{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T15:39:04Z","timestamp":1785771544510,"version":"3.56.0"},"reference-count":54,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T00:00:00Z","timestamp":1715731200000},"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><jats:title>Introduction<\/jats:title><jats:p>The possibility that there is a resident and stable commensal microbiome within the pregnant uterus has been supported and refuted by a series of recent studies. One element of most of the initial studies was that they were based primarily on 16S rRNA gene sequencing from bacteria. To account for this limitation, the current study performed both bacterial culture and 16S rRNA gene sequencing in a side-by-side manner (e.g., same tissues isolated from the same animal).<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The uteruses of 10 mid-pregnant (156\u2009\u00b1\u20095 d of gestation) Holstein heifers and cows were collected following slaughter. The external surface of the reproductive tract (positive control for contamination during tissue collection) as well as tissues within the pregnant uterus (placentome, inter-cotyledonary placenta, inter-caruncular endometrium, amnionic fluid, allantoic fluid, fetal abomasum content, and fetal meconium) were sampled for bacterial culture and 16S rRNA gene sequencing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>There were 87 unique bacterial species cultured from the external surface of the pregnant reproductive tract (contamination control) and 12 bacterial species cultured from pregnancy tissues. Six out of 10 cattle (60%) exhibited bacterial growth in at least one location within the pregnant uterus. For the metataxonomic results (16S rRNA gene sequencing), a low targeted microbial biomass was identified. Analyses of the detected amplicon sequence variants (ASV) revealed that there were: (1) genera that were prevalent on both the external surface and within the pregnant uterus; (2) genera that were prevalent on the external surface but either not detected or had very low prevalence within the pregnant uterus; and (3) genera that were either not detected or had low prevalence on the external surface but found with relatively high prevalence within the pregnant uterus.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>There are a small number of viable bacteria in the pregnant uterus. The 16S rRNA gene sequencing detected a microbial community within the pregnant uterus but with a low biomass. These results are consistent with recent studies of the pregnant bovine uterus and leave open the question of whether there is adequate microbial mass to significantly affect the biology of the normal healthy bovine pregnancy.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2024.1385497","type":"journal-article","created":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T10:41:51Z","timestamp":1715769711000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["The microbiome of the pregnant uterus in Holstein dairy heifers and cows assessed by bacterial culture and 16S ribosomal RNA gene sequencing"],"prefix":"10.3389","volume":"15","author":[{"given":"Joao G. 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Transl. Med."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1128\/mr.59.1.143-169.1995","article-title":"Phylogenetic identification and in situ detection of individual microbial cells without cultivation","volume":"59","author":"Amann","year":"1995","journal-title":"Microbiol. Rev."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"208","DOI":"10.3389\/fimmu.2018.00208","article-title":"Uterine microbiota: residents, tourists, or invaders?","volume":"9","author":"Baker","year":"2018","journal-title":"Front. Immunol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1093\/humupd\/dmy012","article-title":"How uterine microbiota might be responsible for a receptive, fertile endometrium","volume":"24","author":"Benner","year":"2018","journal-title":"Hum. Reprod. Update"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.3945228","article-title":"bokulich-lab\/RESCRIPt: 2020.6.1","author":"Bokulich","year":"2020","journal-title":"Zenodo"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","article-title":"The human skin microbiome","volume":"16","author":"Byrd","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","article-title":"Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample","volume":"108","author":"Caporaso","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.tim.2018.11.003","article-title":"Contamination in low microbial biomass microbiome studies: issues and recommendations","volume":"27","author":"Eisenhofer","year":"2019","journal-title":"Trends Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/clinids\/10.6.1220","article-title":"The intestinal bacteria of the neonate and breast-fed infant. 1884","volume":"10","author":"Escherich","year":"1988","journal-title":"Rev. Infect. Dis."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","article-title":"Conservation evaluation and phylogenetic diversity","volume":"61","author":"Faith","year":"1992","journal-title":"Biol. Conserv."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/j.cell.2018.07.038","article-title":"Microbiome: focus on causation and mechanism","volume":"174","author":"Fischbach","year":"2018","journal-title":"Cell"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"11786","DOI":"10.3168\/jds.2019-17106","article-title":"Symposium review: the uterine microbiome associated with the development of uterine disease in dairy cows","volume":"102","author":"Galv\u00e3o","year":"2019","journal-title":"J. Dairy Sci."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.theriogenology.2008.04.018","article-title":"Infectious causes of embryonic and fetal mortality","volume":"70","author":"Givens","year":"2008","journal-title":"Theriogenology"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"17712","DOI":"10.1038\/s41598-020-74677-7","article-title":"A pioneer calf foetus microbiome","volume":"10","author":"Guzman","year":"2020","journal-title":"Sci. Rep."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"626421","DOI":"10.3389\/fmicb.2021.626421","article-title":"The composition of the microbiota in the full-term fetal gut and amniotic fluid: a bovine cesarean section study","volume":"12","author":"Husso","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/s40168-017-0328-9","article-title":"Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows","volume":"5","author":"Jeon","year":"2017","journal-title":"Microbiome"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1177\/104063879300500114","article-title":"Bacterial agents detected in a 10-year study of bovine abortions and stillbirths","volume":"5","author":"Kirkbride","year":"1993","journal-title":"J. Vet. Diagn. Invest."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"8266","DOI":"10.3390\/ijms21218266","article-title":"The Cervicovaginal mucus barrier","volume":"21","author":"Lacroix","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"6159","DOI":"10.3168\/jds.2020-19554","article-title":"Low microbial biomass within the reproductive tract of mid-lactation dairy cows: a study approach","volume":"104","author":"Lietaer","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1128\/AEM.01996-06","article-title":"Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities","volume":"73","author":"Lozupone","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"Lozupone","year":"2005","journal-title":"AEM"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1177\/104063870902100220","article-title":"Isolation of Propionibacterium acnes from a case of placentitis and abortion in a cow","volume":"21","author":"Lyons","year":"2009","journal-title":"J. Vet. Diagn. Invest."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1146\/annurev-micro-092611-150157","article-title":"Vaginal microbiome: rethinking health and disease","volume":"66","author":"Ma","year":"2012","journal-title":"Ann. Rev. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"27663","DOI":"10.3402\/mehd.v26.27663","article-title":"Analysis of composition of microbiomes: a novel method for studying microbial composition","volume":"26","author":"Mandal","year":"2015","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/2047-217X-1-7","article-title":"The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome","volume":"1","author":"McDonald","year":"2012","journal-title":"Gigascience"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"2886","DOI":"10.3389\/fimmu.2019.02886","article-title":"The unique microbiome and innate immunity during pregnancy","volume":"10","author":"Mei","year":"2019","journal-title":"Front. Immunol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"4953","DOI":"10.3168\/jds.2017-12592","article-title":"Hot topic: 16S rRNA gene sequencing reveals the microbiome of the virgin and pregnant bovine uterus","volume":"100","author":"Moore","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref1002","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-4233045\/v1","article-title":"Systemic antibiotic treatment of cows with metritis early postpartum does not change the progression of uterine disease or the uterine microbiome at 1 month postpartum","author":"Moraes","year":"2024","journal-title":"Res Sq rs.3.rs-4233045."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"12816","DOI":"10.3168\/jds.2021-20502","article-title":"Risk factors for purulent vaginal discharge and its association with reproductive performance of lactating Jersey cows","volume":"104","author":"Moraes","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1111\/1471-0528.15974","article-title":"Re-assessing microbiomes in the low-biomass reproductive niche","volume":"127","author":"O\u2019Callaghan","year":"2020","journal-title":"BJOG"},{"key":"ref35","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2012","journal-title":"J. Mach. Learn. Res."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/s40168-017-0268-4","article-title":"A critical assessment of the \u201csterile womb\u201d and \u201cin utero colonization\u201d hypotheses: implications for research on the pioneer infant microbiome","volume":"5","author":"Perez-Mu\u00f1oz","year":"2017","journal-title":"Microbiome"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0022-5193(66)90013-0","article-title":"The measurement of diversity in different types of biological collections","volume":"13","author":"Pielou","year":"1966","journal-title":"J. Theor. Biol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"7661","DOI":"10.3168\/jds.2017-13858","article-title":"Symposium review: understanding diet-microbe interactions to enhance productivity of dairy cows","volume":"101","author":"Pitta","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"s399","DOI":"10.1017\/S1751731118001921","article-title":"Review: enhancing gastrointestinal health in dairy cows","volume":"12","author":"Plaizier","year":"2018","journal-title":"Animal"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"R41","DOI":"10.1530\/REP-14-0163","article-title":"Innate immunity and inflammation of the bovine female reproductive tract in health and disease","volume":"148","author":"Sheldon","year":"2014","journal-title":"Reproduction"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.theriogenology.2020.01.017","article-title":"Preventing postpartum uterine disease in dairy cattle depends on avoiding, tolerating and resisting pathogenic bacteria","volume":"150","author":"Sheldon","year":"2020","journal-title":"Theriogenology"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s40168-020-00968-w","article-title":"Group therapy on in utero colonization: seeking common truths and a way forward","volume":"9","author":"Silverstein","year":"2021","journal-title":"Microbiome"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nature18846","article-title":"Diet-microbiota interactions as moderators of human metabolism","volume":"535","author":"Sonnenburg","year":"2016","journal-title":"Nature"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.3389\/fmicb.2019.01124","article-title":"The not-so-sterile womb: evidence that the human fetus is exposed to Bacteria prior to birth","volume":"10","author":"Stinson","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1128\/mSphere.00210-20","article-title":"Lack of evidence for microbiota in the placental and fetal tissues of Rhesus macaques","volume":"5","author":"Theis","year":"2020","journal-title":"mSphere"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.chom.2016.12.009","article-title":"Bringing the dynamic microbiome to life with animations","volume":"21","author":"V\u00e1zquez-Baeza","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/2047-217X-2-16","article-title":"EMPeror: a tool for visualizing high-throughput microbial community data","volume":"2","author":"V\u00e1zquez-Baeza","year":"2013","journal-title":"Gigascience"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.vetmic.2014.11.017","article-title":"Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows","volume":"175","author":"Wagener","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s40168-020-00979-7","article-title":"A philosophical perspective on the prenatal in utero microbiome debate","volume":"9","author":"Walter","year":"2021","journal-title":"Microbiome"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"808","DOI":"10.2144\/04365ST04","article-title":"Improved extraction of PCR-quality community DNA from digesta and fecal samples","volume":"36","author":"Yu","year":"2004","journal-title":"BioTechniques"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/s41598-020-80653-y","article-title":"Transfer of oral bacteria to the fetus during late gestation","volume":"11","author":"Yu","year":"2021","journal-title":"Sci. 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