine Carbon Cycle: From Ancient Storage to Future Challenges. Frontiers in Earth Science, 9. https://www.frontiersin.org/article/10.3389/feart.2021.748701
9. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455. https://doi.org/10.1126/science.aac8455
10. Naylor, D., Sadler, N., Bhattacharjee, A., Graham, E. B., Anderton, C. R., McClure, R., Lipton, M., Hofmockel, K. S., & Jansson, J. K. (2020). Soil Microbiomes Under Climate Change and Implications for Carbon Cycling. Annual Review of Environment and Resources, 45(1), 29–59. https://doi.org/10.1146/annurev-environ-012320-082720
11. Ochoa-Hueso, R. (2017). Global Change and the Soil Microbiome: A Human-Health Perspective. Frontiers in Ecology and Evolution, 5. https://www.frontiersin.org/article/10.3389/fevo.2017.00071
12. Paoli, L., Ruscheweyh, H.-J., Forneris, C. C., Kautsar, S., Clayssen, Q., Salazar, G., Milanese, A., Gehrig, D., Larralde, M., Carroll, L. M., Sánchez, P., Zayed, A. A., Cronin, D. R., Acinas, S. G., Bork, P., Bowler, C., Delmont, T. O., Sullivan, M. B., Wincker, P., … Sunagawa, S. (2021). Uncharted biosynthetic potential of the ocean microbiome. BioRxiv, 2021.03.24.436479. https://doi.org/10.1101/2021.03.24.436479
13. Ray, A. E., Zhang, E., Terauds, A., Ji, M., Kong, W., & Ferrari, B. C. (2020). Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.01936
14. Robinson, J.; Watkins, H.; Man, I.; Liddicoat, C.; Cameron, R.; Parker, B.; Cruz, M.; Meagher, L. Microbiome-Inspired Green Infrastructure (MIGI): A Bioscience Roadmap for Urban Ecosystem Health. Preprints 2021, 2021040560 (doi: 10.20944/preprints202104.0560.v1).
15. Trevathan-Tackett, S. M., Kepfer-Rojas, S., Engelen, A. H., York, P. H., Ola, A., Li, J., Kelleway, J. J., Jinks, K. I., Jackson, E. L., Adame, M. F., Pendall, E., Lovelock, C. E., Connolly, R. M., Watson, A., Visby, I., Trethowan, A., Taylor, B., Roberts, T. N. B., Petch, J., … Macreadie, P. I. (2021). Ecosystem type drives tea litter decomposition and associated prokaryotic microbiome communities in freshwater and coastal wetlands at a continental scale. Science of The Total Environment, 782, 146819. https://doi.org/10.1016/j.scitotenv.2021.146819
16. Tripathi, B. M., Kim1, H. M., Jung, J. Y., Nam, S., Ju, H. T., Kim, M., & Lee, Y. K. (2019). Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska. Frontiers in Microbiology, 10. https://www.frontiersin.org/article/10.3389/fmicb.2019.01442
17. Vigneron, A., Lovejoy, C., Cruaud, P., Kalenitchenko, D., Culley, A., & Vincent, W. F. (2019). Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake. Frontiers in Microbiology, 10. https://www.frontiersin.org/article/10.3389/fmicb.2019.01656

The Ocean Microbiome and Marine Life

1. Apprill, A. (2017). Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean. Frontiers in Marine Science, 4. https://www.frontiersin.org/article/10.3389/fmars.2017.00222
2. Doney, S. C., Ruckelshaus, M., Emmett Duffy, J., Barry, J. P., Chan, F., English, C. A., Galindo, H. M., Grebmeier, J. M., Hollowed, A. B., Knowlton, N., Polovina, J., Rabalais, N. N., Sydeman, W. J., & Talley, L. D. (2011). Climate Change Impacts on Marine Ecosystems. Annual Review of Marine Science, 4(1), 11–37. https://doi.org/10.1146/annurev-marine-041911-111611
3. Moran, M. A. (2015). The global ocean microbiome. Science, 350(6266), aac8455. https://doi.org/10.1126/science.aac8455
4. Stévenne, C., Micha, M., Plumier, J.-C., & Roberty, S. (2021). Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.698853
5. Sunagawa, S., Pedro, C. L., Samuel, C., Roat, K. J., Karine, L., Guillem, S., Bardya, D., Georg, Z., R, M. D., Adriana, A., M, C.-C. F., I, C. P., Corinne, C., Francesco, d’Ovidio, Stefan, E., Isabel, F., M, G. J., Lionel, G., Falk, H., … Didier, V. (2015). Structure and function of the global ocean microbiome. Science, 348(6237), 1261359. https://doi.org/10.1126/science.1261359

Soil Microbiomes

1. Gopal, M., & Gupta, A. (2016). Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies. Frontiers in microbiology, 7, 1971. https://doi.org/10.3389/fmicb.2016.01971
2. Omotayo, O. P., & Babalola, O. O. (2021). Resident rhizosphere microbiome’s ecological dynamics and conservation: Towards achieving the envisioned Sustainable Development Goals, a review. International Soil and Water Conservation Research, 9(1), 127–142. https://doi.org/10.1016/j.iswcr.2020.08.002
3. Ray, P., Lakshmanan, V., Labbé, J. L., & Craven, K. D. (2020). Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.622926
4. Tosi, M., Mitter, E. K., Gaiero, J., & Dunfield, K. (2020). It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Canadian Journal of Microbiology, 66(7), 413–433. https://doi.org/10.1139/cjm-2020-0085

Forensic Microbiomes

1. Robinson, J. M., Pasternak, Z., Mason, C. E., & Elhaik, E. (2021). Forensic Applications of Microbiomics: A Review. Frontiers in Microbiology, 11. https://www.frontiersin.org/article/10.3389/fmicb.2020.608101