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)^[1]. 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^[2]. 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 ^[3].

^[1] The enterotype theory doesn’t include viral influence—a major flaw.

^[2] Thus this enterotyping is a bit more broad a designation than that of species, but more specific than that of phyla; it is also more of a functional designation. While we all have hands (our phyla make up) whether you are right or left handed would be your enterotype.

^[3] At this time, it seems that the obvious classifiers of BMI, sex, and age have nothing to do with our enterotypes though researchers have found significant microbial genes that correlate with those factors. It seems that even though the enterotype clustering is determined by a dominant genus, the abundant species in that genus may not necessarily provide the most abundant genes that aid in the metabolic economy. Knowing the most abundant species isn’t enough. Though the validity and benefit of classifying people according to enterotypes is still a subject of hot debate, all agree that a general functional understanding of someone’s GI ecosystem—possibly through enterotyping—could give us the ability to predict how a personal holobiont will respond to various treatments (or even food additives if we think of the infant formula tragedy). Thus, if we can understand how our microbionts function in metabolism, we can better diagnose the entire holobiont’s health state, and—since we then could place a specific hiolobiont into a group of individuals—we may be able to better prescribe a methodology (whether medicine or diet) that will specifically benefit the individual.

^[i] Gary D. Wu et al., “Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes,” Science 334, no. 6052 (October 7, 2011): 105–8, doi:10.1126/science.1208344.

^[ii] Manimozhiyan Arumugam et al., “Enterotypes of the Human Gut Microbiome,” Nature 473, no. 7346 (May 12, 2011): 174–80, doi:10.1038/nature09944.

^[iii] Tanya Yatsunenko et al., “Human Gut Microbiome Viewed across Age and Geography,” Nature 486, no. 7402 (June 14, 2012): 222–27, doi:10.1038/nature11053.

^[iv] Wu et al., “Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes.”

^[v] Alfredo Guarino et al., “Composition and Roles of Intestinal Microbiota in Children,” The Journal of Maternal-Fetal & Neonatal Medicine: The Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 25 Suppl 1 (April 2012): 63–66, doi:10.3109/14767058.2012.663231.

^[vi] Carlotta De Filippo et al., “Impact of Diet in Shaping Gut Microbiota Revealed by a Comparative Study in Children from Europe and Rural Africa,” Proceedings of the National Academy of Sciences 107, no. 33 (August 17, 2010): 14691–96, doi:10.1073/pnas.1005963107.