The bacteria, archaea, viruses, fungi and protozoa living in the gut, collectively called the gut microbiome, have been linked to several diseases including obesity, heart disease, depression, type 2 diabetes, and rheumatoid arthritis (read more here and here).
Each person has a unique gut microbiome consisting of around 160 different bacterial species. In total around 1,200 species have been found in the human gut. These bacteria conduct several beneficial functions for their hosts such as aiding in digestion, producing certain vitamins, suppressing the growth of disease-causing bacteria, and metabolising dietary toxins.
Recent research has indicated that the diversity of the human gut microbiome has declined since humans diverged from Chimpanzees, over 6 million years ago. In fact, humans living in industrialized societies have the lowest gut microbiome diversity of any primate.
The first main transition in human history that resulted in a reduction in gut microbiome diversity was the dietary change from a mainly plant based diet rich in fiber to a diet with a higher proportion of meat. This shift dates back at least 2 million years ago and has left its anatomical mark. The small intestine is much larger in humans than in Great Apes while the opposite is true for the large intestine. The large size of the small intestine and small size of the large intestine are characteristic of carnivores (herbivores in contrast have a small sized small intestine and a large sized large intestine).
When we look at the bacteria that have become less abundant in humans we find many that are involved in the digestion of plant materials. For example, humans have a fivefold lower abundance of Fibrobacter, which as its name suggests helps to break down dietary fiber, compared to African apes. When we compare species we generally find that carnivores have a lower microbiome diversity compared to herbivores.
The agricultural revolution, around 10,000 years ago, caused a shift from a nomadic hunter-gatherer lifestyle towards agriculture and settlement. When the gut microbiomes of modern day hunter-gatherers is compared with that of traditional agricultural societies no difference in the richness of species is found. However, as expected the microbiome composition is different. In contrast, the shift from a traditional lifestyle to a modern (post-)industrial society has lead to a decline in the species richness of the human microbiome. The exact cause for this decrease is not yet known but the increase in food processing, with the resulting decrease in dietary fiber, may play a role. Indeed, the transmission of certain gut bacteria to the offspring was prevented when mice were fed a diet free of fiber. Also the use of antibiotics, especially during early life, and maybe even the increased use of Caesarean sections could contribute to the reduced richness of the gut microbiome. Although a recent study suggested that children born through Caesarean sections do not have a reduced gut microbiome richness.
Have any bacterial species gone extinct in the human gut? This question is hard to answer but one study failed to detect some bacteria, that are present in all African apes, in humans living in the United States but one was found back in humans living in rural Malawi. Some of the lost bacterial species may remain present in understudied human populations while other species may be lost forever.
In conclusion, humans have lost diversity in the gut microbiome since the divergence from Chimpanzees and this decline has become accelerated in the modern (post-)industrial society. This loss in microbiome diversity may increase the risk for infections, autoimmune disorders, and metabolic disorders.
Moeller AH (2017). The shrinking human gut microbiome. Curr Opin Microbiol 38: 30-35.