CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content.

Maxime Borry ,Richard Hagan ,Ingelise Stuijts ,Tanvi P Honap ,Linus Girdland-Flink ,Hélène Carabin ,Alexander Herbig ,Kate Britton ,Courtney A Hofman ,Jada Ko ,Cecil M Lewis ,Marsha C Wibowo ,Alexander Hübner ,Nicolas Méda ,Jie Yu ,David P Jacobson ,Bryan Cordova ,Karl J Reinhard ,Angela R Perri ,Domingo C Salazar‐García ,Robert C Power ,Thérèse Kagoné ,Choongwon Jeong ,Aleksandar D Kostic ,Christina Warinner

doi:10.7717/peerj.9001

Abstract

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

Highlights

The gut microbiome, located in the distal colon and primarily studied through the analysis of feces, is the largest and arguably most influential microbial community within the body (The Human Microbiome Project Consortium, 2012)
In this work we present a bioinformatics method to infer and authenticate the host source of paleofeces from shotgun metagenomic DNA sequencing data: coproID. coproID combines the analysis of putative host ancient DNA with a machine learning prediction of the feces source based on microbiome taxonomic composition
We found that the median percentages of host DNA in Non-Westernized Human/Rural (NWHR), WHU, and Dog (Fig. 3) are significantly different at alpha = 0.05 (Kruskal–Wallis H-test = 117.40, p value < 0.0001)

Summary

Introduction

The gut microbiome, located in the distal colon and primarily studied through the analysis of feces, is the largest and arguably most influential microbial community within the body (The Human Microbiome Project Consortium, 2012). Recent investigations of the human microbiome have revealed that it plays diverse roles in health and disease, and gut microbiome composition has been linked to a variety of human health states, including inflammatory bowel diseases, diabetes, and obesity (Kho & Lal, 2018). To investigate the gut microbiome, metagenomic sequencing is typically used to reveal both the taxononomic composition (i.e., which bacteria are there) and the functions the microbes are capable of performing (i.e., their potential metabolic activities) (Sharpton, 2014). Genetic approaches have long been used to investigate dietary DNA found within human (Gilbert et al, 2008; Poinar et al, 2001) and animal (Poinar et al, 1998; Hofreiter et al, 2000; Bon et al, 2012; Wood et al, 2016) paleofeces, it is only recently that improvements in metagenomic sequencing and bioinformatics have enabled detailed characterization of their microbial communities (Tito et al, 2008, 2012; Warinner et al, 2017)

Methods

Results

Discussion

Conclusion