{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:36:35Z","timestamp":1787067395951,"version":"build-2736575974"},"reference-count":77,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["F31HD104353"],"award-info":[{"award-number":["F31HD104353"]}]},{"DOI":"10.13039\/100000057","name":"HHS | NIH | National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["R35GM133745"],"award-info":[{"award-number":["R35GM133745"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["K99HD090290"],"award-info":[{"award-number":["K99HD090290"]}]},{"name":"March of Dimes Prematurity Research Center"},{"DOI":"10.13039\/100014264","name":"Triangle Center for Evolutionary Medicine","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100014264","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2024,6,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The vaginal microbiome has been linked to negative health outcomes including preterm birth. Specific taxa, including\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      spp. as one species, but the broad diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      has become more apparent. We explore the diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      clades and genomic species in the vaginal microbiome of pregnant women and their associations with microbiome composition and preterm birth. Relative abundance of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      clades and genomic species and other taxa was quantified in shotgun metagenomic sequencing data from three distinct cohorts of pregnant women. We also assessed the diversity and abundance of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      variants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations. Individual microbiomes often contained multiple\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      variants, and the number of clades was associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns were largely consistent across\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      clades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      . The diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. The broad genomic diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      has led to its reclassification as multiple species; here we demonstrate the diversity of\n                      <jats:italic>Gardnerella<\/jats:italic>\n                      found within and between vaginal microbiomes.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        The present study shows that single microbiomes can contain all currently known species of\n                        <jats:italic>Gardnerella<\/jats:italic>\n                        and that multiple similar species can exist within the same environment. Furthermore, surveys of demographically distinct populations suggest that some species appear more commonly in certain populations. Further studies in broad and diverse populations will be necessary to fully understand the ecological roles of each\n                        <jats:italic>Gardnerella<\/jats:italic>\n                        sp., how they can co-exist, and their distinct impacts on microbial communities, preterm birth, and other health outcomes.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.01339-23","type":"journal-article","created":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T09:00:36Z","timestamp":1715850036000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":18,"title":["<i>Gardnerella<\/i>\n                    diversity and ecology in pregnancy and preterm birth"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8616-8167","authenticated-orcid":true,"given":"Hanna L.","family":"Berman","sequence":"first","affiliation":[{"name":"Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela S. Aliaga","family":"Goltsman","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA"},{"name":"Department of Medicine, Stanford University School of Medicine, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Anderson","sequence":"additional","affiliation":[{"name":"Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Relman","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA"},{"name":"Department of Medicine, Stanford University School of Medicine, Stanford, California, USA"},{"name":"Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8752-117X","authenticated-orcid":true,"given":"Benjamin J.","family":"Callahan","sequence":"additional","affiliation":[{"name":"Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA"},{"name":"Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14677-3"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-020-03831-w"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008376"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21010222"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1158\/1940-6207.CAPR-15-0350"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.308.6924.295"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0091-2182(97)00161-4"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1542-2011.2011.00086.x"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1002611107"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiz342"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/0002-9378(55)90095-8"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.9.4607-4612.2005"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1502875112"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1705899114"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0146510"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200625"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cwab024"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0191524"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0450-2"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-12198-6"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.066407-0"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-375"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.034280-0"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.7150\/ijms.6304"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02188-20"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00056-12"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0043009"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.003200"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1373\/clinchem.2019.305474"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-017-2501-y"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00532-19"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0135620"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000543"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.medj.2021.06.001"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11234"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2575"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf436"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-02008-7_13"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0465-8"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.08.014"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.236000.118"},{"key":"e_1_3_5_49_2","unstructured":"Joshi NA Fass JN. 2011. Sickle: a sliding-window adaptive quality-based trimming tool for FastQ files. Version 1.33. Available from: https:\/\/github.com\/najoshi\/sickle"},{"key":"e_1_3_5_50_2","unstructured":"Bushnell B. 2014. BBMap: a fast accurate splice-aware aligner. Available from: https:\/\/www.osti.gov\/biblio\/1241166"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01688-w"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-020-0665-8"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","unstructured":"Karasov TL Neumann M Duque-Jaramillo A Kersten S Bezrukov I Schr\u00f6ppel B Symeonidi E Lundberg DS Regalado J Shirsekar G Bergelson J Weigel D. 2020. The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere. bioRxiv. doi:10.1101\/828814","DOI":"10.1101\/828814"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.12.012"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1111\/1471-0528.15299"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09285-9"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.annepidem.2019.11.004"},{"key":"e_1_3_5_60_2","doi-asserted-by":"publisher","DOI":"10.1055\/s-0035-1565919"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-023-01702-2"},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1654-1103.2003.tb02228.x"},{"key":"e_1_3_5_64_2","unstructured":"R Core Team. 2020. R: a language and environment for statistical computing. Available from: https:\/\/www.R-project.org\/"},{"key":"e_1_3_5_65_2","unstructured":"RStudio Team. 2020. RStudio: integrated development environment for R. Available from: http:\/\/www.rstudio.com\/"},{"key":"e_1_3_5_66_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02188-20"},{"key":"e_1_3_5_67_2","doi-asserted-by":"publisher","unstructured":"Huang C Gin C Fettweis J Foxman B Gelaye B MacIntyre DA Subramaniam A Fraser W Tabatabaei N Callahan B. 2023. Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth. medRxiv. doi:10.1101\/2022.09.26.22280389","DOI":"10.1101\/2022.09.26.22280389"},{"key":"e_1_3_5_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiz474"},{"key":"e_1_3_5_69_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-020-01643-1"},{"key":"e_1_3_5_70_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2019.00374"},{"key":"e_1_3_5_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.02.097"},{"key":"e_1_3_5_72_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00552-21"},{"key":"e_1_3_5_73_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature24460"},{"key":"e_1_3_5_74_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00083"},{"key":"e_1_3_5_75_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0026732"},{"key":"e_1_3_5_76_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0269590"},{"key":"e_1_3_5_77_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0256445"},{"key":"e_1_3_5_78_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep11640"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.01339-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.01339-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T09:08:01Z","timestamp":1718701681000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.01339-23"}},"subtitle":[],"editor":[{"given":"Emily K.","family":"Cope","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,18]]},"references-count":77,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,6,18]]}},"alternative-id":["10.1128\/msystems.01339-23"],"URL":"https:\/\/doi.org\/10.1128\/msystems.01339-23","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,18]]},"assertion":[{"value":"2023-12-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-04-08","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01339-23"}}