Reconstruction of ancient microbial genomes from the human gut

Previous studies have shown losses of gut microbial diversity in industrial populations relative to non-industrial populations. These losses are associated with chronic diseases. To discover bacterial species that might have gone “extinct” in modern populations, we performed shotgun metagenomic sequencing on 11 human coprolites (paleofeces). We reconstructed 591 ancient bacterial genomes, 52% of which are novel species. This is the first large-scale de novo assembly of microbial genomes from ancient microbiome samples. Functional profiling of the coprolites revealed significantly fewer antibiotic resistance genes and virulence factors, and altered carbohydrate transport and metabolism functions relative to the modern, industrial gut microbiome. The coprolites are significantly richer at the gene, pathway, and taxonomic levels, supporting the hypothesis of extinction in the industrial human gut microbiome.