Think about it this way: we all have individual fingerprints on hands that function similarly. If we think about the classification of microbes as a description of what a hand looks like, we can envision how this classification can work on a functional level in our guts and how it can help us better understand how our microbial bionts engage in our metabolism. We all have hands that roughly look the same—four fingers and a thumb: phyla. Then there are some of us who are right-handed or left-handed or both: the dominant functional profile of your ecosystem. Then we have our fingerprints: species composition (which is less reliant on type of species but the diversity of niches that are in the gut).
Your hands, your neighbor’s hands, the hands of people in Finland, and early humans’ hands look roughly the same, and probably so does your microbiota on the phyla level. Here, diversity is not as apparent since composing the five fingers of our microbial hand are four to five phyla with a few miscellaneous phyla tossed in for good measure: Firmicutes, Bacteriodetes, Actinobacteria, Proteobacteria, and Verrumicrobia[i] seem to be the five most prevalent phyla. Of these, Firmicutes and Bacteriodetes comprise 90% of the microbes in our guts (they are the bigger fingers) while Proteobacteria and Verrumicrobia are less than one percent (and the numbers of Verrumicrobia are actually so small, the fifth finger can be classified as “other microbes”). The microbes in these phyla then contribute to the groups of genes (along with our human genes, viral genes, and even the genes of the food we eat) that make up our functional metabolism. The previously mentioned European study claims that out of the millions of genes that can be present in the microbiome, only a fraction (about 300,000) is actually prevalent in all of us. These could be “core housekeeping genes” that code for key metabolic functions that are also similar from individual to individual (think about it: all of our bodies operate basically the same, so our metabolism, on the whole, would look similar) and are proving more and more related to the types of energy we put into our holobiont: our diets.