6533b823fe1ef96bd127eba3
RESEARCH PRODUCT
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
Thérèse KagonéRobert C. PowerRobert C. PowerDavid JacobsonAleksandar KosticAleksandar KosticCourtney A. HofmanWing Tung Jada KoAlexander HerbigRichard W. HaganBryan CordovaChristina WarinnerChristina WarinnerChristina WarinnerMarsha C. WibowoMarsha C. WibowoLinus Girdland-flinkLinus Girdland-flinkTanvi P. HonapJie YuIngelise StuijtsCecil M. LewisKate BrittonKate BrittonMaxime BorryNicolas MedaDomingo Carlos Salazar GarcíaDomingo Carlos Salazar GarcíaChoongwon JeongChoongwon JeongAngela R. PerriAngela R. PerriAlexander HübnerHélène CarabinKarl J. Reinhardsubject
dogsArcheologyMicrobial DNAData Mining and Machine LearningCoprolitemicrobiomeendogenous DNAlcsh:MedicineMorphology (biology)Genomechemistry.chemical_compoundPaleofecesDog0601 history and archaeologyGutArqueologia Metodologia0303 health sciences060102 archaeologyGeneral NeuroscienceGeneral Medicine06 humanities and the artsGenomicsNextflowmachine learningnextflowgutGeneral Agricultural and Biological SciencesShotgun metagenomicsPaleofecesHumanpaleofecesBioinformaticsBiologyMicrobiologyGeneral Biochemistry Genetics and Molecular Biologydiversity03 medical and health sciencesEndogenous DNAMachine learningcoprolitedog molecular analysishumanMicrobiomeancient DNAgenome030304 developmental biology030306 microbiologyHost (biology)lcsh:RcultureAncient DNAarcheologychemistryEvolutionary biologyAnthropologyCoproliteMicrobiomedietDNAdescription
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. This work was supported by the US National Institutes of Health R01GM089886 (to Christina Warinner and Cecil Lewis), the Deutsche Forschungsgemeinschaft EXC 2051 #390713860 (to Christina Warinner), and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2020-04-17 | PeerJ |