{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T11:31:35Z","timestamp":1787916695796,"version":"build-2784847793"},"reference-count":40,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Tissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to\n                      <jats:italic>in silico<\/jats:italic>\n                      contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus\n                      <jats:italic>Sporisorium graminicola<\/jats:italic>\n                      for the heart, the gram-positive bacterium\n                      <jats:italic>Flavonifractor plautii<\/jats:italic>\n                      for the colon tissue, and the gram-negative bacterium\n                      <jats:italic>Bartonella machadoae<\/jats:italic>\n                      for the liver.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2024.1512304","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T07:57:52Z","timestamp":1737964672000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs"],"prefix":"10.3389","volume":"15","author":[{"given":"Anargyros","family":"Skoulakis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgos","family":"Skoufos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Armen","family":"Ovsepian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artemis G.","family":"Hatzigeorgiou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,1,27]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"4048","DOI":"10.1093\/bioinformatics\/btab408","article-title":"PuffAligner: a fast, efficient and accurate aligner based on the pufferfish index","volume":"37","author":"Almodaresi","year":"2021","journal-title":"Bioinformatics"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1038\/s41586-019-1608-2","article-title":"The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL","volume":"574","author":"Aykut","year":"2019","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e65088","DOI":"10.7554\/eLife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bio bakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"eLife"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"e158999","DOI":"10.1172\/JCI158999","article-title":"Bacteria may be in the liver, but the jury is still out","volume":"132","author":"Broderick","year":"2022","journal-title":"J. Clin. Invest."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1099\/ijs.0.016725-0","article-title":"Proposal to unify Clostridium orbiscindens winter et al. 1991 and Eubacterium plautii (S\u00e9guin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. Nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. Nov., comb. nov","volume":"60","author":"Carlier","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"631972","DOI":"10.3389\/fcimb.2021.631972","article-title":"The female vaginal microbiome in health and bacterial vaginosis","volume":"11","author":"Chen","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"p.giab 008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"e3720","DOI":"10.7717\/peerj.3720","article-title":"Atropos: specific, sensitive, and speedy trimming of sequencing reads","volume":"5","author":"Didion","year":"2017","journal-title":"Peer J"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.chom.2020.12.001","article-title":"The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants","volume":"29","author":"Dohlman","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1074\/mcp.M113.035600","article-title":"Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics","volume":"13","author":"Fagerberg","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1214\/aos\/1013203451","article-title":"Greedy function approximation: a gradient boosting machine","volume":"29","author":"Friedman","year":"2001","journal-title":"Ann. Stat."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1080\/1040841X.2018.1501345","article-title":"Human endogenous retrovirus-K (HML-2): a comprehensive review","volume":"44","author":"Garcia-Montojo","year":"2018","journal-title":"Crit. Rev. Microbiol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1016\/j.ccell.2022.09.009","article-title":"Tumor microbiome links cellular programs and immunity in pancreatic cancer","volume":"40","author":"Ghaddar","year":"2022","journal-title":"Cancer Cell"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e01607","DOI":"10.1128\/mbio.01607-23","article-title":"Major data analysis errors invalidate cancer microbiome findings","volume":"14","author":"Gihawi","year":"2023","journal-title":"MBio"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1002\/1096-9071(200104)63:4<277::AID-JMV1002>3.0.CO;2-K","article-title":"Human herpesvirus 7 is latent in gastric mucosa","volume":"63","author":"Gonelli","year":"2001","journal-title":"J. Med. Virol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"30751","DOI":"10.1038\/srep30751","article-title":"The microbiome of aseptically collected human breast tissue in benign and malignant disease","volume":"6","author":"Hieken","year":"2016","journal-title":"Sci. Rep."},{"key":"ref19","doi-asserted-by":"publisher","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":"ref20","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1093\/bioinformatics\/bty648","article-title":"Scaling read aligners to hundreds of threads on general-purpose processors","volume":"35","author":"Langmead","year":"2019","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"e0142334","DOI":"10.1371\/journal.pone.0142334","article-title":"The characterization of novel tissue microbiota using an optimized 16S metagenomic sequencing pipeline","volume":"10","author":"Lluch","year":"2015","journal-title":"PLoS ONE"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The genotype-tissue expression (GTEx) project","volume":"45","author":"Lonsdale","year":"2013","journal-title":"Nat. Genet."},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1101\/2022.10.14.512130","article-title":"Single cell transcriptomics reveals the hidden microbiomes of human tissues","author":"Mahmoudabadi","year":"2022","journal-title":"Bio Rxiv"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"11257","DOI":"10.1038\/ncomms11257","article-title":"Fast and sensitive taxonomic classification for metagenomics with kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat. Commun."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"780","DOI":"10.3389\/fmicb.2019.00780","article-title":"Living at the extremes: extremophiles and the limits of life in a planetary context","volume":"10","author":"Merino","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"133","DOI":"10.5650\/jos.ess14185","article-title":"Mannosylerythritol lipids: production and applications","volume":"64","author":"Morita","year":"2015","journal-title":"J. Oleo Sci."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"e86490","DOI":"10.1371\/journal.pone.0086490","article-title":"Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma Antarctica producing extracellular glycolipids, mannosylerythritol lipids","volume":"9","author":"Morita","year":"2014","journal-title":"PLoS One"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"3789","DOI":"10.1016\/j.cell.2022.09.005","article-title":"Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions","volume":"185","author":"Narunsky-Haziza","year":"2022","journal-title":"Cell"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e0098622","DOI":"10.1128\/msystems.01219-22","article-title":"Host factors associated with gut Mycobiome structure","volume":"8","author":"Natalia","year":"2023","journal-title":"MSystems"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/s41579-022-00821-x","article-title":"The dynamic lung microbiome in health and disease","volume":"21","author":"Natalini","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1126\/science.aay9189","article-title":"The human tumor microbiome is composed of tumor type\u2013specific intracellular bacteria","volume":"368","author":"Nejman","year":"2020","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1038\/nmeth.2658","article-title":"Differential abundance analysis for microbial marker-gene surveys","volume":"10","author":"Paulson","year":"2013","journal-title":"Nat. Methods"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41586-020-2095-1","article-title":"Microbiome analyses of blood and tissues suggest cancer diagnostic approach","volume":"579","author":"Poore","year":"2020","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1111\/1574-6976.12075","article-title":"The first 1000 cultured species of the human gastrointestinal microbiota","volume":"38","author":"Rajili\u0107-Stojanovi\u0107","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1016\/j.cell.2019.07.008","article-title":"Tumor microbiome diversity and composition influence pancreatic cancer outcomes","volume":"178","author":"Riquelme","year":"2019","journal-title":"Cell"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s13059-022-02610-4","article-title":"AGAMEMNON: an accurate metaGenomics and MEtatranscriptoMics quaNtificatiON analysis suite","volume":"23","author":"Skoufos","year":"2022","journal-title":"Genome Biol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"publisher","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":"ref39","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/s41586-019-1238-8","article-title":"The integrative human microbiome project","volume":"569","year":"2019","journal-title":"Nature"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"S38","DOI":"10.1111\/j.1753-4887.2012.00493.x","article-title":"Defining the human microbiome","volume":"70","author":"Ursell","year":"2012","journal-title":"Nutr. Rev."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2334-12-17","article-title":"Granulomatous hepatitis due to Bartonella henselae infection in an immunocompetent patient","volume":"12","author":"Vander Heyden","year":"2012","journal-title":"BMC Infect. Dis."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1512304\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T07:57:55Z","timestamp":1737964675000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1512304\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,27]]},"references-count":40,"alternative-id":["10.3389\/fmicb.2024.1512304"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1512304","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4610181\/v1","asserted-by":"object"}]},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,27]]},"article-number":"1512304"}}