ArticlePloS one2012
Insights from characterizing extinct human gut microbiomes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 214 citations in OpenAlex.
- Gut Prevotella stercorea associates with protection against infection in rural African children.Nature communications · 2025Trial
- Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.Scientific reports · 2026Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- Exploring the Pathogen Profiles of Ancient Feces.bioRxiv : the preprint server for biology · 2025Article
- Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities.PloS one · 2025Article
- Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725-920 CE.PloS one · 2025Article
- Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation.Microbiology and molecular biology reviews : MMBR · 2024Review
- The Role of the Gut Microbiome in Cancer: A Review, With Special Focus on Colorectal Neoplasia and Clostridioides difficile.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Review
- A relational framework for microbiome research with Indigenous communities.Nature microbiology · 2023Review
- Ancient pathogens provide a window into health and well-being.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- TRPV1 in male reproductive system: focus on sperm function.Molecular and cellular biochemistry · 2022Review
- Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes.Proceedings. Biological sciences · 2022Article
- Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations.Microorganisms · 2022Article
- A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration.Frontiers in systems biology · 2022Article
- Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period.Current biology : CB · 2021Article
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- Potential zoonotic pathogens hosted by endangered bonobos.Scientific reports · 2021Article
- Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.Communications biology · 2021Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
Abstract
In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.