Evolutionary Hitchhikers Dwell Within Our Guts

The old saying “you are what you eat” might have been disproved by recent research exploring microbial gut communities. Led by Yale University biochemist Howard Ochman, along with a diverse group of evolutionary ecologists and microbiologists from around the world, the team analyzed the living microorganisms teeming in great ape (humans included!) fecal samples in a study published in PLoS Biology in November 2010. From their stinky samples, the team concluded that the conventional notion – diet primarily governs gut microbiota diversity – no longer holds true. Rather, the creatures living and working within our guts have aided with digestion for a long, long time.

Mammals, including humans, are born with pristine guts free from the bacteria critical to our health and digestive functioning. Our digestive tracts become populated with communities of microbes over time, starting with the first taste of our mother’s milk. Factors, including diet, geography, and disease all influence the microscopic communities inside our digestive systems, but experts still argue over whether these assemblages are most influenced by the external environment or are inherently determined by our specific species’ identity.

Until now, scientists generally regarded our gut communities as an accumulation of free riders from chance dinner encounters. But that conclusion was based on studies that typically surveyed only 100 DNA sequences of microbes. The recent great ape study, on the other hand, took advantage of new technology to more deeply probe their samples. Ochman’s team collected more than 1.5 million ribosomal RNA gene samples and identified nearly 9,000 microbial species from 26 fecal samples of five great ape species, including two humans, one hailing from Africa and one from North America. The number of microbial species found in particular individuals ranged from 265 in a human to 3,247 in a chimpanzee.

With this data, the researchers then performed a parsimony analysis to construct intricate phylogenetic trees illustrating the relationship between hosts and their microbial diversity and abundance. This allowed researchers to compare and contrast the microbial contents found in host guts, both between great ape individuals and species. Going a step further, the researchers then compared host and microbe mitochondrial DNA. Mapping the data about microbes onto the known phylogenetic tree of great apes, they learned that the apes and their gut communities had co-evolved, diverging at an identical pace over the eons. In other words, our specifically tailored microbial communities have been with us for millions of years.

In light of this discovery, a revise to the old mantra is in order: “You are what eons of co-evolution has allowed you to digest.”