200420 fossil faeces preview

The origin of faeces

The archaeological record is littered – aha – with poo, a potential goldmine for insights into ancient health and diet, parasite evolution, and the ecology and evolution of the microbiome.

Coprolites from Xiaosungang archaeological site, Anhui Province, China. Credit: Jada Ko, courtesy of the Anhui Provincial Institute of Cultural Relics and Archaeology

The issue for researchers has always been determining which species’ faeces it is that they’re looking at.

Now, a study published in the journal PeerJ and led by Maxime Borry and Christina Warinner, of the Max Planck Institute for the Science of Human History, Germany, has unveiled “coproID” – a reliable method of inferring sources of paleofaeces.

The specific origin of paleofaeces – often thousands of years old – can be difficult to determine for many reasons. For instance, telling human and dog poo apart is particularly difficult: faecal deposits are similar in size and shape, occur at the same archaeological sites, and have similar compositions.

Further compounding the problem, dogs were a food source for many ancient societies, and given our canine friends’ tendency to scavenge on human faeces, simple genetic analysis becomes problematic because it can return DNA from both species.

Enter coproID (coprolite identification).

The method combines analysis of ancient host DNA with machine-learning software that’s been “trained” on the microbiomes within modern faeces.

Applying coproID to both newly sequenced and previously published datasets, the German-US research team was able to reliably predict the sources of ancient faeces. A combination of host DNA and the distinct colonies of microbes living inside humans and dogs allow their faeces to be accurately distinguished.

“One unexpected finding of our study is the realisation that the archaeological record is full of dog poop,” says Warinner, the study’s senior author.

She also expects coproID to have broader applications, especially in the fields of forensics, ecology and microbiome sciences.

The ability to accurately identify the source of ancient poo enables the direct investigation of changes in the structure and function of the human gut microbiome throughout time. Researchers hope this will provide insights into food intolerances and a host of other issues in human health.

“Identifying human coprolites should be the first step for ancient human microbiome analysis,” says Borry.

“With additional data about the gut metagenomes of non-Westernised rural dogs, we’ll be better able to classify even more ancient dog faeces as in fact being canine, as opposed to ‘uncertain’.”

As the catalogue of human and dog microbiome data grows, coproID will continue to improve its classifications and better aid researchers that encounter paleofaeces in a range of geographic and historical contexts.

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