The human microbiota consists of the 10-100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut; the human microbiome consists of the genes these cells harbor[1
]. Microbiome projects worldwide have been launched with the goal of understanding the roles that these symbionts play and their impacts on human health[2
]. Just as the question, “what is
it to be human?”, has troubled humans from the beginning of recorded history, the question, “what is
the human microbiome?” has troubled researchers since the term was coined by Joshua Lederberg in 2001 [4
]. Specifying the definition of the human microbiome has been complicated by confusion about terminology: for example, “microbiota” (the microbial taxa associated with humans) and “microbiome” (the catalog of these microbes and their genes) are often used interchangeably. In addition, the term “metagenomics” originally referred to shotgun characterization of total DNA, although now it is increasingly being applied to studies of marker genes such as the 16S rRNA gene. More fundamentally, however, new findings are leading us to question the concepts that are central to establishing the definition of the human microbiome, such as the stability of an individual's microbiome, the definition of the OTUs (Operational Taxonomic Units) that make up the microbiota, and whether a person has one microbiome or many. In this review, we cover progress towards defining the human microbiome in these different respects.
Studies of the diversity of the human microbiome started with Antonie van Leewenhoek, who, as early as the 1680s, had compared his oral and fecal microbiota. He noted the striking differences in microbes between these two habitats and also between samples from individuals in states of health and disease in both of these sites [5
].Thus, studies of the profound differences in microbes at different body sites, and between health and disease, are as old as microbiology itself. What is new today is not the ability to observe these obvious differences, but rather the ability to use powerful molecular techniques to gain insight into why these differences exist, and to understand how we can affect transformations from one state to another.
Culture-independent methods for characterizing the microbiota, together with a molecular phylogenetic approach to organizing life's diversity, provided a fundamental breakthrough in allowing researchers to compare microbial communities across environments within a unified phylogenetic context (reviewed in [7
]). Although host-associated microbes are presumably acquired from the environment, the composition of the mammalian microbiota, especially in the gut, is surprisingly different from free-living microbial communities [8
]. In fact, an analysis of bacterial diversity from free-living communities in terrestrial, marine, and freshwater environments as well as communities associated with animals suggests that the vertebrate gut is an extreme [8
]. In contrast, bacterial communities from environments typically considered extreme, such as acidic hot springs and hydrothermal vents, are similar to communities in many other environments[9
]. This suggests that coevolution between vertebrates and their microbial consortia over hundreds of millions of years has selected for a specialized community of microbes that thrive in the gut's warm, eutrophic, and stable environment[8
]. In the human gut and across human-associated habitats, bacteria comprise the bulk of the biomass and diversity, though archaea, eukaryotes, and viruses are also present in smaller numbers and should not be neglected[10
Interestingly, estimates of the human gene catalog and the diversity of the human genome pale in comparison to estimates of the diversity of the microbiome. For example, the Meta-HIT consortium reported a gene catalog of 3.3 million non-redundant genes in the human gut microbiome alone[3
], as compared to the ~22,000 genes present in the entire human genome[12
]. Similarly, the diversity among the microbiome of individuals is immense compared to genomic variation: individual humans are about 99.9% identical to one another in terms of their host genome[13
], but can be 80-90% different from one another in terms of the microbiome of their hand[14
] or gut[15
]. These findings suggest that employing the variation contained within the microbiome will be much more fruitful in personalized medicine, the use of an individual patient's genetic data to inform healthcare decisions, than approaches that target the relatively constant host genome.
Many fundamental questions about the human microbiome were difficult or impossible to address until recently. Some questions, such as the perennially popular “how many species live in a given body site?”, are still hard to answer, due to problems with definitions of bacterial species and with the rate of sequencing error. Other questions, such as “how does the diversity within a person over time compare to the diversity between people?”, or “how does the diversity between sites on the same person's body compare to the diversity between different people at the same site?”, or “is there a core set of microbial species that we all share?”, can now be answered conclusively. In the next section, we discuss some of the tools that have allowed these long-standing questions to be answered.