CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content.
Archeology
Coprolite
Dog
Endogenous DNA
Gut
Human
Machine learning
Microbiome
Nextflow
Paleofeces
Journal
PeerJ
ISSN: 2167-8359
Titre abrégé: PeerJ
Pays: United States
ID NLM: 101603425
Informations de publication
Date de publication:
2020
2020
Historique:
received:
15
01
2020
accepted:
26
03
2020
entrez:
28
4
2020
pubmed:
28
4
2020
medline:
28
4
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32337106
doi: 10.7717/peerj.9001
pii: 9001
pmc: PMC7169968
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e9001Subventions
Organisme : NIDDK NIH HHS
ID : P30 DK036836
Pays : United States
Informations de copyright
© 2020 Borry et al.
Déclaration de conflit d'intérêts
The authors declare that they have no competing interests.
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