Microbiology: Ancient faeces flush with information about human gut microbiome

Notable changes to the human gut microbiome have occurred over the past 2,000 years, according to analyses of ancient faeces from North America reported in Nature this week. The changes reflect differences between pre-industrial and modern diets, highlight an increase in antibiotic-resistance genes, and may explain how the composition of the gut microbiome is linked to the development of chronic diseases.

Comparisons of industrial and non-industrial present-day populations indicate that an industrial lifestyle is linked to a lower diversity of the gut microbiome and an increase in the incidence of chronic illnesses, such as obesity and autoimmune diseases. However, our understanding of the evolution of the gut microbiome over time has been limited by a lack of data on pre-industrial gut microbes, owing to challenges in obtaining well-preserved DNA.

A detailed genetic analysis of eight well-preserved authenticated human faeces samples, which are around 1,000–2,000 years old, that had been discovered in rock shelters in southwestern USA and Mexico provides new insights. From these samples, Aleksandar Kostic and colleagues reconstructed 498 microbial genomes, of which 181 show strong evidence of being ancient and of human gut origin. They find that 61 of these genomes are previously undescribed, indicating the presence of species that are divergent from those seen in modern populations. The researchers compare the genomes to those of present-day samples from industrial and non-industrial populations, and find that the ancient, pre-industrial genomes are more similar to non-industrial human gut microbiomes.

The ancient and non-industrial samples include an enrichment of genes associated with the metabolism of starches, which may be due to the higher consumption of complex carbohydrates compared with present-day industrial populations. Both the industrial and non-industrial modern-day samples are enriched in antibiotic-resistance genes relative to the ancient samples. These insights shed light on the evolutionary history of the human microbiome, and may aid in our understanding of the role of the microbiota in health and disease.

After the embargo ends, the full paper will be available at: https://www.nature.com/articles/s41586-021-03532-0