1
|
Powell AM, Ali Khan FZ, Ravel J, Elovitz MA. Untangling Associations of Microbiomes of Pregnancy and Preterm Birth. Clin Perinatol 2024; 51:425-439. [PMID: 38705650 PMCID: PMC11070640 DOI: 10.1016/j.clp.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
This review illuminates the complex interplay between various maternal microbiomes and their influence on preterm birth (PTB), a driving and persistent contributor to neonatal morbidity and mortality. Here, we examine the dynamics of oral, gastrointestinal (gut), placental, and vaginal microbiomes, dissecting their roles in the pathogenesis of PTB. Importantly, focusing on the vaginal microbiome and PTB, the review highlights (1) a protective role of Lactobacillus species; (2) an increased risk with select anaerobes; and (3) the influence of social health determinants on the composition of vaginal microbial communities.
Collapse
Affiliation(s)
- Anna Maya Powell
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Phipps 249, Baltimore, MD 21287, USA
| | - Fouzia Zahid Ali Khan
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Phipps 249, Baltimore, MD 21287, USA
| | - Jacques Ravel
- Department of Microbiology and Immunology, Institute for Genome Sciences, 670 West Baltimore Street, 3rd Floor, Room 3173, Baltimore, MD 21201, USA
| | - Michal A Elovitz
- Department of Obstetrics and Gynecology, Women's Health Research, Icahn School of Medicine at Mount Sinai, Women's Biomedical Research Institute, 1468 Madison Avenue, New York, NY 10029, USA.
| |
Collapse
|
2
|
Rajasekera TA, Galley JD, Mackos AR, Chen HJ, Mitchell JG, Kleinman JJ, Cappelucci P, Mashburn-Warren L, Lauber CL, Bailey MT, Worly BL, Gur TL. Stress and depression-associated shifts in gut microbiota: A pilot study of human pregnancy. Brain Behav Immun Health 2024; 36:100730. [PMID: 38323225 PMCID: PMC10844036 DOI: 10.1016/j.bbih.2024.100730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
Background Psychosocial stress and mood-related disorders, such as depression, are prevalent and vulnerability to these conditions is heightened during pregnancy. Psychosocial stress induces consequences via several mechanisms including the gut microbiota-brain axis and associated signaling pathways. Previous preclinical work indicates that prenatal stress alters maternal gut microbial composition and impairs offspring development. Importantly, although the fecal and vaginal microenvironments undergo alterations across pregnancy, we lack consensus regarding which shifts are adaptive or maladaptive in the presence of prenatal stress and depression. Clinical studies interrogating these relationships have identified unique taxa but have been limited in study design. Methods We conducted a prospective cohort study of pregnant individuals consisting of repeated administration of psychometrics (Perceived Stress Scale (PSS) and Center for Epidemiological Studies Depression Scale (CES-D)) and collection of fecal and vaginal microbiome samples. Fecal and vaginal microbial community composition across psychometric responses were interrogated using full-length 16S rRNA sequencing followed by α and β-diversity metrics and taxonomic abundance. Results Early pregnancy stress was associated with increased abundance of fecal taxa not previously identified in related studies, and stress from late pregnancy through postpartum was associated with increased abundance of typical vaginal taxa and opportunistic pathogens in the fecal microenvironment. Additionally, in late pregnancy, maternal stress and depression scores were associated with each other and with elevated maternal C-C motif chemokine ligand 2 (CCL2) concentrations. At delivery, concordant with previous literature, umbilical CCL2 concentration was negatively correlated with relative abundance of maternal fecal Lactobacilli. Lastly, participants with more severe depressive symptoms experienced steeper decreases in prenatal vaginal α-diversity. Conclusion These findings a) underscore previous preclinical and clinical research demonstrating the effects of prenatal stress on maternal microbiome composition, b) suggest distinct biological pathways for the consequences of stress versus depression and c) extend the literature by identifying several taxa which may serve critical roles in mediating this relationship. Thus, further interrogation of the role of specific maternal microbial taxa in relation to psychosocial stress and its sequelae is warranted.
Collapse
Affiliation(s)
- Therese A. Rajasekera
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jeffrey D. Galley
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Amy R. Mackos
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Helen J. Chen
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | | | | | - Paige Cappelucci
- College of Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Christian L. Lauber
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Michael T. Bailey
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Center for Microbial Pathogenesis, The Research Institute, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Brett L. Worly
- Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Tamar L. Gur
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
3
|
Mercado-Evans V, Mejia ME, Zulk JJ, Ottinger S, Hameed ZA, Serchejian C, Marunde MG, Robertson CM, Ballard MB, Ruano SH, Korotkova N, Flores AR, Pennington KA, Patras KA. Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota. Nat Commun 2024; 15:1035. [PMID: 38310089 PMCID: PMC10838280 DOI: 10.1038/s41467-024-45336-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. Using a murine GDM model of GBS colonization and perinatal transmission, we find that GDM mice display greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing reveals differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM immune disruptions include reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered maternofetal cytokines. Lastly, we observe distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Here, we show a model of GBS dissemination in GDM hosts that recapitulates several clinical aspects and identifies multiple host and bacterial drivers of GBS perinatal disease.
Collapse
Affiliation(s)
- Vicki Mercado-Evans
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marlyd E Mejia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Samantha Ottinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zainab A Hameed
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Camille Serchejian
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Madelynn G Marunde
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Clare M Robertson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mallory B Ballard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Simone H Ruano
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Natalia Korotkova
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, UTHealth Houston, Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kathleen A Pennington
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kathryn A Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
4
|
Zhou Q, Yu Y, Zhou J, Liu J, Gao J. Relationship of Lactobacillus Vaginal Microbiota Changes and the Risk of Preterm Birth: A Systematic Review and Meta-Analysis. J Womens Health (Larchmt) 2024; 33:228-238. [PMID: 38064523 DOI: 10.1089/jwh.2023.0393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024] Open
Abstract
Objective: With a global incidence of more than 10%, preterm birth (PTB) remains a significant concern. The vaginal microbiome strongly influences the well-being of the female reproductive tract. This study examines the correlation between changes in Lactobacillus vaginal microbiota and the PTB risk. Materials and Methods: A thorough search of PubMed, Web of Science, Cochrane Library, and EMBASE was conducted to locate studies that examined the association between changes in Lactobacillus vaginal microbiota and the risk of PTB from January 1, 2010, to January 30, 2023. The risk of PTB was determined by calculating odds ratios (ORs) with 95% confidence intervals (CIs). Results: In our analysis, there were 11 studies with 1577 pregnant women. The findings revealed a significant negative correlation between higher Lactobacillus abundance and the PTB risk (OR = 0.49, 95% CI: 0.29-0.84, p = 0.009 < 0.05). Similarly, the four individual dominant species, Lactobacillus crispatus (OR = 0.3, 95% CI: 0.14-0.67, p = 0.003 < 0.05), Lactobacillus gasseri (OR = 0.34, 95% CI: 0.17-0.69, p = 0.003 < 0.05), Lactobacillus iners (OR = 0.68, 95% CI: 0.49-0.93, p = 0.016 < 0.05), and Lactobacillus jensenii (OR = 0.43, 95% CI: 0.21-0.89, p = 0.024 < 0.05), were also negatively associated with the PTB risk. The risk of Lactobacillus for PTB was significant in both America (OR = 0.67; 95% CI: 0.50-0.92) and Asia (OR = 0.20; 95% CI: 0.09-0.47), whereas no significant risk was found in Europe (OR = 0.49; 95% CI: 0.11-2.15). Conclusions: Our study demonstrated that the abundance of Lactobacillus and the four dominant individual species (L. crispatus, L. jensenii, L. iners, and L. gasseri) were significantly and negatively associated with the PTB risk.
Collapse
Affiliation(s)
- Qian Zhou
- Department of Obstetrics & Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Yi Yu
- Department of Obstetrics & Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Jingwen Zhou
- Department of Obstetrics & Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Juntao Liu
- Department of Obstetrics & Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Jinsong Gao
- Department of Obstetrics & Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| |
Collapse
|
5
|
Onyango S, Mi JD, Koech A, Okiro P, Temmerman M, von Dadelszen P, Tribe RM, Omuse G. Microbiota dynamics, metabolic and immune interactions in the cervicovaginal environment and their role in spontaneous preterm birth. Front Immunol 2023; 14:1306473. [PMID: 38196946 PMCID: PMC10774218 DOI: 10.3389/fimmu.2023.1306473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Differences in the cervicovaginal microbiota are associated with spontaneous preterm birth (sPTB), a significant cause of infant morbidity and mortality. Although establishing a direct causal link between cervicovaginal microbiota and sPTB remains challenging, recent advancements in sequencing technologies have facilitated the identification of microbial markers potentially linked to sPTB. Despite variations in findings, a recurring observation suggests that sPTB is associated with a more diverse and less stable vaginal microbiota across pregnancy trimesters. It is hypothesized that sPTB risk is likely to be modified via an intricate host-microbe interactions rather than due to the presence of a single microbial taxon or broad community state. Nonetheless, lactobacilli dominance is generally associated with term outcomes and contributes to a healthy vaginal environment through the production of lactic acid/maintenance of a low pH that excludes other pathogenic microorganisms. Additionally, the innate immunity of the host and metabolic interactions between cervicovaginal microbiota, such as the production of bacteriocins and the use of proteolytic enzymes, exerts a profound influence on microbial populations, activities, and host immune responses. These interplays collectively impact pregnancy outcomes. This review aims to summarize the complexity of cervicovaginal environment and microbiota dynamics, and associations with bacterial vaginosis and sPTB. There is also consideration on how probiotics may mitigate the risk of sPTB and bacterial vaginosis.
Collapse
Affiliation(s)
- Stanley Onyango
- Department of Pathology, Aga Khan University, Nairobi, Kenya
- Centre of Excellence Women and Child Health, Aga Khan University, Nairobi, Kenya
| | - Jia Dai Mi
- Faculty of Life Sciences and Medicine, Department of Women and Children’s Health, School of Life Course and Population Sciences, King’s College London, London, United Kingdom
| | - Angela Koech
- Centre of Excellence Women and Child Health, Aga Khan University, Nairobi, Kenya
| | - Patricia Okiro
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | - Marleen Temmerman
- Centre of Excellence Women and Child Health, Aga Khan University, Nairobi, Kenya
| | - Peter von Dadelszen
- Faculty of Life Sciences and Medicine, Department of Women and Children’s Health, School of Life Course and Population Sciences, King’s College London, London, United Kingdom
| | - Rachel M. Tribe
- Faculty of Life Sciences and Medicine, Department of Women and Children’s Health, School of Life Course and Population Sciences, King’s College London, London, United Kingdom
| | - Geoffrey Omuse
- Department of Pathology, Aga Khan University, Nairobi, Kenya
| | | |
Collapse
|
6
|
Zou X, Nakura Y, Kawaguchi H, Nishiumi F, Wu HN, Yanagihara I. Comparison of databases useful for the analysis of vaginal microbiota in Japanese women using next-generation sequencing data (QIIME 2 software). J Appl Microbiol 2023; 134:lxad283. [PMID: 38012110 DOI: 10.1093/jambio/lxad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
AIMS Approximately 10% of children are born prematurely, and bacterial vaginosis during pregnancy is associated with preterm delivery. Highly accurate species-level vaginal microflora analysis helps control bacteria-induced preterm birth. Therefore, we aimed to conduct a bioinformatic analysis of gene sequences using 16S databases and compare their efficacy in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women. METHODS AND RESULTS The 16 s rRNA databases, Silva, Greengenes, and the basic local alignment search tool (BLAST) were compared to determine whether the classification quality could be improved using the V3-V4 region next-generation sequencing (NGS) sequences. It was found that NGS data were aligned using the BLAST database with the QIIME 2 platform, whose classification quality was higher than that of Silva, and the combined Silva and Greengenes databases based on the mutual complementarity of the two databases. CONCLUSIONS The reference database selected during the bioinformatic processing influenced the recognized sequence percentage, taxonomic rankings, and accuracy. This study showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.
Collapse
Affiliation(s)
- Xianya Zou
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
- Department of Pediatric and Neonatal-Perinatal Research, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Haruna Kawaguchi
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
- Department of Obstetrics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Fumiko Nishiumi
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| |
Collapse
|
7
|
Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J. Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Microbiome 2023; 11:259. [PMID: 38031142 PMCID: PMC10688475 DOI: 10.1186/s40168-023-01692-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 10/07/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential. RESULTS MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community. CONCLUSIONS MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.
Collapse
Affiliation(s)
- Johanna B Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Larry Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
8
|
Taylor JY, Barcelona V, Magny-Normilus C, Wright ML, Jones-Patten A, Prescott L, Potts-Thompson S, Santos HP. A roadmap for social determinants of health and biological nursing research in the National Institute of Nursing Research 2022-2026 Strategic Plan: Optimizing health and advancing health equity using antiracist framing. Nurs Outlook 2023; 71:102059. [PMID: 37863707 PMCID: PMC10803078 DOI: 10.1016/j.outlook.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 10/22/2023]
Abstract
BACKGROUND Health equity is essential for improving the well-being of all individuals and groups, and research remains a critical element for understanding barriers to health equity. While considering how to best support research that acknowledges current health challenges, it is crucial to understand the role of social justice frameworks within health equity research and the contributions of minoritized researchers. Additionally, there should be an increased understanding of the influence of social determinants of health on biological mechanisms. PURPOSE Biological health equity research seeks to understand and address health disparities among historically excluded populations. DISCUSSION While there are examples of studies in this area led by minoritized researchers, some individuals and groups remain understudied due to underfunding. Research within minoritized populations must be prioritized to authentically achieve health equity. Furthermore, there should be increased funding from National Institutes of Health to support minoritized researchers working in this area.
Collapse
Affiliation(s)
- Jacquelyn Y Taylor
- Center for Research on People of Color, Columbia University School of Nursing, New York, NY.
| | - Veronica Barcelona
- Center for Research on People of Color, Columbia University School of Nursing, New York, NY
| | | | | | | | - Laura Prescott
- Center for Research on People of Color, Columbia University School of Nursing, New York, NY
| | | | - Hudson P Santos
- School of Nursing & Health Studies, University of Miami, Coral Gables, FL
| |
Collapse
|
9
|
Hadley M, Oppong AY, Coleman J, Powell AM. Structural Racism and Adverse Pregnancy Outcomes Through the Lens of the Maternal Microbiome. Obstet Gynecol 2023; 142:911-919. [PMID: 37678901 PMCID: PMC10510805 DOI: 10.1097/aog.0000000000005345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 09/09/2023]
Abstract
Microbiome science offers a glimpse into personalized medicine by characterizing health and disease states according to an individual's microbial signatures. Without a critical examination of the use of race as a variable, microbiome studies may be susceptible to the same pitfalls as other areas of science grounded in racist biology. We will examine the use of race as a biological variable in pregnancy-related microbiome research. Emerging data from studies that investigate the intestinal microbiome in pregnancy suggest strong influence of a poor diet on adverse pregnancy outcomes. Differences in the vaginal microbiome implicated in adverse pregnancy outcomes are frequently attributed to race. We review evidence that links systemic racism to pregnancy health outcome differences with a focus on the vaginal and intestinal microbiomes as well as diet. We also review how structural racism ultimately contributes to inequitable access to healthy food and higher risk environmental exposures among pregnant people of lower socioeconomic status and exacerbates common pregnancy comorbidities.
Collapse
Affiliation(s)
- Megan Hadley
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland; and the University of Chicago School of Medicine, Chicago, Illinois
| | | | | | | |
Collapse
|
10
|
Gryaznova M, Kozarenko O, Smirnova Y, Burakova I, Syromyatnikov M, Maslov A, Lebedeva O. Cervical and Vaginal Microbiomes in Early Miscarriages and Ongoing Pregnancy with and without Dydrogesterone Usage. Int J Mol Sci 2023; 24:13836. [PMID: 37762139 PMCID: PMC10531357 DOI: 10.3390/ijms241813836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Emerging evidence suggests that the reproductive tract microbiota is a key modulator of local inflammatory and immune pathways throughout pregnancy and may subsequently impact pregnancy outcomes. In this study, our objective was to analyze the cervical and vaginal microbiomes during early pregnancy among three groups: women with healthy ongoing pregnancies, women undergoing dydrogesterone treatment, and those who experienced miscarriages. The experiment involved 51 women at 8-11 weeks of gestation. The microbiome was examined using 16S rRNA sequencing on the Ion Torrent PGM platform. Across all groups, Lactobacillus iners was predominant, suggesting that the vaginal community type CST III is common among the majority of participants. Notably, our data highlighted the significant roles of Gardnerella vaginalis and Mycoplasma girerdii in the pathogenesis of early miscarriage. Conversely, L. iners and Bifidobacterium longum have a protective effect in early pregnancy. Moreover, dydrogesterone intake appeared to influence notable differences between the cervical and vaginal microbiomes. Overall, our study enhanced our understanding of the cervical and vaginal microbiome composition in the eastern European population during early pregnancy.
Collapse
Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Olesya Kozarenko
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Antenatal Care Department, Yakovlevo Central District Hospital, 309070 Stroitel, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Alexander Maslov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Olga Lebedeva
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Obstetrics and Gynecology, Belgorod State National University, 308015 Belgorod, Russia
| |
Collapse
|
11
|
Ene A, Banerjee S, Wolfe AJ, Putonti C. Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris. mSphere 2023; 8:e0056222. [PMID: 37366621 PMCID: PMC10449518 DOI: 10.1128/msphere.00562-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).
Collapse
Affiliation(s)
- Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| |
Collapse
|
12
|
Romero R, Theis KR, Gomez-Lopez N, Winters AD, Panzer JJ, Lin H, Galaz J, Greenberg JM, Shaffer Z, Kracht DJ, Chaiworapongsa T, Jung E, Gotsch F, Ravel J, Peddada SD, Tarca AL. The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity. Microbiol Spectr 2023; 11:e0342922. [PMID: 37486223 PMCID: PMC10434204 DOI: 10.1128/spectrum.03429-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/25/2023] [Indexed: 07/25/2023] Open
Abstract
The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent due, in part, to variation in sample sizes and ethnicity. Thus, an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Here, we report a large longitudinal study (n = 474 women, 1,862 vaginal samples) of a predominantly African-American cohort-a population that experiences a relatively high rate of pregnancy complications-evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The principal factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Other factors are maternal age, parity, obesity, and self-reported Cannabis use. The general pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be modified by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCE There is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a predominantly African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, body mass index, and self-reported Cannabis use, on the vaginal microbiota in pregnancy.
Collapse
Affiliation(s)
- Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Kevin R. Theis
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D. Winters
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jonathan J. Panzer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Huang Lin
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jonathan M. Greenberg
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zachary Shaffer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - David J. Kracht
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Tinnakorn Chaiworapongsa
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Eunjung Jung
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Francesca Gotsch
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shyamal D. Peddada
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Adi L. Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
| |
Collapse
|
13
|
Farr Zuend C, Lamont A, Noel-Romas L, Knodel S, Birse K, Kratzer K, McQueen P, Perner M, Ayele H, Mutch S, Berard AR, Schellenberg JJ, Senturk F, McCorrister S, Westmacott G, Mulhall F, Sandberg B, Yu A, Burnett M, Poliquin V, Burgener AD. Increased genital mucosal cytokines in Canadian women associate with higher antigen-presenting cells, inflammatory metabolites, epithelial barrier disruption, and the depletion of L. crispatus. Microbiome 2023; 11:159. [PMID: 37491398 PMCID: PMC10367425 DOI: 10.1186/s40168-023-01594-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/05/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Cervicovaginal inflammation has been linked to negative reproductive health outcomes including the acquisition of HIV, other sexually transmitted infections, and cervical carcinogenesis. While changes to the vaginal microbiome have been linked to genital inflammation, the molecular relationships between the functional components of the microbiome with cervical immunology in the reproductive tract are understudied, limiting our understanding of mucosal biology that may be important for reproductive health. RESULTS In this study, we used a multi'-omics approach to profile cervicovaginal samples collected from 43 Canadian women to characterize host, immune, functional microbiome, and metabolome features of cervicovaginal inflammation. We demonstrate that inflammation is associated with lower amounts of L. crispatus and higher levels of cervical antigen-presenting cells (APCs). Proteomic analysis showed an upregulation of pathways related to neutrophil degranulation, complement, and leukocyte migration, with lower levels of cornified envelope and cell-cell adherens junctions. Functional microbiome analysis showed reductions in carbohydrate metabolism and lactic acid, with increases in xanthine and other metabolites. Bayesian network analysis linked L. crispatus with glycolytic and nucleotide metabolism, succinate and xanthine, and epithelial proteins SCEL and IVL as major molecular features associated with pro-inflammatory cytokines and increased APCs. CONCLUSIONS This study identified key molecular and immunological relationships with cervicovaginal inflammation, including higher APCs, bacterial metabolism, and proteome alterations that underlie inflammation. As APCs are involved in HIV transmission, parturition, and cervical cancer progression, further studies are needed to explore the interactions between these cells, bacterial metabolism, mucosal immunity, and their relationship to reproductive health. Video Abstract.
Collapse
Affiliation(s)
- Christina Farr Zuend
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA.
| | - Alana Lamont
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Laura Noel-Romas
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Samantha Knodel
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Kateryna Kratzer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Peter McQueen
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Michelle Perner
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Hossaena Ayele
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sarah Mutch
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Alicia R Berard
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - John J Schellenberg
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Faruk Senturk
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
| | - Stuart McCorrister
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Garrett Westmacott
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | | | | | - Adelicia Yu
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Margaret Burnett
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Vanessa Poliquin
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Adam D Burgener
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA.
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada.
- Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
14
|
Mu Y, Hu A, Kan H, Li Y, He Y, Fan W, Liu H, Li Q, Zheng Y. Preterm Prelabor Rupture of Membranes Linked to Vaginal Bacteriome of Pregnant Females in the Early Second Trimester: a Case-Cohort Design. Reprod Sci 2023; 30:2324-2335. [PMID: 36725814 PMCID: PMC9891760 DOI: 10.1007/s43032-022-01153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/13/2022] [Indexed: 02/03/2023]
Abstract
Preterm prelabor rupture of membranes (PPROM) is a major cause of spontaneous preterm birth (sPTB), one of the greatest challenges facing obstetrics with complicated pathogenesis. This case-cohort study investigated the association between vaginal bacteriome of singleton pregnant females in the early second trimester and PPROM. The study included 35,255 and 180 pregnant females with PPROM as cases and term-birth without prelabor rupture of membranes (TWPROM) and term prelabor rupture of membranes (TPROM) pregnant females as controls, respectively. Using 16S rRNA sequencing, the vaginal microbiome traits were analyzed. Females with PPROM had higher alpha and beta diversity (P < 0.05) than TWPROM and TPROM. The presence of L. mulieris was associated with a decreased risk of PPROM (adjusted odds ratio [aOR] = 0.35; 95% confidence interval [CI]: 0.17-0.72) compared with TWPROM. Meanwhile, the presence of Megasphaera genus (aOR = 2.27; 95% CI: 1.09-4.70), Faecalibacterium genus (aOR = 3.29; 95% CI: 1.52-7.13), Bifidobacterium genus (aOR = 3.26; 95% CI: 1.47-7.24), Xanthomonadales genus (aOR = 2.76; 95% CI: 1.27-6.01), Gammaproteobacteria class (aOR = 2.36; 95% CI: 1.09-5.14), and Alphaproteobacteria class (aOR = 2.45; 95% CI: 1.14-5.26) was associated with an increased risk of PPROM compared with TWPROM. Our results indicated that the risk of PPROM can decrease with vaginal L. mulieris but increase with high alpha or beta diversity, and several vaginal bacteria in pregnant females may be involved in the occurrence of PPROM.
Collapse
Affiliation(s)
- Yutong Mu
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Anqun Hu
- Department of Clinical Laboratory, Anqing Municipal Hospital, Anqing, 246003, China
| | - Hui Kan
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Yijie Li
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Yining He
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
- Biostatistics Office, Clinical Research Unit, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Wei Fan
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Haiyan Liu
- Biostatistics Office, Clinical Research Unit, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China.
- Department of Blood Transfusion, Anqing Municipal Hospital, Anqing, 246003, China.
| | - Qing Li
- Department of Obstetrics and Gynecology, Anqing Municipal Hospital, Anqing, 246003, China.
| | - Yingjie Zheng
- Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai, 200032, China.
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
15
|
Baud A, Hillion KH, Plainvert C, Tessier V, Tazi A, Mandelbrot L, Poyart C, Kennedy SP. Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes. Sci Rep 2023; 13:9061. [PMID: 37271782 PMCID: PMC10239749 DOI: 10.1038/s41598-023-36126-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023] Open
Abstract
The vaginal microbiota refers to the microorganisms that reside in the vagina. These microorganisms contribute significantly to a woman's reproductive and general health. A healthy vaginal microbiota is typically a low-diversity environment with a predominance of lactic acid-producing Lactobacillus species. Factors such as antibiotic use, sexual activity, and hormonal changes can disrupt the balance of the vaginal microbiota, leading to conditions such as bacterial vaginosis. The composition of the vaginal microbiota changes and takes on added importance during pregnancy, serving as a barrier against infection for both mother and fetus. Despite the importance of the microorganisms that colonize the vagina, details of how changes in composition and diversity can impact pregnancy outcomes is poorly understood. This is especially true for woman with a high prevalence of Gardnerella vaginalis. Here we report on a diverse cohort of 749 women, enrolled in the InSPIRe cohort, during their final trimester of pregnancy. We show that Lactobacilli, including L. crispatus are important in maintaining low diversity, and that depletion in this critical community is linked with preterm delivery. We further demonstrate that it is overall diversity of the vaginal microbiota, not specific species, which provides the best indicator of risk.
Collapse
Affiliation(s)
- Agnes Baud
- Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015, Paris, France
| | - Kenzo-Hugo Hillion
- Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015, Paris, France
| | - Céline Plainvert
- AP-HP Centre-Université Paris Cité, FHU PREMA, Centre national de référence des streptocoques, Paris, France
| | | | - Asmaa Tazi
- AP-HP Centre-Université Paris Cité, FHU PREMA, Centre national de référence des streptocoques, Paris, France
| | - Laurent Mandelbrot
- Service de gynécologie-obstétrique, Hôpital Louis Mourier, AP-HP, Université de PARIS, IAME INSERM U1137, Paris, France
| | - Claire Poyart
- AP-HP Centre-Université Paris Cité, FHU PREMA, Centre national de référence des streptocoques, Paris, France
- Université de Paris, INSERM, Institut Cochin 1016, Paris, France
| | - Sean P Kennedy
- Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015, Paris, France.
| |
Collapse
|
16
|
Nori W, H-Hameed B. Vaginal microbes confounders and implications on women's health. World J Clin Cases 2023; 11:2119-2122. [PMID: 36998952 PMCID: PMC10044948 DOI: 10.12998/wjcc.v11.i9.2119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/30/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
The vagina has diverse vaginal microbes (Vm). A disturbance in the delicate balance maintained in Vm is linked to women's obstetrical and reproductive tract problems. Vaginal microbes play an essential role in protecting the health of the female reproductive tract by alleviating gynecological infection. However, Vm profiling has many confounders that need to be addressed during sampling, including age, race, pregnancy, medical illness, and smoking. Vm profiling improves reproduction odds, may serve as a marker for genital malignancies and have a therapeutic application in menopausal women and women with cervical cancers.
Collapse
Affiliation(s)
- Wassan Nori
- Department of Obstetrics and Gynecology, Mustansiriyah University, Baghdad 10052, Al Saydyah, Iraq
| | - Ban H-Hameed
- Department of Obstetrics and Gynecology, Mustansiriyah University, Baghdad 10052, Al Saydyah, Iraq
| |
Collapse
|
17
|
Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J. High-resolution functional description of vaginal microbiomes in health and disease. bioRxiv 2023:2023.03.24.533147. [PMID: 36993583 PMCID: PMC10055360 DOI: 10.1101/2023.03.24.533147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background A Lactobacillus-dominated vaginal microbiome provides the first line of defense against numerous adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this limitation, we developed metagenomic community state types (mgCSTs) which uses metagenomic sequences to describe and define vaginal microbiomes based on both composition and function. Results MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella mgSs, as well as a mgSs of L. iners, were associated with a greater likelihood of Amsel bacterial vaginosis diagnosis. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier as an easily applied, standardized method for use by the microbiome research community. Conclusions MgCSTs are a novel and easily implemented approach to reducing the dimension of complex metagenomic datasets, while maintaining their functional uniqueness. MgCSTs enable investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates protection to the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health.
Collapse
Affiliation(s)
- Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Larry Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
18
|
Dixon M, Dunlop AL, Corwin EJ, Kramer MR. Joint effects of individual socioeconomic status and residential neighborhood context on vaginal microbiome composition. Front Public Health 2023; 11:1029741. [PMID: 36761121 PMCID: PMC9902942 DOI: 10.3389/fpubh.2023.1029741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction The vaginal microbiome is a dynamic ecosystem that is important for women's health. Its composition has been associated with risk for menopausal symptoms, sexually transmitted infections, gynecologic cancer, and preterm birth. Conventional risk factors for a vaginal microbiome linked with these adverse health outcomes include sexual behaviors, hygiene practices, individual social factors, and stress levels. However, there has been limited research on socio-contextual determinants, and whether neighborhood context modifies the association with individual socioeconomic factors. Methods Socioeconomically diverse pregnant African American women in Atlanta, Georgia (n = 439) provided residential addresses and first trimester vaginal swab samples, which underwent sequencing, taxonomic classification, and assignment into mutually exclusive CST (community state types) via hierarchical clustering. Linear probability models were used to estimate prevalence differences (PD) for the associations of neighborhood factors with vaginal microbiome CST and to evaluate for additive interaction with maternal level of education, health insurance type, and recruitment hospital. Results Factors such as higher (vs. lower) maternal education, private (vs. public) insurance, and private (vs. public) hospital were associated with higher prevalence of Lactobacillus-dominant vaginal microbiome CSTs typically associated with better health outcomes. When considering the joint effects of these individual socioeconomic status and residential neighborhood factors on vaginal microbiome CST, most combinations showed a greater than additive effect among the doubly exposed; however, in the case of local income homogeneity and local racial homogeneity, there was evidence of a crossover effect between those with less-advantaged individual socioeconomic status and those with more-advantaged individual socioeconomic status. Compared to women at the public hospital who lived in economically diverse neighborhoods, women at the private hospital who lived in economically diverse neighborhoods had a 21.9% higher prevalence of Lactobacillus-dominant CSTs, while women at the private hospital who lived in less economically diverse neighborhoods (the doubly exposed) had only an 11.7% higher prevalence of Lactobacillus-dominant CSTs, showing a crossover effect (interaction term p-value = 0.004). Discussion In this study, aspects of residential neighborhood context were experienced differently by women on the basis of their individual resources, and the joint effects of these exposures on vaginal microbiome CST showed a departure from simple additivity for some factors.
Collapse
Affiliation(s)
- Meredith Dixon
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Anne L. Dunlop
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States,Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | | | - Michael R. Kramer
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States,*Correspondence: Michael R. Kramer ✉
| |
Collapse
|
19
|
Xiao Y, Huang S, Yu W, Ni Y, Lu D, Wu Q, Leng Q, Yang T, Ni M, Xie J, Zhang X. Effects of emergency/nonemergency cervical cerclage on the vaginal microbiome of pregnant women with cervical incompetence. Front Cell Infect Microbiol 2023; 13:1072960. [PMID: 36968117 PMCID: PMC10034410 DOI: 10.3389/fcimb.2023.1072960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Background Evaluation of the therapeutic effects of cerclage on preterm birth (PTB) caused by cervical incompetence remains challenging. The vaginal microbiome is associated with preterm births. Thus, this study aimed to analyse the vaginal microbiota of patients with cervical incompetence, explore the relationship between the composition of the vaginal microbiota before cervical cerclage and at term delivery, and assess the effect of cervical cerclage on the vaginal microbiota. Methods Patients (n = 30) underwent cerclage performed by the same surgical team. Vaginal swabs were obtained pre-surgery and seven days post-surgery. A gestational age-matched cohort of healthy pregnant women (n = 20) (no particular abnormality during pregnancy, delivery at term) was used as the control group and sampled during a comparable pregnancy. All collected vaginal swabs were analysed by 16S rRNA gene sequencing. Results When comparing the healthy control and cervical cerclage groups, the enriched microorganism in the healthy controls was G. Scardovia, and the enriched microorganism of the cerclage was G. Streptococcus. α diversity was significantly increased in patients who received cerclage with preterm delivery compared with those with full-term delivery, and the enriched microorganism was F. Enterococcus. A comparison before and after nonemergency cerclage suggested that the enriched microorganisms were G. Lactobacillus and F. Lactobacillaceae before surgery. After nonemergency cerclage, the enriched microorganisms were F. Enterobacteriaceae and C. Gammaproteobacteria. Vaginal microbiota diversity significantly increased, and the proportion of women with Lactobacillus spp.-depleted microbiomes increased after emergency cerclage. Significant differences in β diversity were found between the groups. Before the emergency cerclage, the enriched microorganisms were G. Lactobacillus, O. Alteromonadales, and P. Firmicutes. After emergency cerclage, the enriched microorganisms were P. Actinobacteria, C. Actinobacteria, P. Proteobacteria, F. Bifidobacteriaceae, O. Bifidobacteriales, G. Gardnerella, and G. Veillonella. Conclusion Cerclage (particularly emergency cerclage) may alter the vaginal microbiota by increasing microbiota diversity, decreasing vaginal Lactobacillus abundance, and increasing the abundance of pathogenic bacteria that are not conducive to pregnancy maintenance, thereby affecting surgical efficacy. Therefore, the role of the vaginal microbiome should be considered when developing treatment strategies for pregnant women with cervical incompetence. Clinical trial registration https://www.chictr.org.cn, identifier ChiCTR2100046305.
Collapse
Affiliation(s)
- Yunshan Xiao
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
- Xiamen Clinical Research Center for Perinatal Medicine, Xiamen, China
| | - Shiting Huang
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Weiwei Yu
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Yan Ni
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Danni Lu
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Quanfeng Wu
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Qin Leng
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Ting Yang
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Meilan Ni
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Jingxian Xie
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
| | - Xueqin Zhang
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Xiamen, China
- Xiamen Clinical Research Center for Perinatal Medicine, Xiamen, China
- *Correspondence: Xueqin Zhang,
| |
Collapse
|
20
|
Zhu B, Tao Z, Edupuganti L, Serrano MG, Buck GA. Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. Microbiol Mol Biol Rev 2022; 86:e0018121. [PMID: 36222685 PMCID: PMC9769908 DOI: 10.1128/mmbr.00181-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The microbiome of the female reproductive tract defies the convention that high biodiversity is a hallmark of an optimal ecosystem. Although not universally true, a homogeneous vaginal microbiome composed of species of Lactobacillus is generally associated with health, whereas vaginal microbiomes consisting of other taxa are generally associated with dysbiosis and a higher risk of disease. The past decade has seen a rapid advancement in our understanding of these unique biosystems. Of particular interest, substantial effort has been devoted to deciphering how members of the microbiome of the female reproductive tract impact pregnancy, with a focus on adverse outcomes, including but not limited to preterm birth. Herein, we review recent research efforts that are revealing the mechanisms by which these microorganisms of the female reproductive tract influence gynecologic and reproductive health of the female reproductive tract.
Collapse
Affiliation(s)
- Bin Zhu
- Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhi Tao
- Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Laahirie Edupuganti
- Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Myrna G. Serrano
- Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Gregory A. Buck
- Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
- Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| |
Collapse
|
21
|
Kan H, He Y, Li Q, Mu Y, Dong Y, Fan W, Zhang M, Wang T, Li Y, Liu H, Hu A, Zheng Y. Differential Effect of Vaginal Microbiota on Spontaneous Preterm Birth among Chinese Pregnant Women. Biomed Res Int 2022; 2022:3536108. [PMID: 36506912 DOI: 10.1155/2022/3536108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022]
Abstract
Objective The effect of vaginal microbiota on spontaneous preterm birth (sPTB) has not been fully addressed, and few studies have explored the associations between vaginal taxa and sPTB in the gestational diabetes mellitus (GDM) and non-GDM groups, respectively. Study Design. To minimize external interference, a total of 41 pregnant women with sPTB and 308 controls (pregnant women without sPTB) from same regain were enrolled in this case-cohort study. Controls were randomly selected at baseline. With the exception of GDM, other characteristics were not significantly different between the two groups. Vaginal swabs were collected at early second trimester. Using 16S amplicon sequencing, the main bioinformatics analysis was performed on the platform of QIIME 2. Vaginal microbiota traits of the sPTB group were compared with controls. Finally, the effects of binary taxa on sPTB in the GDM group and the non-GDM group were analyzed, respectively. Results The proportion of GDM in the sPTB (19.51%) was higher than the controls (7.47%, P = 0.018). The vaginal microbiota of pregnant women with sPTB exhibited higher alpha diversity metrics (observed features, P = 0.001; Faith's phylogenetic diversity, P = 0.013) and different beta diversity metrics (unweighted UniFrac, P = 0.006; Jaccard's distance, P = 0.004), compared with controls. The presence of Lactobacillus paragasseri/gasseri (aOR: 3.12, 95% CI: 1.24-7.84), Streptococcus (aOR: 3.58, 95% CI: 1.68-7.65), or Proteobacteria (aOR: 3.39, 95% CI: 1.55-7.39) was associated with an increased risk of sPTB in the non-GDM group (P < 0.05). However, the relative abundance of novel L. mulieris (a new species of the L. delbrueckii group) was associated with a decreased risk of sPTB (false discovery rate, 0.10) in all pregnant women. Conclusion GDM may modify the association of vaginal taxa with sPTB, suggesting that maternal GDM should be considered when using vaginal taxa to identify pregnant women at high risk of sPTB.
Collapse
|
22
|
Lüth T, Graspeuntner S, Neumann K, Kirchhoff L, Masuch A, Schaake S, Lupatsii M, Tse R, Griesinger G, Trinh J, Rupp J. Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing. J Assist Reprod Genet 2022; 39:2659-2667. [PMID: 36223010 DOI: 10.1007/s10815-022-02628-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis. METHODS Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference. RESULTS The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing. CONCLUSIONS Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.
Collapse
Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.
| | - Kay Neumann
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Laura Kirchhoff
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Antonia Masuch
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Georg Griesinger
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| |
Collapse
|
23
|
Park S, Moon J, Kang N, Kim YH, You YA, Kwon E, Ansari A, Hur YM, Park T, Kim YJ. Predicting preterm birth through vaginal microbiota, cervical length, and WBC using a machine learning model. Front Microbiol 2022; 13:912853. [PMID: 35983325 PMCID: PMC9378785 DOI: 10.3389/fmicb.2022.912853] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
An association between the vaginal microbiome and preterm birth has been reported. However, in practice, it is difficult to predict premature birth using the microbiome because the vaginal microbial community varies highly among samples depending on the individual, and the prediction rate is very low. The purpose of this study was to select markers that improve predictive power through machine learning among various vaginal microbiota and develop a prediction algorithm with better predictive power that combines clinical information. As a multicenter case–control study with 150 Korean pregnant women with 54 preterm delivery group and 96 full-term delivery group, cervicovaginal fluid was collected from pregnant women during mid-pregnancy. Their demographic profiles (age, BMI, education level, and PTB history), white blood cell count, and cervical length were recorded, and the microbiome profiles of the cervicovaginal fluid were analyzed. The subjects were randomly divided into a training (n = 101) and a test set (n = 49) in a two-to-one ratio. When training ML models using selected markers, five-fold cross-validation was performed on the training set. A univariate analysis was performed to select markers using seven statistical tests, including the Wilcoxon rank-sum test. Using the selected markers, including Lactobacillus spp., Gardnerella vaginalis, Ureaplasma parvum, Atopobium vaginae, Prevotella timonensis, and Peptoniphilus grossensis, machine learning models (logistic regression, random forest, extreme gradient boosting, support vector machine, and GUIDE) were used to build prediction models. The test area under the curve of the logistic regression model was 0.72 when it was trained with the 17 selected markers. When analyzed by combining white blood cell count and cervical length with the seven vaginal microbiome markers, the random forest model showed the highest test area under the curve of 0.84. The GUIDE, the single tree model, provided a more reasonable biological interpretation, using the 10 selected markers (A. vaginae, G. vaginalis, Lactobacillus crispatus, Lactobacillus fornicalis, Lactobacillus gasseri, Lactobacillus iners, Lactobacillus jensenii, Peptoniphilus grossensis, P. timonensis, and U. parvum), and the covariates produced a tree with a test area under the curve of 0.77. It was confirmed that the association with preterm birth increased when P. timonensis and U. parvum increased (AUC = 0.77), which could also be explained by the fact that as the number of Peptoniphilus lacrimalis increased, the association with preterm birth was high (AUC = 0.77). Our study demonstrates that several candidate bacteria could be used as potential predictors for preterm birth, and that the predictive rate can be increased through a machine learning model employing a combination of cervical length and white blood cell count information.
Collapse
Affiliation(s)
- Sunwha Park
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
| | - Jeongsup Moon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Nayeon Kang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Young-Han Kim
- Department of Obstetrics and Gynecology, College of Medicine, Yonsei University, Seoul, South Korea
| | - Young-Ah You
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
| | - Eunjin Kwon
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
| | - AbuZar Ansari
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
| | - Young Min Hur
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Statistics, Seoul National University, Seoul, South Korea
- *Correspondence: Taesung Park,
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, Seoul, South Korea
- Young Ju Kim,
| |
Collapse
|
24
|
Greenberg JM, Romero R, Winters AD, Galaz J, Garcia-Flores V, Arenas-Hernandez M, Panzer J, Shaffer Z, Kracht DJ, Gomez-Lopez N, Theis KR. Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing. Microbiol Spectr 2022;:e0128622. [PMID: 35916526 DOI: 10.1128/spectrum.01286-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mice are frequently used as animal models for mechanistic studies of infection and obstetrical disease, yet characterization of the murine microbiota during pregnancy is lacking. The objective of this study was to characterize the microbiotas of distinct body sites of the pregnant mouse—vagina, oral cavity, intestine, and lung—that harbor microorganisms that could potentially invade the murine amniotic cavity, thus leading to adverse pregnancy outcomes. The microbiotas of these body sites were characterized through anoxic, hypoxic, and oxic culture as well as through 16S rRNA gene sequencing. With the exception of the vagina, the cultured microbiotas of each body site varied by atmosphere, with the greatest diversity in the cultured microbiota appearing under anoxic conditions. Only cultures of the vagina were comprehensively representative of the microbiota observed through direct DNA sequencing of body site samples, primarily due to the predominance of two Rodentibacter strains. Identified as Rodentibacter pneumotropicus and Rodentibacter heylii, these isolates exhibited predominance patterns similar to those of Lactobacillus crispatus and Lactobacillus iners in the human vagina. Whole-genome sequencing of these Rodentibacter strains revealed shared genomic features, including the ability to degrade glycogen, an abundant polysaccharide in the vagina. In summary, we report body site-specific microbiotas in the pregnant mouse with potential ecological parallels to those of humans. Importantly, our findings indicate that the vaginal microbiotas of pregnant mice can be readily cultured, suggesting that mock vaginal microbiotas can be tractably generated and maintained for experimental manipulation in future mechanistic studies of host vaginal-microbiome interactions. IMPORTANCE Mice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota during pregnancy has been neglected. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation. Here, we characterized the microbiotas of pregnant mice and established the appropriateness of culture in capturing the microbiota at each site. The high relative abundance of Rodentibacter observed in the vagina is similar to that of Lactobacillus in humans, suggesting potential ecological parallels. Importantly, we report that the vaginal microbiota of the pregnant mouse can be readily cultured under hypoxic conditions, demonstrating that mock microbial communities can be utilized to test the potential ecological parallels between microbiotas in human and murine pregnancy and to evaluate the relevance of the structure of these microbiotas for adverse pregnancy outcomes, especially intra-amniotic infection and preterm birth.
Collapse
|
25
|
Park S, You YA, Kim YH, Kwon E, Ansari A, Kim SM, Lee G, Hur YM, Jung YJ, Kim K, Kim YJ. Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth. Sci Rep 2022; 12:10148. [PMID: 35710793 PMCID: PMC9203766 DOI: 10.1038/s41598-022-13871-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Ureaplasma and Prevotella infections are well-known bacteria associated with preterm birth. However, with the development of metagenome sequencing techniques, it has been found that not all Ureaplasma and Prevotella colonizations cause preterm birth. The purpose of this study was to determine the association between Ureaplasma and Prevotella colonization with the induction of preterm birth even in the presence of Lactobacillus. In this matched case–control study, a total of 203 pregnant Korean women were selected and their cervicovaginal fluid samples were collected during mid-pregnancy. The microbiome profiles of the cervicovaginal fluid were analyzed using 16S rRNA gene amplification. Sequencing data were processed using QIIME1.9.1. Statistical analyses were performed using R software, and microbiome analysis was performed using the MicrobiomeAnalyst and Calypso software. A positive correlation between Ureaplasma and other genera was highly related to preterm birth, but interestingly, there was a negative correlation with Lactobacillus and term birth, with the same pattern observed with Prevotella. Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth, although Ureaplasma and Prevotella are associated with preterm birth. Balanced colonization between Lactobacillus and Ureaplasma and Prevotella is important to prevent preterm birth.
Collapse
Affiliation(s)
- Sunwha Park
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Young-Ah You
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Young-Han Kim
- Department of Obstetrics and Gynecology, College of Medicine, Yonsei University, Seoul, Korea
| | - Eunjin Kwon
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - AbuZar Ansari
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Soo Min Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Gain Lee
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Young Min Hur
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea
| | - Yun Ji Jung
- Department of Obstetrics and Gynecology, College of Medicine, Yonsei University, Seoul, Korea
| | | | - Young Ju Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University, 1071, Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Korea.
| |
Collapse
|
26
|
Yue Y, Hu YJ. A new approach to testing mediation of the microbiome at both the community and individual taxon levels. Bioinformatics 2022; 38:3173-3180. [PMID: 35512399 PMCID: PMC9191207 DOI: 10.1093/bioinformatics/btac310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Understanding whether and which microbes played a mediating role between an exposure and a disease outcome are essential for researchers to develop clinical interventions to treat the disease by modulating the microbes. Existing methods for mediation analysis of the microbiome are often limited to a global test of community-level mediation or selection of mediating microbes without control of the false discovery rate (FDR). Further, while the null hypothesis of no mediation at each microbe is a composite null that consists of three types of null, most existing methods treat the microbes as if they were all under the same type of null, leading to excessive false positive results. RESULTS We propose a new approach based on inverse regression that regresses the microbiome data at each taxon on the exposure and the exposure-adjusted outcome. Then, the P-values for testing the coefficients are used to test mediation at both the community and individual taxon levels. This approach fits nicely into our Linear Decomposition Model (LDM) framework, so our new method LDM-med, implemented in the LDM framework, enjoys all the features of the LDM, e.g. allowing an arbitrary number of taxa to be tested simultaneously, supporting continuous, discrete, or multivariate exposures and outcomes (including survival outcomes), and so on. Using extensive simulations, we showed that LDM-med always preserved the FDR of testing individual taxa and had adequate sensitivity; LDM-med always controlled the type I error of the global test and had compelling power over existing methods. The flexibility of LDM-med for a variety of mediation analyses is illustrated by an application to a murine microbiome dataset, which identified several plausible mediating taxa. AVAILABILITY AND IMPLEMENTATION Our new method has been added to our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ye Yue
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Yi-Juan Hu
- To whom correspondence should be addressed.
| |
Collapse
|
27
|
Gudnadottir U, Debelius JW, Du J, Hugerth LW, Danielsson H, Schuppe-Koistinen I, Fransson E, Brusselaers N. The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis. Sci Rep 2022; 12:7926. [PMID: 35562576 PMCID: PMC9106729 DOI: 10.1038/s41598-022-12007-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/04/2022] [Indexed: 02/02/2023] Open
Abstract
Preterm birth is a major cause of neonatal morbidity and mortality worldwide. Increasing evidence links the vaginal microbiome to the risk of spontaneous preterm labour that leads to preterm birth. The aim of this systematic review and network meta-analysis was to investigate the association between the vaginal microbiome, defined as community state types (CSTs, i.e. dominance of specific lactobacilli spp, or not (low-lactobacilli)), and the risk of preterm birth. Systematic review using PubMed, Web of Science, Embase and Cochrane library was performed. Longitudinal studies using culture-independent methods categorizing the vaginal microbiome in at least three different CSTs to assess the risk of preterm birth were included. A (network) meta-analysis was conducted, presenting pooled odds ratios (OR) and 95% confidence intervals (CI); and weighted proportions and 95% CI. All 17 studies were published between 2014 and 2021 and included 38-539 pregnancies and 8-107 preterm births. Women presenting with "low-lactobacilli" vaginal microbiome were at increased risk (OR 1.69, 95% CI 1.15-2.49) for delivering preterm compared to Lactobacillus crispatus dominant women. Our network meta-analysis supports the microbiome being predictive of preterm birth, where low abundance of lactobacilli is associated with the highest risk, and L. crispatus dominance the lowest.
Collapse
Affiliation(s)
- Unnur Gudnadottir
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.
| | - Justine W Debelius
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden
| | - Luisa W Hugerth
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Science for Life Laboratory, 171 65, Solna, Sweden
| | - Hanna Danielsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Sach's Children's and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Science for Life Laboratory, 171 65, Solna, Sweden
| | - Emma Fransson
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Department of Women's and Children's Health, Uppsala University, 751 85, Uppsala, Sweden
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium.,Department of Head and Skin, Ghent University, 9000, Ghent, Belgium
| |
Collapse
|
28
|
Chen S, Xue X, Zhang Y, Zhang H, Huang X, Chen X, Deng G, Luo S, Gao J. Vaginal Atopobium is Associated with Spontaneous Abortion in the First Trimester: a Prospective Cohort Study in China. Microbiol Spectr 2022; 10:e0203921. [PMID: 35311570 DOI: 10.1128/spectrum.02039-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spontaneous abortion (SA) has received more and more attention in light of its increasing incidence. However, the causes and pathogenesis of SA remain largely unknown, especially for those without any pathological features. In this study, we characterized the vaginal microbiota diversity and composition of pregnant women in their first trimester and evaluated the association between the vaginal microbiota and SA before 12 weeks of gestation. Participants' bacterial profiles were analyzed by 16S rRNA gene sequencing in the V3-V4 regions at 5-8 weeks of gestation. A total of 48 patients with SA at 12 weeks of gestation were included as the study group, while 116 women with normal pregnancies (NPs) were included as a control group. The results indicated that the richness of the vaginal microbiome in SA patients was higher (Chao1, P < 0.05) and different in composition relative to that of women with NPs (unweighted UniFrac, R = 0.15, P < 0.01; binary Jaccard, R = 0.15, P < 0.01). Furthermore, the genus Apotobium was significantly enriched in SA patients. An extreme gradient-boosting (XGBoost) analysis was able to classify Atopobium-induced SA more reliably (area under the receiver operating characteristic curve, 0.69; threshold, 0.01%). Moreover, after adjusting for potential confounders, the results showed a robust association between Apotobium and SA (as a categorical variable [<0.01%]; adjusted odds ratio, 2.9; 95% confidence interval, 1.3 to 6.5; P = 0.01). In conclusion, higher vaginal Apotobium levels were associated with SA in the first trimester. IMPORTANCE Spontaneous abortion (SA) is the most common adverse pregnancy outcome in the first trimester. The causal drivers of SA have become a substantial challenge to reveal and overcome. We hypothesize that vaginal microbial dysbiosis is associated with SA, as it was related to several female reproductive disorders in previous studies. In our study, we characterized the vaginal microbiota of patients with SA at 12 weeks of gestation as the study group, and women with normal pregnancies were enrolled as a control group. Generally, significant differences were discovered in the vaginal microbiota between the two groups. Our study also revealed that Apotobium may play an important role in the pathogenesis of SA. To our knowledge, this study is the first detailed elaboration of the vaginal microbiota composition and vaginal Apotobium in association with SA. We believe that our findings will inspire more researchers to consider dynamic changes in the vaginal microbiota as critical features for further studies of nosogenesis not only for SA but also other reproductive diseases.
Collapse
|
29
|
Juliana NCA, Deb S, Juma MH, Poort L, Budding AE, Mbarouk A, Ali SM, Ouburg S, Morré SA, Sazawal S, Ambrosino E. The Vaginal Microbiota Composition and Genital Infections during and after Pregnancy among Women in Pemba Island, Tanzania. Microorganisms 2022; 10:microorganisms10030509. [PMID: 35336085 PMCID: PMC8951098 DOI: 10.3390/microorganisms10030509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/03/2022] [Accepted: 02/21/2022] [Indexed: 01/25/2023] Open
Abstract
We investigated the vaginal microbiota (VMB) composition, prevalence of genital pathogens and their association among pregnant and post-delivery women in Pemba Island, Tanzania. Vaginal swabs were collected from 90 women, at two time points during pregnancy (<20 weeks of gestational age [GA] and ≥20 weeks GA) and once after delivery, when possible. IS-pro assay was used for VMB characterization. Chlamydia trachomatis (CT), Neisseria gonorrhea (NG), Trichomonas vaginalis (TV), Mycoplasma genitalium (MG) and human papillomavirus (HPV) were detected by qPCRs. VMB were mostly Lactobacillus dominant during pregnancy and non-Lactobacillus dominant post-delivery. A significant decrease in VMB richness was observed during pregnancy among paired and unpaired samples. Shannon diversity was significantly lower during pregnancy than post-delivery among unpaired samples. Klebsiella species and Streptococcus anginosus were the most commonly identified pathobionts at all timepoints. A high abundance of pathobionts was mostly seen in women with non-Lactobacillus dominant VMB. At ≥20 weeks GA timepoint during pregnancy, 63.0% of the women carrying one or more genital pathogen (either HPV, CT, TV, or MG) had L. iners dominant VMB. NG was not detected pre-delivery. This study contributes evidence on VMB composition, its changes during pregnancy and post-delivery, and their association with pathobionts and genital pathogens.
Collapse
Affiliation(s)
- Naomi C. A. Juliana
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Reproduction), Faculty of Health, Medicine & Life Sciences, University of Maastricht, 6200 Maastricht, The Netherlands; (N.C.A.J.); (S.A.M.)
| | - Saikat Deb
- Public Health Laboratory—Ivo de Carneri, Chake Chake 74201, Pemba Island, Tanzania; (S.D.); (M.H.J.); (A.M.); (S.M.A.)
- Centre for Public Health Kinetics, New Delhi 110024, India;
| | - Mohamed H. Juma
- Public Health Laboratory—Ivo de Carneri, Chake Chake 74201, Pemba Island, Tanzania; (S.D.); (M.H.J.); (A.M.); (S.M.A.)
| | - Linda Poort
- inBiome, 1098 Amsterdam, The Netherlands; (L.P.); (A.E.B.)
| | | | - Abdalla Mbarouk
- Public Health Laboratory—Ivo de Carneri, Chake Chake 74201, Pemba Island, Tanzania; (S.D.); (M.H.J.); (A.M.); (S.M.A.)
| | - Said M. Ali
- Public Health Laboratory—Ivo de Carneri, Chake Chake 74201, Pemba Island, Tanzania; (S.D.); (M.H.J.); (A.M.); (S.M.A.)
| | - Sander Ouburg
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location AMC, 1105 Amsterdam, The Netherlands;
| | - Servaas A. Morré
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Reproduction), Faculty of Health, Medicine & Life Sciences, University of Maastricht, 6200 Maastricht, The Netherlands; (N.C.A.J.); (S.A.M.)
| | - Sunil Sazawal
- Centre for Public Health Kinetics, New Delhi 110024, India;
| | - Elena Ambrosino
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Reproduction), Faculty of Health, Medicine & Life Sciences, University of Maastricht, 6200 Maastricht, The Netherlands; (N.C.A.J.); (S.A.M.)
- Correspondence: ; Tel.: +31-04-3388-4081
| |
Collapse
|
30
|
Zhang Y, Chen S, Chen X, Zhang H, Huang X, Xue X, Guo Y, Ruan X, Liu X, Deng G, Luo S, Gao J. Association Between Vaginal Gardnerella and Tubal Pregnancy in Women With Symptomatic Early Pregnancies in China: A Nested Case-Control Study. Front Cell Infect Microbiol 2022; 11:761153. [PMID: 35111691 PMCID: PMC8801712 DOI: 10.3389/fcimb.2021.761153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/20/2021] [Indexed: 12/01/2022] Open
Abstract
The early diagnosis and treatment of ectopic pregnancy (EP) remains a major challenge. Despite a known link between vaginal microbiota and female reproductive health, few studies have focused on the association between vaginal microbiota and pregnancy location. This nested case-control study aimed to characterize the vaginal microbiota in tubal pregnancy (TP) among symptomatic women in early pregnancy. Women with symptomatic early pregnancy of unknown location (PUL) were included in this study. 16S rDNA gene sequencing was performed to assess vaginal microbial diversity and relative abundance. Machine learning and multivariate logistic regression were also used to evaluate the association between Gardnerella and TP. The results indicate that the vaginal microbiome in TP was more diverse (Shannon, p < 0.05) and was different in composition to that of women with intrauterine pregnancy (IUP) (weighted Unifrac, R = 0.08, p = 0.01). The genus Gardnerella was significantly enriched in TP. The XGBoost analysis was able to classify Gardnerella-induced TP more reliably (AUC = 0.621). Moreover, after adjusting potential confounders, our results indicate a robust association between Gardnerella and TP (as a continuous variable, adjusted OR: 12.0, 95% CI: 2.1–67.4, p < 0.01; as a categorical variable (≥0.85%), and adjusted OR: 4.2, 95% CI: 2.0–8.8, p < 0.01). In conclusion, we found that higher virginal Gardnerella levels were associated with TP in women with symptomatic early pregnancy.
Collapse
Affiliation(s)
- Yingxuan Zhang
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Si Chen
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaofeng Chen
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huimin Zhang
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuge Huang
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaomeng Xue
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yinan Guo
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaofeng Ruan
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaorong Liu
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gaopi Deng
- Department of Gynecology, The First Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
| | - Songping Luo
- Department of Gynecology, The First Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
- *Correspondence: Songping Luom, ; Jie Gao,
| | - Jie Gao
- Department of Gynecology, The First Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
- *Correspondence: Songping Luom, ; Jie Gao,
| |
Collapse
|
31
|
Wright ML, Dunlop AL, Dunn AB, Mitchell RM, Wissel EF, Corwin EJ. Factors Associated with Vaginal Lactobacillus Predominance Among African American Women Early in Pregnancy. J Womens Health (Larchmt) 2021; 31:682-689. [PMID: 34448602 PMCID: PMC9133973 DOI: 10.1089/jwh.2021.0148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: Vaginal Lactobacillus is considered protective of some adverse reproductive health outcomes, including preterm birth. However, factors that increase or decrease the likelihood of harboring Lactobacillus in the vaginal microbiome remain largely unknown. In this study, we sought to identify risk and protective factors associated with vaginal Lactobacillus predominance within a cohort of pregnant African American women. Materials and Methods: Vaginal microbiome samples were self-collected by African American women (N = 436) during their 8-14th week of pregnancy. Sociodemographic information and measures of health behaviors, including substance use, antibiotic exposure, sexual practices, frequency of vaginal intercourse, and the use of vaginal products, were collected through participant self-report. The V3-V4 region of the 16S rRNA gene was targeted for amplification and sequencing using Illumina HiSeq, with bacterial taxonomy assigned using the PECAN classifier. Univariate and a series of multivariate logistic regression models identified factors predictive of diverse vaginal microbiota or Lactobacillus predominance. Results: Participants who used marijuana in the past 30 days (aOR 1.80, 95% CI 1.08-2.98) were more likely to have diverse non-Lactobacillus-predominant vaginal microbiota, as were women not living with their partners (aOR 1.90, 95% CI 1.20-3.01). Cohabitating or marijuana usage were not associated with type of Lactobacillus (non-iners Lactobacillus vs. Lactobacillus iners) predominance (aOR 1.11, 95% CI 0.52-2.38 and aOR 0.56, 95% CI 0.21-1.47, respectively). Conclusions: Living with a partner is conducive to vaginal Lactobacillus predominance. As such, cohabitation may be in important covariate to consider in vaginal microbiome studies.
Collapse
Affiliation(s)
- Michelle L Wright
- School of Nursing, The University of Texas at Austin, Austin, Texas, USA.,Department of Women's Health, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
| | - Anne L Dunlop
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Alexis B Dunn
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Rebecca M Mitchell
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA.,Department of Computer Science, College of Arts and Sciences, Emory University, Atlanta, Georgia, USA
| | - Emily F Wissel
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | | |
Collapse
|