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

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e9001
• Main Authors: Borry, Maxime, Cordova, Bryan, Perri, Angela, Wibowo, Marsha, Prasad Honap, Tanvi, Ko, Jada, Yu, Jie, Britton, Kate, Girdland-Flink, Linus, Power, Robert C, Stuijts, Ingelise, Salazar-García, Domingo C, Hofman, Courtney, Hagan, Richard, Samdapawindé Kagoné, Thérèse, Meda, Nicolas, Carabin, Helene, Jacobson, David, Reinhard, Karl, Lewis, Cecil, Kostic, Aleksandar, Jeong, Choongwon, Herbig, Alexander, Hübner, Alexander, Warinner, Christina
• Format: Journal Article
• Language: English
• Published: United States PeerJ, Inc 17-04-2020; PeerJ Inc
• Subjects: Anthropology; Archaeology; Archeology; Bioinformatics; Consortia; Coprolite; Data Mining and Machine Learning; Datasets; Deoxyribonucleic acid; Diabetes; DNA; Dogs; Endogenous DNA; Feces; Genomics; Intestinal microflora; Machine learning; Mesolithic; Metagenomics; Microbiology; Microbiome; Microbiomes; Microbiota; Mitochondrial DNA; Neolithic; Paleofeces; Sediments; Westernization; Mexico; United States > US; Peru; China; Human; Archeology; Paleofeces; Coprolite; Endogenous DNA; Gut; Machine learning; Nextflow; Dog; Microbiome
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.9001

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.