{
    "abstract": "The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.\nBased on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.\nThe VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.",
    "authors": [
        {
            "affiliation": "Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75237, Uppsala, Sweden.\nDepartment of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Nobels V\u00e4g 6, 17177, Stockholm, Sweden.",
            "firstname": "Luisa W",
            "initials": "LW",
            "lastname": "Hugerth"
        },
        {
            "affiliation": "The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Blegdamsvej 9, 2100 Copenhagen and Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark.\nDepartment of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark.\nDepartment of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, Copenhagen, Denmark.",
            "firstname": "Maria Christine",
            "initials": "MC",
            "lastname": "Krog"
        },
        {
            "affiliation": "The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Blegdamsvej 9, 2100 Copenhagen and Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark.\nDepartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre Hospital, Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark.",
            "firstname": "Kilian",
            "initials": "K",
            "lastname": "Vomstein"
        },
        {
            "affiliation": "Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Nobels V\u00e4g 6, 17177, Stockholm, Sweden.",
            "firstname": "Juan",
            "initials": "J",
            "lastname": "Du"
        },
        {
            "affiliation": "The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Blegdamsvej 9, 2100 Copenhagen and Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark.\nDepartment of Obstetrics and Gynecology, Region Zealand, Slagelse Hospital, F\u00e6lledvej 13, 4200, Slagelse, Denmark.",
            "firstname": "Zahra",
            "initials": "Z",
            "lastname": "Bashir"
        },
        {
            "affiliation": "Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden.",
            "firstname": "Vilde",
            "initials": "V",
            "lastname": "Kaldhusdal"
        },
        {
            "affiliation": "Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Nobels V\u00e4g 6, 17177, Stockholm, Sweden.\nDepartment of Women's and Children's Health, Uppsala University, Dag Hammarskj\u00f6lds V\u00e4g\u00e4g 20, 75185, Uppsala, Sweden.",
            "firstname": "Emma",
            "initials": "E",
            "lastname": "Fransson"
        },
        {
            "affiliation": "Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Nobels V\u00e4g 6, 17177, Stockholm, Sweden.",
            "firstname": "Lars",
            "initials": "L",
            "lastname": "Engstrand"
        },
        {
            "affiliation": "The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Blegdamsvej 9, 2100 Copenhagen and Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark. henriette.svarre.nielsen@regionh.dk.\nDepartment of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, Copenhagen, Denmark. henriette.svarre.nielsen@regionh.dk.\nDepartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre Hospital, Ketteg\u00e5rd Alle 30, 2650, Hvidovre, Denmark. henriette.svarre.nielsen@regionh.dk.",
            "firstname": "Henriette Svarre",
            "initials": "HS",
            "lastname": "Nielsen"
        },
        {
            "affiliation": "Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Nobels V\u00e4g 6, 17177, Stockholm, Sweden.",
            "firstname": "Ina",
            "initials": "I",
            "lastname": "Schuppe-Koistinen"
        }
    ],
    "conclusions": null,
    "copyrights": "\u00a9 2024. The Author(s).",
    "doi": "10.1186/s40168-024-01870-5\n10.1038/s41522-022-00295-y\n10.1126/scitranslmed.3003605\n10.1093/humrep/dew026\n10.1016/j.ajog.2018.12.011\n10.1016/j.cmi.2018.04.019\n10.1111/1471-0528.15854\n10.1038/s41598-022-12007-9\n10.1158/2767-9764.CRC-22-0075\n10.1038/s41564-022-01083-2\n10.3389/fimmu.2022.919728\n10.1007/s00284-022-02771-2\n10.3389/fmed.2018.00181\n10.1146/annurev-micro-033121-020757\n10.1038/nature21049\n10.3390/v14020430\n10.3390/v12101143\n10.1038/s41598-020-62184-8\n10.1099/ijsem.0.003200\n10.1186/s40168-023-01692-x\n10.1186/s40168-020-00934-6\n10.1186/2049-2618-1-29\n10.1093/humrep/deac094\n10.1080/1040841X.2021.1905606\n10.1128/JB.00162-20\n10.12703/r/11-8\n10.1097/OLQ.0000000000001744\n10.1371/journal.pcbi.1010400\n10.3390/ijms140612004\n10.1099/jmm.0.041962-0\n10.3390/v13122341\n10.1111/j.1574-6976.2006.00045.x\n10.1099/jmm.0.019794-0\n10.1093/hropen/hoac015\n10.1128/AEM.01403-14\n10.1038/nmeth.3869\n10.1093/nar/gks1219\n10.1186/s13059-019-1891-0\n10.1186/s40168-018-0605-2\n10.1093/bioinformatics/btu153\n10.1371/journal.pone.0185056\n10.1101/gr.213959.116\n10.1038/nmeth.3103\n10.1101/gr.186072.114\n10.1371/journal.pone.0009490\n10.1093/bioinformatics/btv421\n10.1186/s13059-020-02090-4\n10.1038/s41467-020-17041-7\n10.1016/j.jbi.2019.103208",
    "journal": "Microbiome",
    "keywords": [
        "Daily variations",
        "Dysbiosis",
        "Menstrual cycle",
        "Reproductive health",
        "Vaginal microbiome"
    ],
    "methods": null,
    "publication_date": "2024-08-20",
    "pubmed_id": "39160615\n35501321\n22553250\n26911864\n30550767\n29729331\n31237400\n35562576\n35928983\n35246662\n35837395\n35128579\n29951482\n32391287\n34343015\n28099413\n35216023\n33050261\n32277092\n30648938\n31527125\n38031142\n33228810\n24451163\n35553675\n33823747\n32291280\n35509673\n36729966\n35939510\n23739678\n22539000\n34960611\n17096664\n20466841\n35441092\n33208514\n24928874\n27214047\n23193283\n31779668\n30558668\n24642063\n29073143\n28298430\n25218180\n25977477\n20224823\n26198102\n32698896\n27887642\n32665548\n31078660",
    "results": "Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.",
    "title": "Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.",
    "xml": "<Element 'PubmedArticle' at 0x788502799620>"
}