A nutritional anthropology of the human gut microbiota

Undoubtedly, modern humankind is an omnivorous species. Nevertheless, types of diet changed radically over the course of human evolution, from hunter gatherers, through the birth of agriculture and culminating with the modern Western-style diet. The Upper Paleolithic period is the crucial time because of the appearance of anatomically modern humans in Europe. The human gut “metagenome” is a complex consortium of trillions of microbes, whose collective genomes contain at least 100-times as many genes as our own eukaryote genome. This essential “organ” provides the host with enhanced metabolic capabilities, protection against pathogens, education of the immune system and modulation of gastrointestinal development. Historically, the microbial ecosystem of the gastrointestinal tract was specific for an environmental niche, as much as the flora and fauna of an ecosystem are geographically distinct. A clear example of this richness and diversity is that currently in Africa, the microbial composition is very different from that described in the Western world. Globalization of the microbial population of our digestive tracts is due to industrialization and standardization of food chain products that homogenizes the microorganisms that we ingest. Understanding the evolution of human microbe ecosystems greatly benefits from a baseline reflecting an ancestral state of the human microbiome. The study of our closest living cousins, the other great apes, provides one path to reconstruct ancestral microbiomes. Retrieving human microbiome information from samples left behind by our distant ancestors would provide an ideal approach to understanding the coevolution of humans and microbes