The hope is that in examining what lives in our guts on a species level, we will discover just who lives in us and infer from that the functional ability of an individual’s metabolism. Just as in the animal world, microbes have a taxonomy. Humans belong to the phylum Chordata/Vertebrata which groups us with other animals that have a spinal column. Our genus is Homo which groups us with all upright humanoid animals in the past (currently, we are the only species alive in our genus), and our species, of course is Homo sapiens sapiens^[1]. Microbial taxonomy is bit trickier in that we group them according to genetic similarity^[2]; however, we can still examine the functional differences and similarities of these tiny organisms on various taxonomic levels. For example, we can look at the phylum Bacteriodetes, the genus Bacteriodes, and the species of B. fragilis and see how this species operates both as an individual species and within a broader group. Or if you know that one of your microbial inhabitants happens to be the rare Klebsiella terrigena, you would avoid eating melamine (which our human cells can’t process) because K. terrigena converts melamine to an acid that causes kidney stones^[i].  Sadly, in 2008 before we had the means to discover these interactions between microbiota and food, a Chinese infant formula company put melamine into infant formula, hoping to artificially boost the protein content. Many babies became severely ill with kidney stones and a few even died^[ii]. Thus, knowing who is in our guts can help us predict and determine, in certain cases, functional aspects of a specific human holobiont and know if some substance (melamine or a medication or supplement) will be changed by our microbes into something harmful.

It makes intuitive sense that microbes within the same genus would be functionally similar. So, with the shift in thought that humans are a holobiont and the technology to identify the presence or absence of uncultureable microbes, the focus of many research endeavors has been to characterize exactly who lives in our internal metropolis. However, determining a “core” or shared set of microbes between all humans is proving to be a trickier task than first imagined. It seems that just as environmental pressures are never exactly the same between two holobionts—no two guts are exactly alike. The same species in two different hosts can activate a variety of genes to occupy different roles in that host’s metabolism or maybe that species may be completely absent yet the functional niche is filled with another species. As the body of research on the human gut grows, we are learning that metabolic function (driven by the type of nutrient energy put into it) is more important to understanding holobiont health than looking for a specific species, genus, or even phylum of microbes to make us all healthy.

^[1] Even for macro-species, as we refine how we look at genes, the Linnaeus taxonomy is becoming outdated as we learn from looking at genomes that dogs and wolves are actually the same species and that hippopotami and giraffes are more closely related than we previously thought.

^[2] The concepts of species and genus and phyla are determined in microbes not by physical or visible characteristics but by the genetic similarities of their 16S rDNA sequence.  Microbes whose 16S rDNA sequences are at least 97% identical are typically classified together as a species; those who sequences are at least 93% identical are assigned to the same genus.  Phyla assignation then is given once the species and/or genus is identified. [modified from coral book]

^[i] Xiaojiao Zheng et al., “Melamine-Induced Renal Toxicity Is Mediated by the Gut Microbiota,” Science Translational Medicine 5, no. 172 (February 13, 2013): 172ra22–172ra22, doi:10.1126/scitranslmed.3005114.

^[ii] Jim Yardley, “Chinese Baby Formula Scandal Widens as 2nd Death Is Announced,” The New York Times, September 16, 2008, sec. International / Asia Pacific, http://www.nytimes.com/2008/09/16/world/asia/16milk.html.