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Comparative metagenomic analysis of the vaginal microbiome in healthy women

Synthetic and Systems Biotechnology 2021年第2期6卷 77-84页

作者： Fei Liu Yingshun Zhou Lisi Zhu Zhiyi Wang LiangKun Ma Yuan He Pengcheng Fu CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of Pathogenic Biology Pathogenic Biology platformSchool of Basic Medical SciencesSouthwest Medical UniversityLuzhou646000Sichuan ProvinceChina Laboratory of Clinical Genetics Medical Research CenterState Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina CAS Key Laboratory of Microbial Physiological and Metabolic Engineering Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Peking Union Medical College Hospital(Dongdan Campus) No.1 Shuai Fu YuanBeijing100730China National Human Genetic Resources Center National Research Institute for Health and Family PlanningBeijingChina Mybiome(Beijing)Medical Consulting Co.LTD China

The composition of these vaginal microbiome has a significant impact on women’s ***,few studies have characterized the vaginal microbiome of healthy Chinese women using metagenomic ***,we carried out a comparative metagenomic analysis to survey taxonomic,functional levels,and microbial communities’genome content in healthy women’s vaginal ***,we observed a total of 111 species,including all dominant vaginal Lactobacillus species,such as ***,***,***,and *** microbial taxa,several pathways were ubiquitous and prevalent across individuals,including adenosine ribonucleotides de novo biosynthesis and pyruvate fermentation to acetate and lactate Ⅱ.Notably,our diversity analysis confirmed a significant difference in healthy women from different ethnic ***,we binned vaginal assemblies into 62 high-quality genomes,including 9 ***,7 ***,5 ***,and 5 *** identified the pan and core genomes of *** and *** and revealed the genetic *** differences between strains were the hypothetical genes and mobile element-like *** results provide a framework for understanding the implications of the female reproductive tract’s composition and functional potential and highlight the importance of genome-resolved metagenomic analysis to further understand the human vaginal microbiome.

关键词： vaginal microbiome Metagenome Metabolic pathways Genome Strains

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Influence of group B streptococcus and vaginal cleanliness on the vaginal microbiome of pregnant women

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World Journal of Clinical Cases 2022年第34期10卷 12578-12586页

作者： Qi Liao Xiao-Fen Zhang Xin Mi Feng Jin Hong-Min Sun Qing-Xuan Wang Department of Obstetrics and Gynecology Shunyi Maternal and Children’s Hospital of Beijing Children’s HospitalBeijing 101300China Department of Genetics and Reproductive Medicine Shunyi Maternal and Children’s Hospital of Beijing Children’s HospitalBeijing 101300China

BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their *** B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are closely associated with vaginal *** To explore the effects of GBS status and vaginal cleanliness on vaginal *** We collected 160 vaginal swabs from pregnant women and divided them into the following four groups based on GBS status and vaginal cleanliness:GBS-positive+vaginal cleanliness I–II degree,GBS-negative+vaginal cleanliness I–II degree,GBS-positive+vaginal cleanliness III–IV degree,and GBS-negative+vaginal cleanliness III–IV *** were subjected to 16S rRNA gene amplicon *** Alpha diversity analysis showed that the Shannon index did not significantly differ between the four *** identified significant variation in taxa abundance between the GBS-positive and GBS-negative groups and between the vaginal cleanliness I–II degree and III–IV degree *** coordinate analysis and non-metric multidimensional scaling analysis further confirmed the microbial diversity of the four ***,the linear discriminant analysis demonstrated that Lactobacillus jensenii and Actinobacteria were strongly associated with GBS-positive status,and Lactobacillus iners,Lactobacillaceae,Lactobacillus,Lactobacillales,Bacilli and Firmicutes were closely correlated with GBS-negative *** GBS status and vaginal cleanliness significantly affect vaginal microbiome differences in pregnant *** findings provide instructional information for clinical antibiotic treatment in pregnant women with different GBS statuses and vaginal cleanliness degrees.

关键词： vaginal microbiome Pregnant women 16S rRNA gene amplicon sequencing Group B Streptococcus vaginal cleanliness

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The Utility of Voided Urine Samples as a Proxy for the vaginal microbiome and for the Prediction of Bacterial Vaginosis

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Infectious Microbes & Diseases 2022年第4期4卷 149-156页

作者： Bin Zhu Christopher Diachok Laahirie Edupuganti David J.Edwards Jeffrey R.Donowitz Katherine Tossas Andrey Matveyev Katherine M.Spaine Vladimir Lee Myrna G.Serrano Gregory A.Buck Department of Microbiology and Immunology School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Center for microbiome Engineering and Data Analysis Virginia Commonwealth UniversityRichmondVirginiaUSA Department of Statistical Sciences and Operations Research College of Humanities and SciencesVirginia Commonwealth UniversityRichmondVirginiaUSA Department of Pediatric Infectious Diseases Children's Hospital of Richmond at Virginia Commonwealth UniversityRichmondVirginiaUSA Department of Infectious Diseases and International Health University of VirginiaCharlottesvilleVirginiaUSA Department of Health Behavior and Policy School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Department of Family Medicine and Population Health School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Computer Science Department College of EngineeringVirginia Commonwealth UniversityRichmondVirginiaUSA Genomics Core Virginia Commonwealth UniversityRichmondVirginiaUSA

Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological ***,collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained *** contrast,urine sample collection is routine and noninvasive and does not require involvement of a *** sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal *** urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic *** examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes.A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal ***,the relative abundances of common vaginal taxa were linearly correlated with those in the paired *** similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginalmicrobiome with likely clinical ***,a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.

关键词： 16S rRNA vaginal microbiome urine microbiome bacterial vaginosis reproductive and gynecologic health

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Longitudinal analysis reveals characteristically high proportions of bacterial vaginosis-associated bacteria and temporal variability of vaginal microbiota in northern pig-tailed macaques （Macaca leonina）

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Zoological Research 2015年第5期36卷 285-298页

作者： Lin ZHU Ai-Hua LEI Hong-Yi ZHENG Long-Bao LYU Zhi-Gang ZHANG Yong-Tang ZHENG Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan 650204 China School of Life Sciences University of Science and Technology of China Hefei Anhui 230026 China Kunming Primate Research Center Chinese Academy of Sciences Kunming Yunnan 650223 China

The complex and dynamic vaginal microbial ecosystem is critical to both health and disease of the host. Studies focusing on how vaginal microbiota influences HIV-1 infection may face limitations in selecting proper animal models. Given that northern pig-tailed macaques （Macaca leonina） are susceptible to HIV-1 infection, they may be an optimal animal model for elucidating the mechanisms by which vaginal microbiota contributes to resistance and susceptibility to HIV-1 infection. However, little is known about the composition and temporal variability of vaginal microbiota of the northern pig-tailed macaque. Here, we present a comprehensive catalog of the composition and temporal dynamics of vaginal microbiota of two healthy northern pig-tailed macaques over 19 weeks using 454-pyrosequencing of 16S rRNA genes. We found remarkably high proportions of a diverse array of anaerobic bacteria associated with bacterial vaginosis. Atopobium and Sneathia were dominant genera, and interestingly, we demonstrated the presence of Lactobacillus-dominated vaginal microbiota. Moreover, longitudinal analysis demonstrated that the temporal dynamics of the vaginal microbiota were considerably individualized. Finally, network analysis revealed that vaginal pH may influence the temporal dynamics of the vaginal microbiota, suggesting that inter-subject variability of vaginal bacterial communities could be mirrored in inter-subject variation in correlation profiles of species with each other and with vaginal pH over time. Our results suggest that the northern pig-tailed macaque could be an ideal animal model for prospective investigation of the mechanisms by which vaginal microbiota influence susceptibility and resistance to HIV-1 infection in the context of highly polymicrobial and Lactobacillus-dominated states.

关键词： Macaque vaginal microbiome Bacterialvaginosis Temporal dynamics Networks

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Multi-omic microbiome Profiles in the Female Reproductive Tract in Early Pregnancy

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Infectious Microbes & Diseases 2019年第2期1卷 49-60页

作者： Sophonie Jean Bernice Huang Hardik I.Parikh David J.Edwards J.Paul Brooks Naren Gajenthra Kumar Nihar U.Sheth Vishal Koparde Ekaterina Smirnova Snehalata Huzurbazar Philippe H.Girerd Dayanjan S.Wijesinghe Jerome F.StraussIII Myrna G.Serrano Jennifer M.Fettweis Kimberly K.Jefferson Gregory A.Buck Department of Microbiology and Immunology Virginia Commonwealth UniversityRichmondVA Center for microbiome Engineering and Data Analysis Virginia Commonwealth UniversityRichmondVA Department of Statistical Sciences and Operations Research Virginia Commonwealth UniversityRichmondVA Supply Chain Management and Analytics School of BusinessVirginia Commonwealth UniversityRichmondVA Life Sciences Virginia Commonwealth UniversityRichmondVA DNAnexus Inc. Mountain ViewCA Frederick National Laboratory for Cancer Research FrederickMD Department of Biostatistics Virginia Commonwealth UniversityRichmondVA Department of Statistics University of WyomingLaramieWY Obstetrics and Gynecology Virginia Commonwealth UniversityRichmondVA Pharmacotherapy and Outcomes Science Virginia Commonwealth UniversityRichmondVA Department of Computer Science Virginia Commonwealth UniversityRichmondVA.

The vaginal microbiome likely influences host signaling compounds within the reproductive tract,including pro-inflammatory signals,which may play an important role during *** lactobacilli are associated with positive pregnancy outcome,whereas bacterial vaginosis,a dysbiosis of the vaginal microbiome,is associated with an increased risk of adverse pregnancy outcomes including preterm *** the host response could be predicted based on the taxonomic composition of the vaginal microbiome,particularly early in pregnancy,then those predictions could potentially be used to personalize intervention methods to reduce preterm birth and other adverse *** this proof of principle study,we apply multivariate strategies to analyze 16S rRNA-based taxonomic surveys in conjunction with targeted immuno-proteomic and lipidomic data from vaginal samples from 58 women enrolled in the Multi-Omic microbiome Study-Pregnancy Initiative during early *** between the vaginal microbiome and the vaginal lipidome have not been previously *** from this study reveal significant multiple pairwise associations between microbial taxa,specific eicosanoids and sphingomyelins,and *** the biologic significance of these associations is not yet known,these results support the utility of such multi-omic approaches as a means to predict the impact of the microbiome on the host.

关键词： vaginal microbiome preterm birth multi-omics metagenomics cytokine profiles lipidomics

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Alteration of vaginal microbiota in patients with unexplained recurrent miscarrige

Alteration of vaginal microbiota in patients with unexplaine...

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2018年浙江省医学会妇产科学与围产医学学术年会暨2018年浙江省医师协会妇产科医师分会学术年会

作者：张锋绍兴市妇幼保健院

Objective: The presence of an abnormal vaginal microflora in early pregnancy is a risk factor for recurrent *** the means by which balanced vaginal microbiomes help prevent gynecological diseases in women and maintain health are poorly *** gain insight into this,the vaginal bacterial communities of 10 patients with unexplained recurrent miscarriage and 10 healthy volunteers were ***,we compared the microbiomes of bacterial profile of RM patients and healthy volunteers by pyrosequencing the V3-V4 regions of the bacterial16 S ribosomal RNA gene using the Illumina MiSeq *** diversity(PCoA) analysis showed that bacterial community structure segregate between RM and control *** diversity estimations revealed lower microbiota diversity in samples from RM *** analysis illustrated that abundance of three phyla(Firmicutes,Actinobacteria,Bacteroidetes) was significantly ***,in the genus level,Lactobacillus is the most dominated *** observed statistically significant difierences in 5 *** MT group,3 bacterial taxa were significantly more abundant(Atopobium,Prevotella,Streptococcus),while only 2 taxa were overrepresented in MC group(Lactobacillus,Gardnerella).According to the data of the KEGG database,it was found that there was no significant difference in the function of the two *** present findings provide preliminary experimental evidence supporting vaginal flora dysbiosis in women with *** this might indicate an association between the vaginal microbiota and RM.

关键词： unexplained recurrent miscarriage vaginal microbiome bacterial diversity 16S rRNA

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