19.1: An Introduction to Microbiomes

Learning Objectives

• Contrast the terms microbiome and microbiota
• Describe the major types of microbes that make up the human microbiome
• Discuss how multi-omics approaches (e.g., genomics, metagenomics, transcriptomics, proteomics, and metabolomics) are used to study the microbiome

An Introduction to Microbiomes

Microorganisms represent the fundamentals of life and interact with almost every facet of it. Yet, for the majority of their existence they have been largely ignored, or rather unseen by humans. The unraveling of the complex interactions between all life forms is an endless duty and seems to generate more questions than answers. However, the cracks in knowledge produced by peering into the unknown offers insight into our life and the world around us. These minute creatures have shaped Earth’s evolution since their dawn almost three-and-a-half billion years ago, and continuously affect our environment and health. The importance of the planet’s collection of microbes is realized more and more each day, and our unceasing investigation of them will surely unlock secrets of life we could never imagine.

The study of microbiomes is fairly novel in the context of understanding and applying their communal existence to ourselves and surroundings. Though scientists have recognized symbiotic relationships and traditionally focused on individual microbes and their interactions with human health, environmental impact, industrial applications, etc., their respective communities and influence as a whole in these areas have only just begun to be elucidated. That is in no small part due to the daunting task of cataloging the immense and complex interplay between the multitude of different microorganisms in a given environment, though rapid advances in technology have begun to ease analysis.

What is a microbiome?

A microbiome can be best described as a collective polymicrobial community, or ‘microbiota’, and its associated activity with genetic and physio-chemical constituents in a defined spaciotemporal habitat (Figure 1). These members of the microbiota include bacteria, archaea, algae, protozoa, fungi, and viruses (though the latter is somewhat debated since viruses and their derivatives aren’t technically living). Within this symbiotic context with a particular eukaryotic host, the entire entity is termed a ‘holobiont’ and the aggregate of genetic material termed the ‘hologenome’. Interactions between these partners may have long occurred, shaping the evolution of each, whereas others may be novel or transient, sometimes resulting in prompt change and infectious diseases. The change in the normal microbiota, or dysbiosis, can result in a variety of different diseases. As so, their study has been especially important in the fields of life sciences, human health, and medicine.

Figure 1. A schematic highlighting the composition of the term microbiome containing both the microbiota (community of microorganisms) and their “theatre of activity” (structural elements, metabolites/signal molecules, and the surrounding environmental conditions). (Berg et al., 2020 adapted by Dylan Parks).

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Our fascination with microorganisms begun before we even fully understood them or were even able to see them. Their implications concerning human health were primarily explored during the ‘golden age of microbiology’ with the work of Louis Pasteur and Robert Koch. Their experiments and discoveries shed light on not only the ubiquitous nature of microbes, but their importance in our everyday lives. Other significant milestones and historical microbiological development can be viewed in Figure 2. Human health and infectious diseases were central to the field of microbiology, though food microbiology, industrial applications, and microbial ecology became increasingly explored. Over the last couple centuries, a microbial catalog of knowledge has slowly grown, but much of these findings were limited to those organisms that could be cultured and measured.

The advent of sequencing and ‘multi-omics’ technologies has since allowed researchers to document microorganisms that were previously missed or ignored with traditional techniques, and with further advances, larger microbial communities and symbioses can be better understood. Multi-omics refers to the analysis of genes, proteins, metabolism, etc. on a system level. For example, genomics refers to the sequencing of the whole genome; proteomics refers to the analysis of all the proteins in cells; and metabolomics is the study of all metabolites in cells.

The ‘microbiome’ was first defined in the late 1980s when a group of microbial ecologists were studying the rhizosphere, which provided context to better describe these polymicrobial communities (Whipps et al., 1988). Many other similar definitions have been published since then with varying specifics on genetic expression, symbioses, and ecological interactions (Lederberg & McCray, 2001, Marchesi & Ravel, 2015, Berg et al., 2020). The ‘holobiont’ concept stems from Adolf Meyer-Abich’s ‘theory of holobiosis’ proposed in 1943 and was independently conceived and popularized in the early 1990s by Lynn Margulis, though it only described the host and a single symbiont (Margulis, 1991, Baedke et al., 2020). Since then has been expanded to include the entire microbiota in multiple symbiotic contexts (Simon et al., 2019). In recent decades there has been a steady increase in microbiome publications as the subject has grown in popularity. Along with that, there has been more analytical breakdown as certain microbiomes are being described with emphasis on specific members, such as the ‘bacteriome’, ‘archaeome’, ‘mycobiome’, ‘protistome’, and ‘virome’, and these terms are best used to refer to the distinct contribution of those particular microbes within the entire microbiome context. In general, though, most microbiomes are delineated by their specific host or type of environment, with the human microbiome being the most popular example.

Figure 2. The history of microbiome research from seventieth century until our days, highlighting the shift of the paradigm from microbes as unsocial organisms causing diseases to the holistic view of microorganisms being the center of the One Health Concept: positively interconnecting all areas of our lives. (Berg et al., 2020).

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Key Concepts and Summary

• Microbiota refers to the community of microorganisms (bacteria, archaea, fungi, viruses, etc.) living in a specific environment, such as the human gut or soil.

• Microbiome includes both the microbiota and their collective genetic material, metabolic activity, and environmental context—also known as their “theater of activity.”

• The concept of the holobiont represents a host organism together with its associated microbiota; their combined genetic information is referred to as the hologenome.

• Microbiomes are diverse, dynamic ecosystems that influence and are influenced by their hosts, often shaping health, disease, and evolution.

• The term dysbiosis refers to an imbalance in the normal microbiota, which may contribute to disease.

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