{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:51:37Z","timestamp":1791334297921,"version":"4.3.1"},"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["5T32ES007018"],"award-info":[{"award-number":["5T32ES007018"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    DNA analysis of ancient, desiccated feces \u2013 termed paleofeces \u2013 can unlock insights into the lives of ancient peoples, including through examination of the gut microbiome and identification of specific pathogens and parasites. We collected desiccated feces from the Cave of the Dead Children (La Cueva de Los Muertos Chiquitos) in the Rio Zape Valley in Mexico dated to 725\u2013920 CE, for targeted pathogen analysis. First, we extracted DNA with methods previously optimized for paleofeces. Then, we applied highly sensitive modern molecular tools (i.e., PCR pre-amplification followed by multi-parallel qPCR) to assess the presence of 30 enteric pathogens and gut microbes. We detected \u22651 pathogen or gut microbe associated gene in each of the ten samples and a mean of 3.9 targets per sample. The targets detected included\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    spp. (n\u2009=\u20097), atypical enteropathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (n\u2009=\u20097),\n                    <jats:italic>Enterobius vermicularis<\/jats:italic>\n                    (n\u2009=\u20096),\n                    <jats:italic>Entamoeba<\/jats:italic>\n                    spp. (n\u2009=\u20095), enterotoxigenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (n\u2009=\u20095),\n                    <jats:italic>Shigella<\/jats:italic>\n                    spp.\/enteroinvasive\n                    <jats:italic>E. coli<\/jats:italic>\n                    (n\u2009=\u20093),\n                    <jats:italic>Giardia<\/jats:italic>\n                    spp. (n\u2009=\u20092), and\n                    <jats:italic>E. coli<\/jats:italic>\n                    O157:H7 (n\u2009=\u20091). The protozoan pathogens we detected (i.e.,\n                    <jats:italic>Giardia<\/jats:italic>\n                    spp. and\n                    <jats:italic>Entamoeba<\/jats:italic>\n                    spp.) have been previously detected in paleofeces via enzyme-linked immunoassay (ELISA), but not via PCR. This work represents the first detection of\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    spp. atypical enteropathogenic\n                    <jats:italic>E. coli,<\/jats:italic>\n                    enterotoxigenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    ,\n                    <jats:italic>Shigella<\/jats:italic>\n                    spp.\/enteroinvasive\n                    <jats:italic>E. coli<\/jats:italic>\n                    , and\n                    <jats:italic>E. coli<\/jats:italic>\n                    O157:H7 in paleofeces. These results suggest that enteric infection may have been common among the Loma San Gabriel people, who lived in the Rio Zape Valley in Mexico during this period.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0318140","type":"journal-article","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T17:22:17Z","timestamp":1761153737000},"page":"e0318140","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725\u2013920 CE"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2138-6382","authenticated-orcid":true,"given":"Drew","family":"Capone","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4055-7164","authenticated-orcid":true,"given":"David","family":"Holcomb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Meade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl","family":"Reinhard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joe","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,10,22]]},"reference":[{"issue":"29","key":"pone.0318140.ref001","article-title":"Pre-Clovis 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Rabinow","year":"2022","journal-title":"J Archaeological Science: Reports"},{"issue":"9","key":"pone.0318140.ref010","article-title":"Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures","volume":"9","author":"RJ Cano","year":"2014","journal-title":"PLoS One"},{"issue":"4","key":"pone.0318140.ref011","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1080\/01459740.1997.9966143","article-title":"Hookworm: not a pre-Columbian pathogen","volume":"17","author":"K Fuller","year":"1997","journal-title":"Med Anthropol"},{"issue":"6","key":"pone.0318140.ref012","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1016\/0035-9203(80)90205-9","article-title":"The finding of eggs and larvae of parasitic helminths in archaeological material from Unai, Minas Gerais, Brazil","volume":"74","author":"LF Ferreira","year":"1980","journal-title":"Trans R Soc Trop Med 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Handelsman","year":"1998","journal-title":"Chem Biol"},{"key":"pone.0318140.ref019","first-page":"263","article-title":"Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction","volume-title":"Cold Spring Harbor symposia on quantitative biology","author":"K Mullis","year":"1986"},{"issue":"2","key":"pone.0318140.ref020","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/ajpa.23978","article-title":"Comparison of extraction methods for recovering ancient microbial DNA from paleofeces","volume":"171","author":"RW Hagan","year":"2020","journal-title":"Am J Phys Anthropol"},{"issue":"1","key":"pone.0318140.ref021","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.03173-20","article-title":"Metagenomic Quantification of Genes with Internal Standards","volume":"12","author":"E Crossette","year":"2021","journal-title":"mBio"},{"issue":"1","key":"pone.0318140.ref022","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s13104-024-07027-9","article-title":"Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study","volume":"18","author":"W Taylor","year":"2025","journal-title":"BMC Res Notes"},{"issue":"11","key":"pone.0318140.ref023","article-title":"Phylotyping and functional analysis of two ancient human microbiomes","volume":"3","author":"RY Tito","year":"2008","journal-title":"PLoS One"},{"issue":"2","key":"pone.0318140.ref024","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0088376","article-title":"Polyphasic analysis of a middle ages coprolite microbiota, Belgium","volume":"9","author":"S Appelt","year":"2014","journal-title":"PLoS One"},{"issue":"3","key":"pone.0318140.ref025","doi-asserted-by":"crossref","first-page":"356","DOI":"10.2307\/277801","article-title":"Plant Material from a Cave on the Rio Zape, Durango, Mexico","volume":"27","author":"RH Brooks","year":"1962","journal-title":"Am antiq"},{"key":"pone.0318140.ref026","author":"y Meade T i m o t h","year":"1994"},{"key":"pone.0318140.ref027","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.ijpp.2017.06.002","article-title":"Reestablishing rigor in archaeological parasitology","volume":"19","author":"K Reinhard","year":"2017","journal-title":"Int J Paleopathol"},{"key":"pone.0318140.ref028","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.9001","article-title":"CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content","volume":"8","author":"M Borry","year":"2020","journal-title":"PeerJ"},{"issue":"7","key":"pone.0318140.ref029","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0133710","article-title":"Agave Chewing and Dental Wear: Evidence from Quids","volume":"10","author":"EE Hammerl","year":"2015","journal-title":"PLoS 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the16S rDNA gene associated with fecal bacteria","volume":"59","author":"N Rousselon","year":"2004","journal-title":"J Microbiol Methods"},{"issue":"24","key":"pone.0318140.ref034","doi-asserted-by":"crossref","first-page":"7505","DOI":"10.1128\/AEM.02578-14","article-title":"Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples","volume":"80","author":"S Ishii","year":"2014","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"pone.0318140.ref035","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1128\/JCM.05987-11","article-title":"Engineered combined-positive-control template for real-time reverse transcription-PCR in multiple-pathogen-detection assays","volume":"50","author":"M Kodani","year":"2012","journal-title":"J Clin Microbiol"},{"key":"pone.0318140.ref036","doi-asserted-by":"crossref","first-page":"116085","DOI":"10.1016\/j.watres.2020.116085","article-title":"A novel droplet digital PCR human mtDNA assay for fecal source tracking","volume":"183","author":"K Zhu","year":"2020","journal-title":"Water Res"},{"key":"pone.0318140.ref037","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13099-016-0103-7","article-title":"Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples","volume":"8","author":"A Glassing","year":"2016","journal-title":"Gut Pathog"},{"issue":"1","key":"pone.0318140.ref038","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1111\/lam.13091","article-title":"Identification and removal of contaminating microbial DNA from PCR reagents: impact on low-biomass microbiome analyses","volume":"68","author":"LF Stinson","year":"2019","journal-title":"Lett Appl Microbiol"},{"issue":"5","key":"pone.0318140.ref039","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1128\/JCM.38.5.1747-1752.2000","article-title":"Contamination and sensitivity issues with a 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Rio Zape Valley, Durango, Mexico","volume":"102","author":"JJ Morrow","year":"2016","journal-title":"J Parasitol"},{"issue":"9","key":"pone.0318140.ref043","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1136\/gut.35.9.1159","article-title":"Enterobius vermicularis infection","volume":"35","author":"GC Cook","year":"1994","journal-title":"Gut"},{"key":"pone.0318140.ref044","volume-title":"Analysis of ancient feces: a discussion and annotated bibliography","author":"PJ Wilke","year":"1975"},{"key":"pone.0318140.ref045","first-page":"245","article-title":"Coprolite analysis: a biological perspective on archaeology","volume":"4","author":"KJ Reinhard","year":"1992","journal-title":"Archaeological method and theory"},{"issue":"6","key":"pone.0318140.ref046","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1021\/acs.estlett.2c00140","article-title":"Elevated fecal mitochondrial dna from symptomatic norovirus infections suggests potential health relevance of human mitochondrial dna in fecal source tracking","volume":"9","author":"KJ Zhu","year":"2022","journal-title":"Environ Sci Technol Lett"},{"key":"pone.0318140.ref047","article-title":"Risk Factors for Enteric Pathogen Exposure among Children in Black Belt Region of Alabama, USA","author":"D Capone","year":"2023","journal-title":"Emerg Infect Dis"},{"key":"pone.0318140.ref048","first-page":"1","article-title":"Excreta disposal for rural areas and small communities","volume":"39","author":"EG WAGNER","year":"1958","journal-title":"Monogr Ser World Health Organ"},{"issue":"20","key":"pone.0318140.ref049","doi-asserted-by":"crossref","first-page":"11537","DOI":"10.1021\/acs.est.7b02811","article-title":"Exposure to Animal Feces and Human Health: A Systematic Review and Proposed Research Priorities","volume":"51","author":"G Penakalapati","year":"2017","journal-title":"Environ Sci 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