{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T21:40:38Z","timestamp":1791582038674,"version":"4.3.4"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T00:00:00Z","timestamp":1704931200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T00:00:00Z","timestamp":1704931200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Urology Care Foundation Residency Research Award Program and the Russell Scott, Jr., MD, Urology Research Fund"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    There has recently been an explosion of studies implicating the human microbiome in playing a critical role in many disease and wellness states. The etiology of abnormal semen analysis (SA) parameters is not identified in 30% of cases; investigations involving the semen microbiome may bridge this gap. Here, we explore the relationship between the semen microbiome and alterations of sperm parameters. We recruited men presenting for fertility evaluation or vasectomy consultation with proven biological paternity. SA and next generation sequencing was performed. Differential abundance testing using Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) was performed along with canonical correlational analysis for microbial community profiling. Men with abnormal (N\u2009=\u200927) sperm motility showed a higher abundance of\n                    <jats:italic>Lactobacillus iners<\/jats:italic>\n                    compared to those with normal (N\u2009=\u200946) sperm motility (mean proportion 9.4% versus 2.6%,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.046). This relationship persisted on canonical correlational analysis (r\u2009=\u20090.392,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.011). Men with abnormal sperm concentration (N\u2009=\u200920) showed a higher abundance of\n                    <jats:italic>Pseudomonas stutzeri<\/jats:italic>\n                    (2.1% versus 1.0%,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.024) and\n                    <jats:italic>Pseudomonas fluorescens<\/jats:italic>\n                    (0.9% versus 0.7%,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.010), but a lower abundance of\n                    <jats:italic>Pseudomonas putida<\/jats:italic>\n                    (0.5% versus 0.8%,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.020), compared to those with normal sperm concentration (N\u2009=\u200953). Major limitations are related to study design (cross-sectional, observational). Our results suggest that a small group of microorganisms may play a critical role in observed perturbations of SA parameters. Some of these microbes, most notably\n                    <jats:italic>Lactobacillus iners<\/jats:italic>\n                    , have been described extensively within other, fertility-related, contexts, whereas for others, this is the first report where they have potentially been implicated. Advances in our understanding of the semen microbiome may contribute to potentially new therapeutic avenues for correcting impairments in sperm parameters and improving male fertility.\n                  <\/jats:p>","DOI":"10.1038\/s41598-024-51686-4","type":"journal-article","created":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T05:02:07Z","timestamp":1704949327000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Semen microbiota are dramatically altered in men with abnormal sperm parameters"],"prefix":"10.1038","volume":"14","author":[{"given":"Vadim","family":"Osadchiy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre","family":"Belarmino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reza","family":"Kianian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John T.","family":"Sigalos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob S.","family":"Ancira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trisha","family":"Kanie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah F.","family":"Mangum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig D.","family":"Tipton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tung-Chin M.","family":"Hsieh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesse N.","family":"Mills","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sriram V.","family":"Eleswarapu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,1,11]]},"reference":[{"key":"51686_CR1","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1093\/humrep\/dew284","volume":"32","author":"M Punab","year":"2017","unstructured":"Punab, M. et al. Causes of male infertility: A 9-year prospective monocentre study on 1737 patients with reduced total sperm counts. Hum. Reprod. 32, 18\u201331. https:\/\/doi.org\/10.1093\/humrep\/dew284 (2017).","journal-title":"Hum. Reprod."},{"key":"51686_CR2","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/j.eururo.2021.08.014","volume":"80","author":"S Minhas","year":"2021","unstructured":"Minhas, S. et al. European association of urology guidelines on male sexual and reproductive health: 2021 update on male infertility. Eur. Urol. 80, 603\u2013620. https:\/\/doi.org\/10.1016\/j.eururo.2021.08.014 (2021).","journal-title":"Eur. Urol."},{"key":"51686_CR3","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1007\/s11930-020-00273-5","volume":"12","author":"V Osadchiy","year":"2020","unstructured":"Osadchiy, V., Mills, J. N., Mayer, E. A. & Eleswarapu, S. V. The seminal microbiome and male factor infertility. Curr. Sex Health Rep. 12, 202\u2013207. https:\/\/doi.org\/10.1007\/s11930-020-00273-5 (2020).","journal-title":"Curr. Sex Health Rep."},{"key":"51686_CR4","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.cgh.2018.10.002","volume":"17","author":"V Osadchiy","year":"2019","unstructured":"Osadchiy, V., Martin, C. R. & Mayer, E. A. The gut-brain axis and the microbiome: mechanisms and clinical implications. Clin. Gastroenterol. Hepatol. 17, 322\u2013332. https:\/\/doi.org\/10.1016\/j.cgh.2018.10.002 (2019).","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"51686_CR5","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1016\/j.eururo.2021.01.014","volume":"79","author":"SD Lundy","year":"2021","unstructured":"Lundy, S. D. et al. Functional and taxonomic Dysbiosis of the gut, urine, and semen microbiomes in male infertility. Eur. Urol. 79, 826\u2013836. https:\/\/doi.org\/10.1016\/j.eururo.2021.01.014 (2021).","journal-title":"Eur. Urol."},{"key":"51686_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.xfss.2023.06.001","author":"K Campbell","year":"2023","unstructured":"Campbell, K. et al. Next generation sequencing analysis of semen microbiome taxonomy in men with non-obstructive azoospermia vs fertile controls: A pilot study. F. S. Sci. https:\/\/doi.org\/10.1016\/j.xfss.2023.06.001 (2023).","journal-title":"F. S. Sci."},{"key":"51686_CR7","doi-asserted-by":"publisher","DOI":"10.1111\/evj.13884","author":"ME Lowman","year":"2022","unstructured":"Lowman, M. E., Tipton, C. D., Labordere, A. L. & Brown, J. A. Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing. Equine Vet J https:\/\/doi.org\/10.1111\/evj.13884 (2022).","journal-title":"Equine Vet J"},{"key":"51686_CR8","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.euf.2022.11.010","volume":"9","author":"MC Suarez Arbelaez","year":"2023","unstructured":"Suarez Arbelaez, M. C. et al. Pilot study: Next-generation sequencing of the semen microbiome in vasectomized versus nonvasectomized men. Eur. Urol. Focus 9, 75\u201382. https:\/\/doi.org\/10.1016\/j.euf.2022.11.010 (2023).","journal-title":"Eur. Urol. Focus"},{"key":"51686_CR9","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460\u20132461. https:\/\/doi.org\/10.1093\/bioinformatics\/btq461 (2010).","journal-title":"Bioinformatics"},{"key":"51686_CR10","doi-asserted-by":"publisher","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","volume":"27","author":"RC Edgar","year":"2011","unstructured":"Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194\u20132200. https:\/\/doi.org\/10.1093\/bioinformatics\/btr381 (2011).","journal-title":"Bioinformatics"},{"key":"51686_CR11","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","volume":"30","author":"J Zhang","year":"2014","unstructured":"Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614\u2013620. https:\/\/doi.org\/10.1093\/bioinformatics\/btt593 (2014).","journal-title":"Bioinformatics"},{"key":"51686_CR12","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792\u20131797. https:\/\/doi.org\/10.1093\/nar\/gkh340 (2004).","journal-title":"Nucleic Acids Res."},{"key":"51686_CR13","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2\u2013approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490. https:\/\/doi.org\/10.1371\/journal.pone.0009490 (2010).","journal-title":"PLoS One"},{"key":"51686_CR14","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1111\/2041-210X.13780","volume":"13","author":"LE Drake","year":"2022","unstructured":"Drake, L. E. et al. An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data. Methods Ecol. Evolut. 13, 694\u2013710. https:\/\/doi.org\/10.1111\/2041-210X.13780 (2022).","journal-title":"Methods Ecol. 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Microorganisms https:\/\/doi.org\/10.3390\/microorganisms11061443 (2023).","journal-title":"Microorganisms"},{"key":"51686_CR26","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00460-13","author":"SS Witkin","year":"2013","unstructured":"Witkin, S. S. et al. Influence of vaginal bacteria and D- and L-lactic acid isomers on vaginal extracellular matrix metalloproteinase inducer: Implications for protection against upper genital tract infections. mBio https:\/\/doi.org\/10.1128\/mBio.00460-13 (2013).","journal-title":"mBio"},{"key":"51686_CR27","doi-asserted-by":"publisher","first-page":"2451","DOI":"10.3389\/fmicb.2019.02451","volume":"10","author":"F De Seta","year":"2019","unstructured":"De Seta, F., Campisciano, G., Zanotta, N., Ricci, G. & Comar, M. The vaginal community state types microbiome-immune network as key factor for bacterial vaginosis and aerobic vaginitis. 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Genet 40, 125\u2013135. https:\/\/doi.org\/10.1007\/s10815-022-02688-6 (2023).","journal-title":"J. Assist. Reprod. Genet"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-51686-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-51686-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-51686-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T05:04:26Z","timestamp":1704949466000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-51686-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,11]]},"references-count":29,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["51686"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-51686-4","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,11]]},"assertion":[{"value":"25 October 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 January 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"JNM is a consultant for Halozyme Pharma, Boston Scientific, and Endo Pharmaceuticals. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1068"}}