Our Ancient Microbiome

Share on facebook
Share on twitter
Share on email

Our guts are much less diverse than they used to be 2000 years ago. Scientists believe that our ancient gut microbiomes may give clues for the chronic conditions of today.

Loss of diversity in the gut microbiome is connected with chronic disease1. Inspired by this knowledge, researchers decided to investigate our ancestral gut microbiome.

Our Ancestral Gut

To date, we don’t know much about what our gut microbiomes used to look like. Researchers wanted to find out. They believe it might help us better understand why modern microbiomes are more prone to disease such as obesity and diabetes.
 
In this study, researchers performed large-scale analyses of ancestral microbial genomes. The samples were up to 2000 years old, and taken from rock shelters in USA and Mexico.
 
The team analysed 8 fossilised human faecal samples – known as coprolites.
 
Coprolites can be valuable sources of information. They can tell us how we used to live, including insights on our ancestral diet and disease prevalence. 

The scientists found microbes that were completely absent from the gut microbiome today.

These samples contain certain gut microbes. So anyone with proper tools can compile a snapshot of the microbiome. That’s exactly what microbiologists decided to do!
 
The scientists first validated the coprolites using dietary and radiocarbon analyses. Afterwards, they extracted preserved DNA to identify the microbes.
 
They able to reconstruct 498 microbial genomes – 181 of which appear to originate in the human gut, rather than the soil.
 
The scientists found microbes that were completely absent from the gut microbiome today.
 
In total, 158 of these sequences seem to represent a distinct microbial species.

Our Microbiomes Changed

The results were remarkable. The team discovered species never been seen in the modern microbiome. Out of 158 genomes, 61 were completely unknown to science – almost 40 percent!

Out of 158 genomes, 61 were completely unknown to science – almost 40 percent!

Overall, the ancestral guts more similar to non-industrialized microbiomes, and had:

  • Lower abundance of antibiotic-resistance genes
  • Fewer genes that make proteins to degrade glycans (sugar molecules found in mucus.) Mucus degradation in the colon is associated with diseases such as Crohn’s disease, Celiac disease and Ulcerative Colitis.
  • Higher numbers of transposases – enzymes that can cut, paste and replicate elements of DNA, which help with adaptation.

Mucus degradation in the colon is associated with diseases such as Crohn’s disease, Celiac disease and Ulcerative Colitis.

Ultimately, it appears the ancestral microbes were adapting to environmental shifts that were much more frequent than today. More transposases would therefore be necessary.

Diet & Diversity

Microbiome diversity, the researchers believe, has something to do with diet diversity.

“In ancient cultures, the foods you’re eating are very diverse and can support a more eclectic collection of microbes,” says microbiologist Alexsandar Kostic of the Joslin Diabetes Center. “But as you move toward industrialization and more of a grocery-store diet, you lose a lot of nutrients that help to support a more diverse microbiome.”

“In ancient cultures, the foods you’re eating are very diverse and can support a more eclectic collection of microbes.”

The way our evolving microbiome influence our health remains unclear, but – even with a small sample size – this study does show that studying our ancestral guts can offer insights we can use to improve our health in the future.

As the team concludes: “Similar future studies tapping into the richness of palaeofeces will not only expand our knowledge of the human microbiome, but may also lead to the development of approaches to restore present-day gut microbiomes to their ancestral state.”

References

  1. Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol17, 461–463 (2017). DOI: 10.1038/nri.2017.77
  2. Wibowo, M.C., Yang, Z., Borry, M. et al. Reconstruction of ancient microbial genomes from the human gut. Nature (2021). DOI: 10.1038/s41586-021-03532-0