{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:01:54Z","timestamp":1791378114734,"version":"4.3.2"},"reference-count":107,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:00:00Z","timestamp":1763683200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008483","name":"NOMIS Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008483","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010304","name":"The Pershing Square Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010304","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.celrep.2025.116724","type":"journal-article","created":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T06:32:15Z","timestamp":1766125935000},"page":"116724","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation"],"prefix":"10.1016","volume":"45","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8105-9607","authenticated-orcid":false,"given":"Francesco","family":"Beghini","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilana L.","family":"Brito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas A.","family":"Christakis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2025.116724_bib1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/s41586-024-08222-1","article-title":"Gut microbiome strain-sharing within isolated village social networks","volume":"637","author":"Beghini","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib2","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2024.114442","article-title":"Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages","volume":"43","author":"Shridhar","year":"2024","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2025.116724_bib3","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/s41586-022-04567-7","article-title":"Environmental factors shaping the gut microbiome in a Dutch population","volume":"604","author":"Gacesa","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib4","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3001536","article-title":"Public human microbiome data are dominated by highly developed countries","volume":"20","author":"Abdill","year":"2022","journal-title":"PLoS Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib5","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2017947118","article-title":"The human gut microbiome and health inequities","volume":"118","author":"Amato","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116724_bib6","doi-asserted-by":"crossref","first-page":"R611","DOI":"10.1016\/j.cub.2015.05.040","article-title":"Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity","volume":"25","author":"Segata","year":"2015","journal-title":"Curr. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib7","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaw9255","article-title":"Vulnerability of the industrialized microbiota","volume":"366","author":"Sonnenburg","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116724_bib8","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/s41579-019-0191-8","article-title":"The ancestral and industrialized gut microbiota and implications for human health","volume":"17","author":"Sonnenburg","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.celrep.2025.116724_bib9","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/s41591-020-01183-8","article-title":"Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals","volume":"27","author":"Asnicar","year":"2021","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2025.116724_bib10","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","article-title":"Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life","volume":"17","author":"B\u00e4ckhed","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116724_bib11","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nature18927","article-title":"Mobile genes in the human microbiome are structured from global to individual scales","volume":"535","author":"Brito","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib12","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giz004","article-title":"The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches","volume":"8","author":"Dhakan","year":"2019","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116724_bib13","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13073-017-0490-5","article-title":"A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients","volume":"9","author":"Hall","year":"2017","journal-title":"Genome Med."},{"key":"10.1016\/j.celrep.2025.116724_bib14","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib15","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/s41564-017-0089-z","article-title":"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome","volume":"3","author":"Schirmer","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2025.116724_bib16","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0231197","article-title":"Metagenomics analysis reveals features unique to Indian distal gut microbiota","volume":"15","author":"Kaur","year":"2020","journal-title":"PLoS One"},{"key":"10.1016\/j.celrep.2025.116724_bib18","article-title":"Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis","volume":"6","author":"Liu","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2025.116724_bib19","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0211139","article-title":"Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels","volume":"14","author":"Lokmer","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.celrep.2025.116724_bib20","doi-asserted-by":"crossref","first-page":"6505","DOI":"10.1038\/ncomms7505","article-title":"Subsistence strategies in traditional societies distinguish gut microbiomes","volume":"6","author":"Obregon-Tito","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib21","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib22","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/nature17672","article-title":"Interconnected microbiomes and resistomes in low-income human habitats","volume":"533","author":"Pehrsson","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib23","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"Qin","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib24","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature13568","article-title":"Alterations of the human gut microbiome in liver cirrhosis","volume":"513","author":"Qin","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib25","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1016\/j.cub.2015.04.055","article-title":"Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota","volume":"25","author":"Rampelli","year":"2015","journal-title":"Curr. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib26","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s40168-018-0416-5","article-title":"Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia","volume":"6","author":"Rosa","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.celrep.2025.116724_bib27","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-020-02020-4","article-title":"Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians","volume":"21","author":"Rubel","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib28","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1126\/science.aan4834","article-title":"Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania","volume":"357","author":"Smits","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116724_bib29","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1038\/s41467-021-27917-x","article-title":"Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa","volume":"13","author":"Tamburini","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib30","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.chom.2019.08.018","article-title":"The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations","volume":"26","author":"Tett","year":"2019","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116724_bib31","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1038\/s41591-019-0458-7","article-title":"Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer","volume":"25","author":"Yachida","year":"2019","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2025.116724_bib32","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.chom.2018.06.007","article-title":"Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life","volume":"24","author":"Yassour","year":"2018","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116724_bib33","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/s40168-018-0520-6","article-title":"A metagenomic study of the gut microbiome in Behcet\u2019s disease","volume":"6","author":"Ye","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.celrep.2025.116724_bib34","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1136\/gutjnl-2015-309800","article-title":"Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer","volume":"66","author":"Yu","year":"2017","journal-title":"Gut"},{"key":"10.1016\/j.celrep.2025.116724_bib35","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.cell.2015.11.001","article-title":"Personalized nutrition by prediction of glycemic responses","volume":"163","author":"Zeevi","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib36","doi-asserted-by":"crossref","first-page":"766","DOI":"10.15252\/msb.20145645","article-title":"Potential of fecal microbiota for early-stage detection of colorectal cancer","volume":"10","author":"Zeller","year":"2014","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib37","doi-asserted-by":"crossref","first-page":"1612","DOI":"10.1038\/s41467-020-15457-9","article-title":"Metagenome-wide association of gut microbiome features for schizophrenia","volume":"11","author":"Zhu","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib38","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4","volume":"41","author":"Blanco-M\u00edguez","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib39","doi-asserted-by":"crossref","first-page":"1804","DOI":"10.1016\/j.chom.2023.09.013","article-title":"Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions","volume":"31","author":"Blanco-M\u00edguez","year":"2023","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116724_bib40","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1016\/j.cell.2018.10.029","article-title":"US immigration westernizes the human gut microbiome","volume":"175","author":"Vangay","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib41","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1136\/gutjnl-2020-323071","article-title":"Gut microbiota-derived metabolites as central regulators in metabolic disorders","volume":"70","author":"Agus","year":"2021","journal-title":"Gut"},{"key":"10.1016\/j.celrep.2025.116724_bib42","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/s41586-021-03532-0","article-title":"Reconstruction of ancient microbial genomes from the human gut","volume":"594","author":"Wibowo","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib43","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1126\/science.abm7759","article-title":"Codiversification of gut microbiota with humans","volume":"377","author":"Suzuki","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116724_bib44","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1101\/gr.216242.116","article-title":"Microbial strain-level population structure and genetic diversity from metagenomes","volume":"27","author":"Truong","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116724_bib45","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib46","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1038\/s41564-021-01020-9","article-title":"A catalogue of 1,167 genomes from the human gut archaeome","volume":"7","author":"Chibani","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2025.116724_bib47","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib48","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib49","article-title":"Expanding the human gut microbiome atlas of Africa","author":"Maghini","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2025.116724_bib50","doi-asserted-by":"crossref","first-page":"3111","DOI":"10.1016\/j.cell.2023.05.046","article-title":"Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes","volume":"186","author":"Carter","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib51","article-title":"Prevalence and subtype distribution of Blastocystis sp. infecting children from a rural community in Panama","volume":"9","author":"Perea","year":"2020","journal-title":"Parasite Epidemiol. Control"},{"key":"10.1016\/j.celrep.2025.116724_bib52","doi-asserted-by":"crossref","first-page":"2848","DOI":"10.1038\/ismej.2017.139","article-title":"Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome","volume":"11","author":"Beghini","year":"2017","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2025.116724_bib53","doi-asserted-by":"crossref","DOI":"10.1155\/2018\/3916263","article-title":"Genetic diversity and distribution of Blastocystis subtype 3 in human populations, with special reference to a rural population in central Mexico","volume":"2018","author":"Rojas-Vel\u00e1zquez","year":"2018","journal-title":"BioMed Res. Int."},{"key":"10.1016\/j.celrep.2025.116724_bib54","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00007-18","article-title":"Asymptomatic intestinal colonization with protist Blastocystis is strongly associated with distinct microbiome ecological patterns","volume":"3","author":"Nieves-Ram\u00edrez","year":"2018","journal-title":"mSystems"},{"key":"10.1016\/j.celrep.2025.116724_bib55","unstructured":"Health Organization, W. (2012). Accelerating work to overcome the global impact of neglected tropical diseases a roadmap for implementation. https:\/\/apps.who.int\/iris\/bitstream\/handle\/10665\/338712\/WHO-HTM-NTD-2012.5-eng.pdf."},{"key":"10.1016\/j.celrep.2025.116724_bib56","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1101\/gr.228429.117","article-title":"Genome-reconstruction for eukaryotes from complex natural microbial communities","volume":"28","author":"West","year":"2018","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116724_bib57","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1128\/JCM.02520-15","article-title":"Blastocystis in Health and Disease: Are We Moving from a Clinical to a Public Health Perspective?","volume":"54","author":"Andersen","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.celrep.2025.116724_bib58","doi-asserted-by":"crossref","first-page":"4554","DOI":"10.1016\/j.cell.2024.06.018","article-title":"Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries","volume":"187","author":"Piperni","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib59","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009253","article-title":"New insights into the interactions between Blastocystis, the gut microbiota, and host immunity","volume":"17","author":"Deng","year":"2021","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.celrep.2025.116724_bib60","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1186\/s13071-020-04392-9","article-title":"Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia","volume":"13","author":"Casta\u00f1eda","year":"2020","journal-title":"Parasit. Vectors"},{"key":"10.1016\/j.celrep.2025.116724_bib61","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib62","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1038\/s41564-021-00928-6","article-title":"Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome","volume":"6","author":"Nayfach","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2025.116724_bib63","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib64","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1038\/s41467-021-21350-w","article-title":"Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features","volume":"12","author":"Yutin","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib65","doi-asserted-by":"crossref","DOI":"10.1126\/science.1237439","article-title":"The long-term stability of the human gut microbiota","volume":"341","author":"Faith","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116724_bib66","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/nm.4517","article-title":"Current understanding of the human microbiome","volume":"24","author":"Gilbert","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2025.116724_bib67","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1016\/j.cell.2021.03.024","article-title":"The long-term genetic stability and individual specificity of the human gut microbiome","volume":"184","author":"Chen","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116724_bib68","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003925","article-title":"Reconstructing the population genetic history of the Caribbean","volume":"9","author":"Moreno-Estrada","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116724_bib69","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.3390\/genes13071224","article-title":"MicrobiomeGWAS: A tool for identifying host genetic variants associated with microbiome composition","volume":"13","author":"Hua","year":"2022","journal-title":"Genes"},{"key":"10.1016\/j.celrep.2025.116724_bib70","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2022.104011","article-title":"Gut microbial similarity in twins is driven by shared environment and aging","volume":"79","author":"Vilchez-Vargas","year":"2022","journal-title":"EBioMedicine"},{"key":"10.1016\/j.celrep.2025.116724_bib71","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.chom.2016.04.017","article-title":"Genetic Determinants of the Gut Microbiome in UK Twins","volume":"19","author":"Goodrich","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116724_bib72","article-title":"PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets","author":"Cantu","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.celrep.2025.116724_bib73","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib74","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4","author":"Blanco-Miguez","year":"2022","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2025.116724_bib75","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.celrep.2025.116724_bib76","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib77","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116724_bib78","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib79","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41587-020-00777-4","article-title":"Improved metagenome binning and assembly using deep variational autoencoders","volume":"39","author":"Nissen","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib80","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2025.116724_bib81","series-title":"galah: More scalable dereplication for metagenome assembled genomes","author":"Woodcroft","year":"2024"},{"key":"10.1016\/j.celrep.2025.116724_bib82","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"10.1016\/j.celrep.2025.116724_bib83","article-title":"CoverM: Read alignment statistics for metagenomics","author":"Aroney","year":"2025","journal-title":"arXiv"},{"key":"10.1016\/j.celrep.2025.116724_bib84","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s13059-021-02295-1","article-title":"Gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models","volume":"22","author":"Zimmermann","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib85","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib86","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1038\/s41467-020-16366-7","article-title":"Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0","volume":"11","author":"Asnicar","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib87","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib88","series-title":"Fast Genome-wide Functional Annotation through Orthology Assignment by eggNOG-Mapper","author":"Huerta-Cepas","year":"2016"},{"key":"10.1016\/j.celrep.2025.116724_bib89","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.celrep.2025.116724_bib90","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","article-title":"BUSCO: Assessing genome assembly and annotation completeness","volume":"1962","author":"Seppey","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib91","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/s41467-022-28581-5","article-title":"Genome binning of viral entities from bulk metagenomics data","volume":"13","author":"Johansen","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib92","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116724_bib93","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116724_bib94","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41588-020-00756-0","article-title":"Efficient phasing and imputation of low-coverage sequencing data using large reference panels","volume":"53","author":"Rubinacci","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2025.116724_bib95","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116724_bib96","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"10.1016\/j.celrep.2025.116724_bib97","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1093\/bioinformatics\/btq559","article-title":"Robust relationship inference in genome-wide association studies","volume":"26","author":"Manichaikul","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib98","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1093\/bioinformatics\/bts163","article-title":"Matrix eQTL: ultra fast eQTL analysis via large matrix operations","volume":"28","author":"Shabalin","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib99","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/nmeth.4468","article-title":"Accessible, curated metagenomic data through ExperimentHub","volume":"14","author":"Pasolli","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116724_bib100","doi-asserted-by":"crossref","first-page":"eadi5147","DOI":"10.1126\/science.adi5147","article-title":"Induction of social contagion for diverse outcomes in structured experiments in isolated villages","volume":"384","author":"Airoldi","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116724_bib101","unstructured":"BMTagger ftp:\/\/ftp.ncbi.nlm.nih.gov\/pub\/agarwala\/bmtagger\/."},{"key":"10.1016\/j.celrep.2025.116724_bib102","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41586-022-05620-1","article-title":"The person-to-person transmission landscape of the gut and oral microbiomes","volume":"614","author":"Valles-Colomer","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116724_bib103","doi-asserted-by":"crossref","first-page":"4845","DOI":"10.1038\/s41467-021-25213-2","article-title":"Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations","volume":"12","author":"Stra\u017ear","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116724_bib104","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1038\/s41587-020-0501-8","article-title":"A complete domain-to-species taxonomy for Bacteria and Archaea","volume":"38","author":"Parks","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2025.116724_bib105","doi-asserted-by":"crossref","first-page":"3029","DOI":"10.1093\/bioinformatics\/btab184","article-title":"Fast and sensitive taxonomic assignment to metagenomic contigs","volume":"37","author":"Mirdita","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2025.116724_bib106","series-title":"CoverM: Read Coverage Calculator for Metagenomics","author":"Aroney","year":"2024"},{"key":"10.1016\/j.celrep.2025.116724_bib107","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725014962?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725014962?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:24:54Z","timestamp":1791260694000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124725014962"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":107,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S2211124725014962"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116724","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116724","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116724"}}