Fundamentals of Microbiome Science

How Microbes Shape Animal Biology

Angela E. Douglas

• Publisher: Princeton University Press
• Year: 2018
• ISBN:
  9781400889822
• Topic: Biological Sciences
• Subtopic: Microbiology
• Index: Biological Sciences

An essential introduction to microbiome science, a new cutting-edge discipline that is transforming the life sciences This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. Resident microbes in healthy animals--including humans—can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens; it can structure host metabolism in animals as diverse as reef corals and hibernating mammals; and it may influence animal behavior, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales.Drawing on concepts and data across a broad range of disciplines and systems, Angela Douglas provides a conceptual framework for understanding these animal-microbe interactions while shedding critical light on the scientific challenges that lie ahead. Douglas explains why microbiome science demands creative and interdisciplinary thinking—the capacity to combine microbiology with animal physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.An essential introduction to a cutting-edge field that is revolutionizing the life sciences, this book explains why microbiome science presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for many medical conditions and new strategies for pest control.

1

Introduction

ANIMALS IN A MICROBIAL WORLD

1.1. What Is An Animal?

We can answer this question in two ways. One answer is relatively straightforward and is provided in the following paragraph, and a first attempt at the really interesting answer occupies the rest of this book.

The animals are a monophyletic group of eukaryotes with a multicellular common ancestor that fed holozoically (i.e., on particulate food) and comprised cells that lacked a cell wall and included multiple morphologically and functionally different cell types. These traits set animals apart from the only other major group of ancestrally multicellular eukaryotes, the terrestrial plants, and other eukaryotes with multicellular representatives, e.g., the fungi and red algae, which have saprophytic or photosynthetic lifestyles and are composed of cells enclosed within a cell wall. Early in their diversification, two key innovations evolved in the animals: the gut, permitting exploitation of large food items; and the nervous system, laying the foundation for the complex behavior displayed by many animals. A further defining feature of the animals is that, as a group, they lack key metabolic capabilities common to various other organisms, including the capacity to photosynthesize, fix nitrogen, synthesize many amino acids contributing to protein, and produce various cofactors required for the function of enzymes central to metabolism. In other words, many animals are morphologically complex and some are clever, but all are metabolically impoverished.

This description of animals is not incorrect, but it is incomplete. It omits 1–10% of the biomass and half or more of the cells in the animal body. The missing cells are the microbial communities that live persistently with the animal. Most of these microorganisms are bacteria, but they also include unicellular eukaryotes; and large animals additionally bear multicellular eukaryotes, including mycelial fungi, mites, helminth worms, etc. Traditionally, these inhabitants of animals have been ignored unless they are injurious to the health of their animal host, and because many are difficult to culture, their ubiquity and diversity are grossly underestimated by routine culture-based microbiological methods.

The study of microorganisms associated with animals has been transformed by culture-independent methods to identify and study the function of microorganisms. The key technology has been high throughput DNA sequencing (also known as next generation sequencing), by which all the DNA, expressed genes, or specific genomic regions of interest in a sample can be sequenced simultaneously. It is now possible to determine the taxa in the microbial community and their functional traits, for example from a biopsy taken from the lung or intestine of a human patient, from a single soil microarthropod, or from the gills of a bivalve mollusk brought up from a deep sea hydrothermal vent. These ever-improving technologies have supported a decade or more of research on the microbiological natural history of animal bodies. It is now apparent that animals are the habitat for a previously unsuspected diversity and abundance of microbial residents, and this unfolding discovery has empowered experimental science, revealing that these microorganisms are critical to the health and well-being of their animal hosts.

So, what is an animal? It is a multiorganismal entity, comprising animal cells and microbial cells. The phenotype of an animal is not the product of animal genes, proteins, cells, tissues, and organs alone, but the product of the interactions between all of these animal functions with communities of microorganisms, whose composition and function vary with the age, physiological condition, and genotype of their animal host. Following from the growing appreciation of the significance of the microbiology of animals, many aspects of animal biology are being rewritten (McFall-Ngai et al., 2013). The biomedical sciences are increasingly recognizing the pervasive effects of resident microorganisms on human health. These effects extend beyond local impacts, for example of gut microorganisms on gut health and disease, to microbial effects on cardiovascular health, the integrity of the circadian rhythm, and psychiatric health. Many evolutionary biologists are realizing that the response of animals to selection is influenced by the impact of microbial partners on the trait under selection and the heritability of the microorganisms. Applied biologists are appreciating that microbes can shape the capacity of insects, such as mosquitoes, to vector disease agents (e.g., the malaria parasite, dengue virus) and their susceptibility to certain pest control agents. Furthermore, reliable predictions of the impacts of climate change on animal distributions will require consideration of the environmental requirements and dispersal capability of the microbial partners as well as the animal.

But, before we go any further, we need to address some issues of terminology. As with so many scientific disciplines, multiple terms are being used, sometimes interchangeably but often with different shades of meaning that can sow confusion and misunderstanding. Section 1.2 provides a guide to how some terms are used in this book, as well as why some terms are eschewed.

1.2. Terminology: Dismantling the Tower of Babel

Terms are important not only because they communicate agreed concepts within a discipline but also because they can encapsulate an entire conceptual framework. In this respect, the term “microbiome,” coined to describe the catalog of microorganisms and their genes (Lederberg and McCray, 2001), is of central importance. The microbiome is a global, all-encompassing term for the microbiology of an animal, and is particularly useful where, as in shot-gun sequencing, individual genes cannot readily be assigned to particular microbial taxa. A related term is “microbiota,” which refers specifically to the microbial taxa associated with an animal. The terms microbiome and microbiota are sometimes used interchangeably when referring to taxa. Alternatively, the microbiome can be used exclusively to refer to genes and genomes, with the microbiota as a taxonomic descriptor. It is usually obvious from the context how the term microbiome is being used. In this book, I will use both terms, with microbiome to describe inventories of genes, especially in relation to function, and microbiota when referring to the organisms.

The terms microbiome and microbiota have meaning for a science that is founded on molecular biology and genomics. A major driver of microbiome research over the last decade has been large consortium projects that have generated microbial sequences associated with humans, and their potential biomedical importance. However, microbiome research is also founded on many decades of pregenomic research on interactions between healthy animals and their resident microorganisms (Sapp, 1994). Although this research endeavor has been largely independent of biomedical science, the melding of the terminology of the pregenomic science of animal-microbial interactions with the terminology of -omic science has, to a large extent, been successful. But there have been some difficulties, and this is has caused some confusion and miscommunication.

A key pregenomic term is “symbiosis,” which—as for microbiome—was invented to fulfil a scientific need. Symbiosis was coined in the 1870s to encapsulate the new discovery of multipartner organisms. It was initially used by Albert Franck to describe the composite nature of lichens, comprising a fungus and alga, and generalized in 1879 by Anton de Bary to describe the “living together of different species.” Over the following century, most research on interactions between healthy animals and microorganisms focused on associations that were readily detected morphologically, including highly specialized interactions involving single microbial taxa housed in specific tissues or organs. These associations were categorized as symbioses (or sometimes endosymbioses), with the animal described as the host and microbial partner as the symbiont. The microbial symbionts in these “one-host-one-symbiont” or occasionally “one-host-two/three-symbionts” associations include the zooxanthellae (dinoflagellate algal cells) in corals, luminescent bacteria in the light organs of some fish and squid, and dense bacterial aggregations in specialized organs (bacteriomes) of certain insects. The text of Buchner (1965), together with two multiauthor volumes (Jennings, 1975; Nutman and Mosse, 1963), provide a superb overview of premolecular research on these associations.

Today, the terms microbiome and microbiota are generally used with reference to multitaxon microbial communities, and the microbial partner(s) tend to be called symbiont(s) where the interactions are limited to one or a few microbial taxa. There is a general presumption that, where the animal host is healthy, the terms microbiota and symbionts do not refer to pathogens. However, the impact of many microorganisms on the animal host can be context-dependent, varying with the developmental age, physiological condition, and genotype of the host, as well as environmental conditions. This was appreciated by Elie Metchnikoff who, in the early twentieth century, coined a further term “dysbiosis” as an antonym of symbiosis, to describe a microbial community that is deleterious to host health (Stecher et al., 2013). In the same vein, individual members of a microbial community that display context-dependent pathogenicity are often known as pathobionts (Hornef, 2015).

In the biomedical literature, the term “commensal” is widely used to describe individual taxa of the microbiota. This term poses some important problems. Strictly speaking, the term commensal refers to “eating at the same table,” and has come to describe an organism that derives benefit from an association with no discernible effect on the fitness of its partner, akin to the sparrow feeding on the breadcrumbs dropped from a man’s dining-table. The term commensal is not widely used in the symbiosis literature because it has all the standard difficulties of a negative definition: if only one used a more sensitive assay or studied the association under different conditions, perhaps benefit or harm would be detected, and the organism would, no longer, be a commensal. Microorganisms associated with the gut and skin of humans used to be called commensals, in the erroneous belief that they are of no significance. It is unfortunate that commensal has persisted into the era of microbiome research with the full knowledge that these microorganisms are crucial to the health of humans and other animals. Needless to say, verbal modifiers such as “beneficial commensal” further compound the terminological confusion. In the light of the complexities surrounding the term commensal, it is preferable to avoid this term. Alternative terms, such as microorganisms, microbial communities, etc. are sufficient; where it is important to emphasize that pathogens are specifically excluded from consideration, the term “nonpathogenic microorganisms” can be used to avoid any ambiguity.

There is one further set of terms that needs to be addressed: holobiont and hologenome. Lynn Margulis coined new terms for the partners in a symbiosis as “bionts” and the association as a “holobiont” (Margulis, 1991) to emphasize the evolutionary persistence of the association and how selection may operate at the level of the association (or holobiont). This terminology has been brought into the -omic era with a further new term, the hologenome, which refers explicitly to the host genome plus microbiome as the unit of select...