Gut Microbiota: Interactive Effects on Nutrition and Health

9.

Chapter 1

An Overview of the Human Microbiome

Abstract

The human body exists in a close, mutually beneficial relationship with its resident microorganisms: bacteria, archaea, fungi, and viruses. Methods that enable the study of the human microbiome have developed over the past several centuries—from Antonie van Leeuwenhoek's discovery of single-celled microorganisms, to Koch's innovations in isolating and studying bacterial cultures, to Woese and colleagues' pioneering work on sequencing small subunit ribosomal RNAs. In the current era, metagenomics techniques enable researchers to identify the bacteria that exist in an entire population and the functions encoded by the bacterial genes. Several large-scale projects have begun to characterize the range of variation of the human microbiome in healthy individuals: in particular, the Human Microbiome Project and the Metagenomics of the Human Intestinal Tract project (MetaHIT). Researchers continue to investigate aspects of the human microbiome in further large-scale projects around the world.

Keywords

Human microbiome; Microbiota; Host; Culture-dependent microbiology; Culture-independent microbiology; Metagenomics; Microbiota composition; Microbiota function; Normal microbiome; Human microbiome project; MetaHIT

Objectives

•To understand the relationship between the human body and its associated microorganisms.

•To become familiar with the terminology of the human microbiome and with the methods that enable it to be studied.

•To learn about large-scale projects aimed at characterizing the normal human microbiome.

What is a Human?

The human species, Homo sapiens, is usually defined as a large-brained bipedal primate with a capacity for language and a knack for using complex tools. A human’s 22,000 genes account for hair and eye color, predisposition to disease, cognitive ability, and even aspects of personality. Yet recent discoveries indicate that this description of a human is incomplete.

Humans are covered, inside and out, with a living layer of microbes: bacteria, archaea, fungi, and viruses. Although these microbes are too small to be seen with the naked eye, they are a fundamental part of our human biology. No human or human ancestor has lived without this collection of microbes (Moeller et al., 2016); it has evolved with us over millions of years and is thought to be as necessary for health and survival as a major organ system. These microbes live in an ecosystem with the human at its core; the human is the host, providing the resources the microbes need to sustain themselves.

Microbiological Methods

Setting the Stage for Discovery of the Human Microbiome

Antonie van Leeuwenhoek—a cloth merchant by trade—is credited for the discovery of single-celled microorganisms, which he called wee animalcules (little animals) (Dobell, 1932). With a simple, personally handcrafted microscope, in the late 1600s, he documented the presence of microorganisms in samples collected from a variety of sources. Leeuwenhoek was the first to observe microorganisms in the human body; he found them in dental plaque and in a stool sample on one occasion when he was ill with diarrhea. About two centuries would pass before techniques were developed to explore the significance of Leeuwenhoek’s observations.

Robert Koch’s extraordinary research career spanned the greater part of an era dubbed the golden age of bacteriology, 1876–1906 (Blevins et al., 2010). In 1876, Koch published a paper demonstrating that anthrax was caused by the bacterium Bacillus anthracis, providing the first proof for the germ theory of disease (Blevins et al., 2010). But his original methods for laboratory cultivation of bacteria were crude and inadequate for routine use, hindering his further progress. To obtain pure cultures—that is, cultures composed of a single bacterial species—he required a solid medium that would support bacterial growth. His attempts to grow bacteria on the surface of slices of potato or on media solidified with gelatin were unsuccessful. The breakthrough occurred when Fannie Angelina Hesse, the wife of Koch’s associate Walther Hesse, suggested the use of agar to solidify liquid bacteriologic media (Hesse & Gröschel, 1992). Armed with this new medium, Koch and his colleagues developed methods for isolating and studying pure cultures of bacteria. The impact on medical microbiology was immediate, and between 1878 and 1906, nineteen new bacterial pathogens were linked to specific infectious diseases. These techniques, augmented and supplemented with advances in microscopy and microbial biochemistry, endure in modern microbiology laboratories. They not only have formed the basis for the culture-dependent microbiology but also have fostered the expansion of microbiology beyond pathogenicity into diverse fields like biochemistry, genetics, ecology, and biotechnology.

By the 1980s, however, the growing awareness of the great abundance, diversity, and environmental ubiquity of microorganisms (Whitman et al., 1998) prompted a shift in research strategy. The complexity of microbial communities in their natural habitats was exemplified by the observation that most of the microscopically observable microorganisms in an environmental sample could not be cultured in the laboratory. This discrepancy between microbes that could be observed and those that could be cultured was a phenomenon termed the great plate count anomaly (Staley & Konopka, 1985). Usually, between 1.0% and 0.1% of the total bacteria could be accounted for by the standard plating method. Thus, scientists realized that culture-dependent methods alone would be completely inadequate for studying complex populations such as those populating the human body. This prompted a search for alternative methods.

Culture-Independent Microbiology for Exploring the Human Microbiome

Several significant discoveries paved the way for the development of culture-independent methods, which, for the first time, allowed access to the unculturable fraction of natural microbial populations like the human microbiota. The most significant early contribution was made by Carl Woese (Pace et al., 2012). In the 1960s, Woese began studying the evolution of microorganisms—asking seemingly intractable questions that could not be answered by classic paleontology methods. Microbes, after all, not only were unicellular and microscopic but also were soft-bodied and left no fossil record except in a few extremely rare instances. Even if they were successfully fossilized, they would hardly ever display unique recognizable morphological characteristics distinctive enough to permit species identification. Woese consequently used a molecular phylogenetic approach for tracing evolutionary history. In this approach to tracking microorganisms’ evolution, he took cellular ribosomes (the most abundant organelles in all forms of cellular life, performing the essential function of protein biosynthesis) and undertook a comparative analysis of the sequences of one component: the small subunit ribosomal RNAs or SSU rRNAs. Woese reasoned that the similarities and differences between these sequences (i.e., the order of the four chemical bases—adenine, uracil (or thymine in DNA), cytosine, and guanine) would reflect the phylogenetic relationships of the organisms from which they were obtained.

Over many years, Woese and his associates collected and comparatively analyzed the sequences of SSU rRNAs from numerous species of microorganisms. SSU rRNA turned out to be, in Woese’s own words, the ultimate molecular chronometer (Woese, 1987). There are two forms of SSU rRNAs, designated 18S and 16S. Eukaryotic cells, characterized by genomes enclosed within nuclear membranes, have 18S rRNA, and the morphologically simpler prokaryotic cells that lack nuclear envelopes have 16S rRNA. From analyses of 16S rRNA sequences, Woese and his coworkers discovered that there were actually two distinct groups of prokaryotic cells: the bacteria (originally named eubacteria) and a newly recognized group that was named the archaebacteria (Woese & Fox, 1977). In 1990, the group proposed a new taxonomic scheme to cover all forms of life on Earth, composed of three domains—the domain Eucaryota that included all eukaryotic cells and the two prokaryotic domains, the Bacteria and the Archaea (Woese et al., 1990). The SSU rRNA sequences not only contained unique short sequences that defined the three domains but also contained unique sequences that permitted assignment of cells to specific phyla (Woese, 1987). A universal phylogenetic tree based on SSU rRNA sequences is shown in Fig. 1.1.

Fig. 1.1 The universal phylogenetic tree based on SSU rRNA sequence analyses accounts for all life forms on Earth. At the root of the tree is the hypothetical last universal common ancestor, and each branch is represented by different phylogenetic groups. The lengths of the branches reflect the amount of evolutionary time separating them. (From Maulucioni (CC BY-SA 3.0).)

The original pioneering studies by Woese involved laborious direct sequencing of SSU rRNA purified from ribosomes. Several key developments expanded the range of applications for SSU rRNA analysis (Escobar-Zepeda et al., 2015). The inventions of DNA sequencing by Sanger in 1977 and of polymerase chain reaction (a method permitting the amplification of small amounts of any desired DNA sequence by several orders of magnitude) by Mullis in 1980 permitted the cloning and sequencing of SSU rRNA genes from DNA samples extracted directly from environmental samples. For the first time, this procedure allowed for the characterization of complex microbial communities without need for prior microbial cultivation. The 21st century brought on rapid technological advances such as high-throughput next-generation DNA sequencing and enhanced computational methods to interpret the DNA sequence information. These methods significantly expanded the analysis of microbial community DNA extracted directly from environmental samples beyond SSU rRNA genes; it enabled the sequencing of entire genomes, a procedure termed metagenomics (Handelsman, 2004). In whole-genome shotgun sequencing, DNA sequences are randomly broken up (shotgunned) into smaller DNA fragments; computer programs reassemble the complete sequence by taking these fragments and looking for regions of overlap. Metagenome sequences provide information about which bacteria exist in a microbial population and at least a partial prediction of what functions are encoded by its genes. These new methods led to an era in which microbiologists had broken away from culture dependence and could now see the vast majority of nonculturable microbes that constituted complex microbial communities like the human gut microbiome, and the genetic potentials of the individual community members (Qin et al., 2010). Of particular interest are the metabolic capabilities of the microbiome, their interaction with human metabolism, and their influence on human health.

The Return to Culture Dependence

Microbiome research, ironically, has returned to a phase where culturability will be desirable or even necessary: for example, to determine the individual phenotypes of the many species that constitute the gut microbiota. The murine gut species segmented filamentous bacteria (SFB), for example, which have unique interactions with the immune system (stimulating maturation of B and T cells and increasing small intestinal Th17 responses), were finally cultured after more than 50 years of attempts (Schnupf et al., 2015; Ericsson et al., 2015). A recent report indicated that, in contrast with common belief, the majority of bacteria in fresh fecal samples can indeed be cultured. Researchers cultured these bacteria on a single medium following a relatively simple procedure (Browne et al., 2016). Interestingly, over half of the bacteria isolated were capable of forming resistant spores. The researchers demonstrated that this property significantly promoted survival of the bacteria outside of the gut environment, and they suggested that this may play a role in person-to-person dissemination of these species.

Terminology

Four basic categories of microorganisms live in and on the human body: bacteria, archaea, eukaryotes (which include fungi), and viruses. The words microbes and microorganisms are used interchangeably to refer to all four