Since not all species of microbe are created equal, we can assume that certain microbial genera and species do have genetic endowments that allow them to better function in a niche than others. Nature is very smart about conservation of resources; therefore, despite the elusiveness of a solid core of microbes or genes on the species level, there must be some sort of underlying similarity between certain guts that share certain environmental similarities. Certainly, many studies have indicated just that; but rather than a specific grouping, they have been able to make a broad generalization about where people fall in the gut microbiota spectrum by determining a dominant genus. Some scientists call these groupings of species enterotypes[i]. Though the validity of that classification under debate, the idea of enterotypes is useful in that it lets us link types of microbes to certain functions that are related to how we eat. Defining your gut ecosystem by an enterotype would be characterizing it by the prevalent type of food energy you put into it (diet) and by the way your microbiota processed that energy (metabolic skills). It is similar to designating the difference between San Francisco and New York. Both are cities; both engage in similar aspects of necessary commerce; but both possess unique cultural, economic, and geographic differences.
One of the reasons classifying an individual holobiont into an enterotype is complicated is that the groups are not the nothing/either/or/both of blood types but a description of a dense population of microbes that—just like a city—experience some areas of sprawl with a concentrated and (according to the theory) classifiable urban center. Enterotypes are defined as a dominant presence of a specific genus of microbes. The team of researchers who first characterized enterotypes found that three genera seemed to be the loci of enterotypes: Bacteriodes, Prevotella, and Ruminococcus[ii]. Each of these has genes that code for specialized ability to process certain energy currency, and thus, we can use them to generally describe the functionality of the ecosystem. Bacteriodes have more genes that enable them to better extract energy from carbohydrates and protein through fermentation and are associated with a high fat/high protein diet. Prevotella and Ruminococcus both have a capability to degrade carbohydrates in the mucus (mucin) in the gut and are associated with diets that are heavy in plant matter[iii]. The latter (a more rare enterotype) also has more membrane transporters for sugars on their cells.
Scientists are still not completely clear on what drives these clusters; some claim that long-term diet[iv] has a huge effect while others claim that method of initial inoculation[v] matters more. Both of these claims may be correct in part. For example, one study of the microbiota of children from Europe (chosen to represent the modern Western diet) versus the microbiota of children in the rural African village of Burkina Faso (chosen to represent the diets of ancient humans) showed that the European children fell into the enterotype most associated with a high fat, high animal protein diets (Bacteroides) while the Burkina Faso children’s enterotype was that associated with high carbohydrate, plant-based diet with low animal protein and dairy (Prevotella)[vi]; further the microbes from breastfed babies in both groups were similar to each other and not to their solid food-eating siblings, thus demonstrating that diet (and not environment) was the driving factor in establishing enterotypes .