Using metagenomic analysis to look at 16S rRNA signatures, we know that our internal residents are either in the phylum Bacteriodetes or Firmicutes. And many studies have been done to determine if there is a magic ratio between these types that confers more (or less) health to the host[i]. The logic here is that if we know the genetic narrative of a gut homesteader, we’ll be able to predict how it behaves in the gut ecosystem. However, this examination of just 16S rRNA signatures doesn’t accommodate the diversity that bacteria in the same species can have in their genes. Just as one group of researchers thinks they understand how a specific microbe or cadre of microbe behaves and works in one group of guts, other researchers find that the same exact microbes do a completely different job in another group. Rather than thinking in terms of individual microbial species that must live in a specific place and can perform a function, it is better to envision a functional niche that can be filled by a variety of microbial types across individuals.
We can see this niche variation on a larger level when looking at how a city works: a conglomerate of humans who do different tasks to keep the region vital. Individuals of same species occupy different niches and develop different skills best perform in that niche. Early man grows wheat in the river valley while his woman tends goats and sheep in the hills. Modern humans get their wheat already processed into bread and beer which was done by other humans before being delivered by yet another human to the grocery store. Like humans in a city, our gut microbes have developed a balance that allows their combined metabolic functions to make them thrive and to aid our bodies in extracting energy from non-digestible sources. After millennia of symbiosis, we both as a human biont and as a holobiont cannot survive without our microbes’ participation in our metabolism. Without them, we would not be able to extract much needed nutrients from our diet nor have access to vital nutrients (like certain vitamins) we can’t make ourselves as studies with gnotobiotic (germ free) mice indicate. Without microbiota, these mice fail to thrive and gain weight on any type of diet[ii]. In mice who do have a thriving microbiota (both of the mousey type or the human type), scientists have shown that if the balance of microbes is disrupted, the entire holobiont including the host biont can become diseased. This disruption in homeostasis manifests in the form of infection, obesity, diabetes, various bowel disorders, various autoimmune disorders, and cardiac disorders that are prevalent in the Western world. It appears that the microbes in our guts have been carefully selected less for who they are and more for what they can do, and that our changing diets and lives constantly refine this selection.
 Remember from the previous section: Metagenomic analysis refers to the study of all genes from various organisms that make up a system. In our case, metagenomics is examination of the total DNA from us as well as the bacteria, yeast, and Archaea that live in and on us. Through metagenomics we can look at the aggregate effect of the population, not just how one organism functions. That way we can get an idea of the genetic and metabolic capacity of the community as a whole. This technique is particularly vital when you realize that microbes (and humans) do not function in a vacuum. They have a lot of cross-talk among members of their own species, members of other species, and host cells. What we get then, is not the genome of one particular organism, but the genome of the entire community. This use of “meta-omes” (metagenome, metabolome, meta-proteome) is the acknowledgement that nothing operates in isolation. Therefore, we can gain more valuable information about function and effect by looking at everything together rather than looking at something by itself.
 Remember the Hadza!
[i] Ruth E. Ley et al., “Microbial Ecology: Human Gut Microbes Associated with Obesity,” Nature 444, no. 7122 (December 21, 2006): 1022–23, doi:10.1038/4441022a; Peter J Turnbaugh et al., “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest,” Nature 444, no. 7122 (December 21, 2006): 1027–31, doi:10.1038/nature05414; Fredrik Bäckhed et al., “The Gut Microbiota as an Environmental Factor That Regulates Fat Storage,” Proceedings of the National Academy of Sciences of the United States of America 101, no. 44 (November 2, 2004): 15718–23, doi:10.1073/pnas.0407076101.
[ii] Turnbaugh et al., “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest.”