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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Feng D, Zhang F, Cai J, Zhang Y, Yan H, Yang Y, Zhong H, Ye H. Functional testing is a complementary tool for the diagnosis of vaginitis. BMC Womens Health 2024; 24:224. [PMID: 38582823 PMCID: PMC10998416 DOI: 10.1186/s12905-024-03035-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/08/2024] Open
Abstract
OBJECTIVE Vaginal microbiota evaluation is a methodology widely used in China to diagnose various vaginal inflammatory diseases. Although vaginal microbiota evaluation has many advantages, it is time-consuming and requires highly skilled and experienced operators. Here, we investigated a six-index functional test that analyzed pH, hydrogen peroxide (H2O2), leukocyte esterase (LEU), sialidase (SNA), β-glucuronidase (GUS), and acetylglucossidase (NAG), and determined its diagnostic value by comparing it with morphological tests of vaginal microbiota. MATERIALS AND METHODS The research was conducted using data extracted from the Laboratory Information System of Women and Children's Hospital. A total of 4902 subjects, ranging in age from 35.4 ± 9.7 years, were analyzed. During the consultation, a minimum of two vaginal swab specimens per patient were collected for both functional and morphological testing. Fisher's exact was used to analyze data using SPSS. RESULTS Of the 4,902 patients, 2,454 were considered to have normal Lactobacillus morphotypes and 3,334 were considered to have normal dominant microbiota. The sensitivity and specificity of H2O2-indicating Lactobacillus morphotypes were 91.3% and 25.28%, respectively, while those of pH-indicating Lactobacillus morphotypes were 88.09% and 59.52%, respectively. The sensitivity and specificity of H2O2-indicating dominant microbiota were 91.3% and 25.3%, respectively, while those of pH-indicating dominant microbiota were 86.27% and 64.45%, respectively. The sensitivity and specificity of NAG for vulvovaginal candidiasis were 40.64% and 84.8%, respectively. For aerobic vaginitis, GUS sensitivity was low at 0.52%, while its specificity was high at 99.93%; the LEU sensitivity and specificity values were 94.73% and 27.49%, respectively. Finally, SNA sensitivity and specificity for bacterial vaginosis were 80.72% and 96.78%, respectively. CONCLUSION Functional tests (pH, SNA, H2O2, LEU) showed satisfactory sensitivity for the detection of vaginal inflammatory diseases. However, these tests lacked specificity, making it difficult to accurately identify specific pathologies. By contrast, NAG and GUS showed excellent specificity in identifying vaginal inflammatory diseases, but their sensitivity was limited. Therefore, functional tests alone are not sufficient to diagnose various vaginal inflammatory diseases. When functional and morphological tests are inconsistent, morphological tests are currently considered the preferred reference method.
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Affiliation(s)
- Danqin Feng
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Fuhui Zhang
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Jianguo Cai
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yansheng Zhang
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Honghong Yan
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yichi Yang
- Department of Social Medicine, Graduate School of Medicine, Hirosaki University, Hirosaki, Japan
| | - Hongxiu Zhong
- Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.
| | - Huiming Ye
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.
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Zhang J, Yu D, Wang T, Gao N, Shi L, Wang Y, Huo Y, Ji Z, Li J, Zhang X, Zhang L, Yan J. Body fluids should be identified before estimating the time since deposition (TsD) in microbiome-based stain analyses for forensics. Microbiol Spectr 2024; 12:e0248023. [PMID: 38470485 PMCID: PMC10986545 DOI: 10.1128/spectrum.02480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Identification and the time since deposition (TsD) estimation of body fluid stains from a crime scene could provide valuable information for solving the cases and are always difficult for forensics. Microbial characteristics were considered as a promising biomarker to address the issues. However, changes in the microbiota may damage the specific characteristics of body fluids. Correspondingly, incorrect body fluid identification may result in inaccurate TsD estimation. The mutual influence is not well understood and limited the codetection. In the current study, saliva, semen, vaginal secretion, and menstrual blood samples were exposed to indoor conditions and collected at eight time points (from fresh to 30 days). High-throughput sequencing based on the 16S rRNA gene was performed to characterize the microbial communities. The results showed that a longer TsD could decrease the discrimination of different body fluid stains. However, the accuracies of identification still reached a quite high value even without knowing the TsD. Correspondingly, the mean absolute error (MAE) of TsD estimation significantly increased without distinguishing the types of body fluids. The predictive TsD of menstrual blood reached a quite low MAE (1.54 ± 0.39 d). In comparison, those of saliva (6.57 ± 1.17 d), semen (6.48 ± 1.33 d), and vaginal secretion (5.35 ± 1.11 d) needed to be further improved. The great effect of individual differences on these stains limited the TsD estimation accuracy. Overall, microbial characteristics allow for codetection of body fluid identification and TsD estimation, and body fluids should be identified before estimating TsD in microbiome-based stain analyses.IMPORTANCEEmerged evidences suggest microbial characteristics could be considered a promising tool for identification and time since deposition (TsD) estimation of body fluid stains. However, the two issues should be studied together due to a potential mutual influence. The current study provides the first evidence to understand the mutual influence and determines an optimal process for codetection of identification and TsD estimation for unknown stains for forensics. In addition, we involved aged stains into our study for identification of body fluid stains, rather than only using fresh stains like previous studies. This increased the predictive accuracy. We have preliminary verified that individual differences in microbiotas limited the predictive accuracy of TsD estimation for saliva, semen, and vaginal secretion. Microbial characteristics could provide an accurate TsD estimation for menstrual blood. Our study benefits the comprehensive understanding of microbiome-based stain analyses as an essential addition to previous studies.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Linyu Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yaya Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
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Aguadé-Gorgorió G, Arnoldi JF, Barbier M, Kéfi S. A taxonomy of multiple stable states in complex ecological communities. Ecol Lett 2024; 27:e14413. [PMID: 38584579 DOI: 10.1111/ele.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024]
Abstract
Natural systems are built from multiple interconnected units, making their dynamics, functioning and fragility notoriously hard to predict. A fragility scenario of particular relevance concerns so-called regime shifts: abrupt transitions from healthy to degraded ecosystem states. An explanation for these shifts is that they arise as transitions between alternative stable states, a process that is well-understood in few-species models. However, how multistability upscales with system complexity remains a debated question. Here, we identify that four different multistability regimes generically emerge in models of species-rich communities and other archetypical complex biological systems assuming random interactions. Across the studied models, each regime consistently emerges under a specific interaction scheme and leaves a distinct set of fingerprints in terms of the number of observed states, their species richness and their response to perturbations. Our results help clarify the conditions and types of multistability that can be expected to occur in complex ecological communities.
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Affiliation(s)
| | - Jean-François Arnoldi
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Matthieu Barbier
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sonia Kéfi
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
- France Santa Fe Institute, Santa Fe, New Mexico, USA
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Tsang HF, Cheung YS, Yu CSA, Chan CSS, Wong CBT, Yim KYA, Pei X, Wong SCC. Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool. Diagnostics (Basel) 2024; 14:686. [PMID: 38611599 PMCID: PMC11012019 DOI: 10.3390/diagnostics14070686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. METHOD Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. RESULTS MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. CONCLUSIONS In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.
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Affiliation(s)
- Hin-Fung Tsang
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong SAR, China
| | - Yui-Shing Cheung
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China; (Y.-S.C.); (C.-S.S.C.)
| | - Chi-Shing Allen Yu
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Chung-Sum Sammy Chan
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China; (Y.-S.C.); (C.-S.S.C.)
| | - Chi-Bun Thomas Wong
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Kay-Yuen Aldrin Yim
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Xiaomeng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Sze-Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China;
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Maduta CS, McCormick JK, Dufresne K. Vaginal community state types (CSTs) alter environmental cues and production of the Staphylococcus aureus toxic shock syndrome toxin-1 (TSST-1). J Bacteriol 2024; 206:e0044723. [PMID: 38334326 PMCID: PMC10955855 DOI: 10.1128/jb.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024] Open
Abstract
Menstrual toxic shock syndrome (mTSS) is a rare but life-threatening disease associated with the use of high-absorbency tampons. The production of the Staphylococcus aureus toxic shock syndrome toxin-1 (TSST-1) superantigen is involved in nearly all cases of mTSS and is tightly controlled by regulators responding to the environment. In the prototypic mTSS strain S. aureus MN8, the major repressor of TSST-1 is the carbon catabolite protein A (CcpA), which responds to glucose concentrations in the vaginal tract. Healthy vaginal Lactobacillus species also depend on glucose for both growth and acidification of the vaginal environment through lactic acid production. We hypothesized that interactions between the vaginal microbiota [herein referred to as community state types (CSTs)] and S. aureus MN8 depend on environmental cues and that these interactions subsequently affect TSST-1 production. Using S. aureus MN8 ΔccpA growing in various glucose concentrations, we demonstrate that the supernatants from different CSTs grown in vaginally defined medium (VDM) could significantly decrease tst expression. When co-culturing CST species with MN8 ∆ccpA, we show that Lactobacillus jensenii completely inhibits TSST-1 production in conditions mimicking healthy menstruation or mTSS. Finally, we show that growing S. aureus in "unhealthy" or "transitional" CST supernatants results in higher interleukin 2 (IL-2) production from T cells. These findings suggest that dysbiotic CSTs may encourage TSST-1 production in the vaginal tract and further indicate that the CSTs are likely important for the protection from mTSS.IMPORTANCEIn this study, we investigate the impact of the vaginal microbiota against Staphylococcus aureus in conditions mimicking the vaginal environment at various stages of the menstrual cycle. We demonstrate that Lactobacillus jensenii can inhibit toxic shock syndrome toxin-1 (TSST-1) production, suggesting the potential for probiotic activity in treating and preventing menstrual toxic shock syndrome (mTSS). On the other side of the spectrum, "unhealthy" or "transient" bacteria such as Gardnerella vaginalis and Lactobacillus iners support more TSST-1 production by S. aureus, suggesting that community state types are important in the development of mTSS. This study sets forward a model for examining contact-independent interactions between pathogenic bacteria and the vaginal microbiota. It also demonstrates the necessity of replicating the environment when studying one as dynamic as the vagina.
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Affiliation(s)
- Carla S. Maduta
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - John K. McCormick
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Karine Dufresne
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
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Chen P, Hu T, Zheng Z, E. Garfield R, Yang J. Characteristics of cervicovaginal microflora at different cervical maturity during late pregnancy: A nested case-control study. PLoS One 2024; 19:e0300510. [PMID: 38507418 PMCID: PMC10954133 DOI: 10.1371/journal.pone.0300510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
OBJECTIVE The mechanism of cervical ripening in late pregnancy is still unclear. The vaginal microbiome has been reported to correlate with the preterm birth and short cervix in pregnant women. However, the associations between the cervical maturity and the vaginal microbiome are still poorly understood. We aim to analyze the cervicovaginal microflora in women with ripe cervix and in those who are unripe when delivering at term. METHODS Cervicovaginal swabs were collected between 40 and 41 weeks of gestation from the following 2 different groups of patients: ripe group (n = 25) and unripe group (n = 25). Samples were tested using 16S ribosomal RNA gene high-throughput sequencing and analyzed by bioinformatics platform. RESULTS This study highlights the relationship between cervical maturity during late pregnancy and the composition of the cervicovaginal microflora. Both α- and β-diversity analyses demonstrated significant differences between women with a ripe cervix and those with an unripe cervix. Notably, the Lactobacillus profile was found to be closely linked to cervical maturity. There was a significant difference in the vaginal community state type, with CST IV being more prevalent in women with an unripe cervix. Furthermore, the association between CST IV and the unripe cervix group, as indicated by the odds ratio of 8.6, underscores its relevance in evaluating cervical maturity, when compared to other Lactobacillus-dominant community state types. Additionally, several bacterial taxa, particularly Lactobacillus, exhibited differential relative abundances between the two groups. CONCLUSION This study provided significant evidence regarding the relationship between the vaginal microbiome and cervical maturity, highlighting the differential diversity, community state types, and specific bacterial taxa, such as Lactobacillus, that are associated with cervical maturation status. These findings contributed to our understanding of the dynamics of the cervicovaginal microflora during late pregnancy and its implications for cervical health.
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Affiliation(s)
- Ping Chen
- Department of Gastroenterology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tingting Hu
- Department of Gastroenterology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zheng Zheng
- Guangzhou Women and Children’s Medical Center, Guangzhou, Guangdong, China
| | - Robert E. Garfield
- Department of Obstetrics and Gynecology, University of Arizona College of Medicine Phoenix, Phoenix, AZ, United States of America
| | - Jinying Yang
- Department of Obstetrics, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, Guangdong, China
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Liu X, Chen X, Wang C, Song J, Xu J, Gao Z, Huang Y, Suo H. Mechanisms of probiotic modulation of ovarian sex hormone production and metabolism: a review. Food Funct 2024; 15:2860-2878. [PMID: 38433710 DOI: 10.1039/d3fo04345b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Sex hormones play a pivotal role in the growth and development of the skeletal, neurological, and reproductive systems. In women, the dysregulation of sex hormones can result in various health complications such as acne, hirsutism, and irregular menstruation. One of the most prevalent diseases associated with excess androgens is polycystic ovary syndrome with a hyperandrogenic phenotype. Probiotics have shown the potential to enhance the secretion of ovarian sex hormones. However, the underlying mechanism of action remains unclear. Furthermore, comprehensive reviews detailing how probiotics modulate ovarian sex hormones are scarce. This review seeks to shed light on the potential mechanisms through which probiotics influence the production of ovarian sex hormones. The role of probiotics across various biological axes, including the gut-ovarian, gut-brain-ovarian, gut-liver-ovarian, gut-pancreas-ovarian, and gut-fat-ovarian axes, with a focus on the direct impact of probiotics on the ovaries via the gut and their effects on brain gonadotropins is discussed. It is also proposed herein that probiotics can significantly influence the onset, progression, and complications of ovarian sex hormone abnormalities. In addition, this review provides a theoretical basis for the therapeutic application of probiotics in managing sex hormone-related health conditions.
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Affiliation(s)
- Xiao Liu
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
| | - Xiaoyong Chen
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing 400715, P. R. China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, P. R. China
| | - Chen Wang
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing 400715, P. R. China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, P. R. China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing 400715, P. R. China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, P. R. China
| | - Jiahui Xu
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
| | - Zhen Gao
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
| | - Yechuan Huang
- College of Bioengineering, Jingchu University of Technology, Jingmen 448000, P. R. China.
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing 400715, P. R. China.
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing 400715, P. R. China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, P. R. China
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Gao H, Liu Q, Wang X, Li T, Li H, Li G, Tan L, Chen Y. Deciphering the role of female reproductive tract microbiome in reproductive health: a review. Front Cell Infect Microbiol 2024; 14:1351540. [PMID: 38562966 PMCID: PMC10982509 DOI: 10.3389/fcimb.2024.1351540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Relevant studies increasingly indicate that female reproductive health is confronted with substantial challenges. Emerging research has revealed that the microbiome interacts with the anatomy, histology, and immunity of the female reproductive tract, which are the cornerstone of maintaining female reproductive health and preventing adverse pregnancy outcomes. Currently, the precise mechanisms underlying their interaction and impact on physiological functions of the reproductive tract remain elusive, constituting a prominent area of investigation within the field of female reproductive tract microecology. From this new perspective, we explore the mechanisms of interactions between the microbiome and the anatomy, histology, and immunity of the female reproductive tract, factors that affect the composition of the microbiome in the female reproductive tract, as well as personalized medicine approaches in managing female reproductive tract health based on the microbiome. This study highlights the pivotal role of the female reproductive tract microbiome in maintaining reproductive health and influencing the occurrence of reproductive tract diseases. These findings support the exploration of innovative approaches for the prevention, monitoring and treatment of female reproductive tract diseases based on the microbiome.
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Affiliation(s)
- Hong Gao
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada
| | - Qiao Liu
- School of Nursing, University of South China, Hengyang, China
| | - Xiaolan Wang
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Li
- Department of Obstetrics, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Huanhuan Li
- Department of Gynaecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Genlin Li
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Lingling Tan
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yahui Chen
- School of Nursing, University of South China, Hengyang, China
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Vidhate P, Wakchoure P, Borole S, Khan AA. Lactobacillus as probiotics: opportunities and challenges for potential benefits in female reproductive health. Am J Transl Res 2024; 16:720-729. [PMID: 38586104 PMCID: PMC10994795 DOI: 10.62347/igwr5474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
The growing interest of the scientific community in the study of probiotics has gathered valuable data about its beneficial effects for multiple clinical conditions. This data also provides evidence for the functions and properties of probiotics and how they contribute to health benefits by influencing normal microbiota. Lactobacillus is an important genus which has long been utilized in the food industry and is also found as normal oral, intestinal and vaginal microbiota. Lactobacillus has shown multiple health benefits but its relative importance as a probiotic is majorly explored for gastrointestinal health. Healthy vaginal microbiota typically harbors Lactobacillus spp. providing several health benefits for female reproductive health, but there is more data required in order to compare the relative benefits with probiotic Lactobacillus added through either natural food sources or with standard probiotics supplements. The present article discusses the current status of knowledge about vaginal Lactobacillus as a probiotic and also compares the potential of probiotics from natural sources and through supplements along with recent approaches in this area.
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Affiliation(s)
- Pallavi Vidhate
- Division of Microbiology, ICMR-National AIDS Research Institute Pune, Maharashtra, India
| | - Pooja Wakchoure
- Division of Microbiology, ICMR-National AIDS Research Institute Pune, Maharashtra, India
| | - Samiksha Borole
- Division of Microbiology, ICMR-National AIDS Research Institute Pune, Maharashtra, India
| | - Abdul Arif Khan
- Division of Microbiology, ICMR-National AIDS Research Institute Pune, Maharashtra, India
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Gonçalves-Nobre JG, Matos A, Carreira M, Santos AC, Veiga LC, Ginete C, Brito M, Pires M, Pereira H, Cardoso C, Bicho M, Bicho MC. The interplay between HPV, other Sexually Transmissible Infections and genital microbiome on cervical microenvironment (MicroCervixHPV study). Front Cell Infect Microbiol 2024; 13:1251913. [PMID: 38532749 PMCID: PMC10963500 DOI: 10.3389/fcimb.2023.1251913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024] Open
Abstract
Background The importance of Cervicovaginal Microbiota in protecting against infections (such as HPV) is already well established, namely through Lactobacillus spp., as well as the mechanism through which HPV leads to Cervical Neoplasia. However, it is not possible to classify HPV as a complete carcinogen. Thus, the importance of exploring Cervicovaginal dysbiosis with the intention of deciphering this interaction with HPV, takes on greater relevance. The main objectives of this study were: 1) Comparison of the MCV composition of women with or without HPV and women with ASCUS or LSIL; 2) Characterization of cytokines present in the vaginal microenvironment; 3) Evaluation of the blood count ratios as prognostic systemic inflammatory biomarkers; 4) Correlation between MCV, HPV serotypes and cytokines. Methods This was a retrospective, observational, multicenter, cross-sectional study. CVM analysis was performed by isolation RNA and sequencing on a NGS platform. Cytokine concentrations of CVM were obtained through Multiplex platform. Statistical analysis was performed in SPSS v 26.0. An α of 0.05 was considered statistically significant. Results Highlighting the core of the study, CVM types of CST I and CST IV were found to influence the emergence of cervical lesions. Neutrophil-to-Lymphocyte ratio was found to impact the prognosis of ASCUS. Within CVM, Lactobacillus prevent the growth of other CST IV species, while the latter express symbiotic relationships with each other and show affinity for specific HPV serotypes. At last, RANTES chemokine is significantly elevated in cervicovaginal infections. Conclusion The importance of using vaginal cytokine profiles and CVM is highlighted in the hypothesis of prevention of Cervical Neoplasia development, as well as in its use as a prognostic biomarker. Taken together, these insights are one step closer to personalized medicine.
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Affiliation(s)
- J. Guilherme Gonçalves-Nobre
- Institute of Environmental Health (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Preventive Medicine and Public Health (IMPSP), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- PTSurg – Portuguese Surgical Research Collaborative, Lisbon, Portugal
- Instituto de Investigação Científica Bento da Rocha Cabral, Lisboa, Portugal
| | - Andreia Matos
- Institute of Environmental Health (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Preventive Medicine and Public Health (IMPSP), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Investigação Científica Bento da Rocha Cabral, Lisboa, Portugal
- Tumour & Microenvironment Interactions Group i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, Universidade de Porto, Porto, Portugal
| | - Mariana Carreira
- Amedes MVZ Müenchen GmbH fier Gynaekologie und Pathologie, Munich, Germany
| | - Ana Carolina Santos
- Institute of Environmental Health (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Preventive Medicine and Public Health (IMPSP), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Investigação Científica Bento da Rocha Cabral, Lisboa, Portugal
| | - Luisa Carvalho Veiga
- Health and Technology Research Center, Escola superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Catarina Ginete
- Health and Technology Research Center, Escola superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Miguel Brito
- Health and Technology Research Center, Escola superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Marina Pires
- Joaquim Chaves Saúde, Laboratório de Análises Clínicas, Carnaxide, Portugal
| | - Hermínia Pereira
- Joaquim Chaves Saúde, Laboratório de Análises Clínicas, Carnaxide, Portugal
| | - Carlos Cardoso
- Joaquim Chaves Saúde, Laboratório de Análises Clínicas, Carnaxide, Portugal
| | - Manuel Bicho
- Institute of Environmental Health (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Preventive Medicine and Public Health (IMPSP), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Investigação Científica Bento da Rocha Cabral, Lisboa, Portugal
| | - Maria Clara Bicho
- Institute of Environmental Health (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Preventive Medicine and Public Health (IMPSP), Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Investigação Científica Bento da Rocha Cabral, Lisboa, Portugal
- Joaquim Chaves Saúde, Laboratório de Análises Clínicas, Carnaxide, Portugal
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Ponciano JM, Gómez JP, Ravel J, Forney LJ. Inferring stability and persistence in the vaginal microbiome: A stochastic model of ecological dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.581600. [PMID: 38464272 PMCID: PMC10925280 DOI: 10.1101/2024.03.02.581600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The interplay of stochastic and ecological processes that govern the establishment and persistence of host-associated microbial communities is not well understood. Here we illustrate the conceptual and practical advantages of fitting stochastic population dynamics models to multi-species bacterial time series data. We show how the stability properties, fluctuation regimes and persistence probabilities of human vaginal microbial communities can be better understood by explicitly accommodating three sources of variability in ecological stochastic models of multi-species abundances: 1) stochastic biotic and abiotic forces, 2) ecological feedback and 3) sampling error. Rooting our modeling tool in stochastic population dynamics modeling theory was key to apply standardized measures of a community's reaction to environmental variation that ultimately depends on the nature and intensity of the intra-specific and inter-specific interaction strengths. Using estimates of model parameters, we developed a Risk Prediction Monitoring (RPM) tool that estimates temporal changes in persistence probabilities for any bacterial group of interest. This method mirrors approaches that are often used in conservation biology in which a measure of extinction risks is periodically updated with any change in a population or community. Additionally, we show how to use estimates of interaction strengths and persistence probabilities to formulate hypotheses regarding the molecular mechanisms and genetic composition that underpin different types of interactions. Instead of seeking a definition of "dysbiosis" we propose to translate concepts of theoretical ecology and conservation biology methods into practical approaches for the management of human-associated bacterial communities.
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Affiliation(s)
| | - Juan P. Gómez
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD
| | - Larry J. Forney
- Institute for Interdisciplinary Data Science and Department of Biological Sciences, University of Idaho, Moscow, ID
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63
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Das S, Konwar BK. Influence of connatural factors in shaping vaginal microflora and ensuring its health. Arch Gynecol Obstet 2024; 309:871-886. [PMID: 37676318 DOI: 10.1007/s00404-023-07200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Vaginal canal (VC) is exposed to the external environment affected by habitual factors like hygiene and sexual behaviour as well as physiological factors like puberty, menstrual cycle, pregnancy, child birth and menopause. Healthy VC harbours beneficial microflora supported by vaginal epithelium and cervical fluid. Connatural antimicrobial peptide (AMPs) of female reproductive tract (FRT) conjunctly with these beneficial microbes provide protection from a large number of infectious diseases. Such infections may either be caused by native microbes of the VC or transitory microbes like bacteria or virus which are not a part of VC microflora. This review highlight's the role of hormones, enzymes, innate immunological factors, epithelial cells and vaginal mucus that support beneficial microbes over infectious ones thus, helping to maintain homeostasis in VC and further protect the FRT. We also discuss the prospective use of vaginal probiotics and AMPs against pathogens which can serve as a potential cure for vaginal infections.
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Affiliation(s)
- Shreaya Das
- Department of MBBT, Tezpur University, Napaam, Assam, 784028, India.
| | - Bolin K Konwar
- Department of MBBT, Tezpur University, Napaam, Assam, 784028, India
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Wu Y, Liu P, Liao Q, Jin T, Wu Z, Guomin W, Wang H, Chu PK. Cotton Fibers with a Lactic Acid-Like Surface for Re-establishment of Protective Lactobacillus Microbiota by Selectively Inhibiting Vaginal Pathogens. Adv Healthc Mater 2024; 13:e2302736. [PMID: 38061349 DOI: 10.1002/adhm.202302736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Failure to reconstruct the Lactobacillus microbiota is the major reason for the recurrence of vaginal infection. However, most empiric therapies focus on the efficacy of pathogen elimination but do not sufficiently consider the viability of Lactobacillus. Herein, cotton fibers with a lactic acid-like surface (LC) are fabricated by NaIO4 oxidation and L-isoserine grafting. The lactic acid analog chain ends and imine structure of LC can penetrate cell walls to cause protein cleavage in Escherichia coli and Candida albicans and inhibit vaginal pathogens. Meanwhile, the viability of Lactobacillus acidophilus is unaffected by the LC treatment, thus revealing a selective way to suppress pathogens as well as provide a positive route to re-establish protective microbiota in the vaginal tract. Moreover, LC has excellent properties such as good biosafety, antiadhesion, water absorption, and weight retention. The strategy proposed here not only is practical, but also provides insights into the treatment of vaginal infections.
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Affiliation(s)
- Yuzheng Wu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Pei Liu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Qing Liao
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- School of Nuclear Science and Technology and CAS Key Laboratory of Geospace Environment, University of Science and Technology of China, Hefei, 230026, China
| | - Tao Jin
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- School of Nuclear Science and Technology and CAS Key Laboratory of Geospace Environment, University of Science and Technology of China, Hefei, 230026, China
| | - Zhengwei Wu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Wang Guomin
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Huaiyu Wang
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Paul K Chu
- Department of Physics, Department of Materials Science and Engineering, and Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
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Marquis KA, Merenstein C, Bushman FD. 2-Hydroxyisovalerate Is Produced During Bacterial Vaginosis and Boosts HIV Infection in Resting T Cells. AIDS Res Hum Retroviruses 2024; 40:158-170. [PMID: 37548528 PMCID: PMC10924192 DOI: 10.1089/aid.2022.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection and the ensuing acquired immunodeficiency syndrome (AIDS) disproportionally affect young women, yet understanding of the factors promoting heterosexual transmission in the female genital tract is limited. Colonization with highly diverse, Lactobacillus-deficient communities (HDCs) increases a woman's risk of acquiring HIV-1 compared with colonization with Lactobacillus-dominated low diversity communities (LDCs). The polymicrobial nature of these communities has made it challenging to elucidate the microbial mechanisms responsible for modulating HIV susceptibility. Here, we analyzed conserved changes in small-molecule metabolites present in the cervicovaginal lavage fluid collected from women colonized with HDCs and LDCs with the goal of identifying possible chemicals influencing HIV infection. As in previous studies, we found that the catabolite of the branched-chain amino acid valine, 2-hydroxyisovalerate (2-HV), was a consistent component of dysbiotic HDC microbiota. Effects of 2-HV on HIV infection were assessed. In experimental infections with HIV, treatment with 2-HV increased infections of resting CD4+ T cells. To understand bacterial production of 2-HV in more detail, we cultured purified HDC and LDC bacteria and used mass spectrometry to identify two HDC bacteria that synthesize high levels of 2-HV. In contrast, protective vaginal Lactobacilli did not produce high levels of 2-HV. A genomic analysis of genes encoding 2-HV synthetic pathways showed a correlation between high-level production of 2-HV and pathways for synthesis of the immediate precursor 2-ketoisovalerate. Thus, 2-HV is a candidate mediator linking vaginal microbiome structure and heterosexual HIV transmission in women.
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Affiliation(s)
- Kaitlin A. Marquis
- Chan Zuckerberg Biohub, University of California San Francisco, San Francisco, California, USA
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Cocomazzi G, Del Pup L, Contu V, Maggio G, Parmegiani L, Ciampaglia W, De Ruvo D, Faioli R, Maglione A, Baldini GM, Baldini D, Pazienza V. Gynecological Cancers and Microbiota Dynamics: Insights into Pathogenesis and Therapy. Int J Mol Sci 2024; 25:2237. [PMID: 38396914 PMCID: PMC10889201 DOI: 10.3390/ijms25042237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, the relationship between the microbiota and various aspects of health has become a focal point of scientific investigation. Although the most studied microbiota concern the gastrointestinal tract, recently, the interest has also been extended to other body districts. Female genital tract dysbiosis and its possible impact on pathologies such as endometriosis, polycystic ovary syndrome (PCOS), pelvic inflammatory disease (PID), and gynecological cancers have been unveiled. The incursion of pathogenic microbes alters the ecological equilibrium of the vagina, triggering inflammation and compromising immune defense, potentially fostering an environment conducive to cancer development. The most common types of gynecological cancer include cervical, endometrial, and ovarian cancer, which occur in women of any age but especially in postmenopausal women. Several studies highlighted that a low presence of lactobacilli at the vaginal level, and consequently, in related areas (such as the endometrium and ovary), correlates with a higher risk of gynecological pathology and likely contributes to increased incidence and worse prognosis of gynecological cancers. The complex interplay between microbial communities and the development, progression, and treatment of gynecologic malignancies is a burgeoning field not yet fully understood. The intricate crosstalk between the gut microbiota and systemic inflammation introduces a new dimension to our understanding of gynecologic cancers. The objective of this review is to focus attention on the association between vaginal microbiota and gynecological malignancies and provide detailed knowledge for future diagnostic and therapeutic strategies.
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Affiliation(s)
- Giovanna Cocomazzi
- Division of Gastroenterology, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy;
| | - Lino Del Pup
- Gynecological Endocrinology and Fertility, University Sanitary Agency Friuli Central (ASUFC), Via Pozzuolo, 330, 33100 Udine, FVG, Italy;
| | - Viviana Contu
- Integrative Medicine Unit, Humanitas Gradenigo, Corso Regina Margherita 8/10, 10153 Torino, FC, Italy;
| | - Gabriele Maggio
- Pia Fondazione Cardinale Giovanni Panico, Via S. Pio X, 4, 73039 Tricase, LE, Italy;
| | - Lodovico Parmegiani
- Next Fertility GynePro, NextClinics International Via T. Cremona 8, 40137 Bologna, RE, Italy; (L.P.); (W.C.)
| | - Walter Ciampaglia
- Next Fertility GynePro, NextClinics International Via T. Cremona 8, 40137 Bologna, RE, Italy; (L.P.); (W.C.)
| | - Daniele De Ruvo
- Gynaecology, Obstetrics and Reproductive Medicine Affidea Promea, Via Menabrea 14, 10126 Torino, TO, Italy;
| | - Raffaele Faioli
- Gynecology and Obstetrics, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, FG, Italy; (R.F.); (A.M.)
| | - Annamaria Maglione
- Gynecology and Obstetrics, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, FG, Italy; (R.F.); (A.M.)
| | - Giorgio Maria Baldini
- IVF Center, Momò Fertilife, 76011 Bisceglie Via Cala dell’Arciprete, 76011 Bisceglie, BT, Italy; (G.M.B.); (D.B.)
| | - Domenico Baldini
- IVF Center, Momò Fertilife, 76011 Bisceglie Via Cala dell’Arciprete, 76011 Bisceglie, BT, Italy; (G.M.B.); (D.B.)
| | - Valerio Pazienza
- Division of Gastroenterology, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy;
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Matějková T, Dodoková A, Kreisinger J, Stopka P, Stopková R. Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice. Microbiol Spectr 2024; 12:e0203723. [PMID: 38171017 PMCID: PMC10846187 DOI: 10.1128/spectrum.02037-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.
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Affiliation(s)
- Tereza Matějková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Alica Dodoková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Romana Stopková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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Long C, Deng J, Nguyen J, Liu YY, Alm EJ, Solé R, Saavedra S. Structured community transitions explain the switching capacity of microbial systems. Proc Natl Acad Sci U S A 2024; 121:e2312521121. [PMID: 38285940 PMCID: PMC10861894 DOI: 10.1073/pnas.2312521121] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors, it remains unclear the extent to which internal community dynamics affect the switching capacity of microbial systems. Here, we integrate ecological theory and empirical data to demonstrate that structured community transitions increase the dependency of future communities on the current taxon membership, enhancing the switching capacity of microbial systems. Following a structuralist approach, we propose that each community is feasible within a unique domain in environmental parameter space. Then, structured transitions between any two communities can happen with probability proportional to the size of their feasibility domains and inversely proportional to their distance in environmental parameter space-which can be treated as a special case of the gravity model. We detect two broad classes of systems with structured transitions: one class where switching capacity is high across a wide range of community sizes and another class where switching capacity is high only inside a narrow size range. We corroborate our theory using temporal data of gut and oral microbiota (belonging to class 1) as well as vaginal and ocean microbiota (belonging to class 2). These results reveal that the topology of feasibility domains in environmental parameter space is a relevant property to understand the changing behavior of microbial systems. This knowledge can be potentially used to understand the relevant community size at which internal dynamics can be operating in microbial systems.
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Affiliation(s)
- Chengyi Long
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jie Deng
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jen Nguyen
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL61801
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Ricard Solé
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona08003, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona08010, Spain
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona08003, Spain
- Santa Fe Institute, Santa Fe, NM87501
| | - Serguei Saavedra
- Institució Catalana de Recerca i Estudis Avançats, Barcelona08010, Spain
- Santa Fe Institute, Santa Fe, NM87501
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Muzny CA, Elnaggar JH, Sousa LGV, Lima Â, Aaron KJ, Eastlund IC, Graves KJ, Dong C, Van Gerwen OT, Luo M, Tamhane A, Long D, Cerca N, Taylor CM. Microbial interactions among Gardnerella, Prevotella and Fannyhessea prior to incident bacterial vaginosis: protocol for a prospective, observational study. BMJ Open 2024; 14:e083516. [PMID: 38316599 PMCID: PMC10859992 DOI: 10.1136/bmjopen-2023-083516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
INTRODUCTION The aetiology of bacterial vaginosis (BV), a biofilm-associated vaginal infection, remains unknown. Epidemiologic data suggest that it is sexually transmitted. BV is characterised by loss of lactic acid-producing lactobacilli and an increase in facultative and strict anaerobic bacteria. Gardnerella spp are present in 95%-100% of cases; Gardnerella vaginalis has been found to be more virulent than other BV-associated bacteria (BVAB) in vitro. However, G. vaginalis is found in women with normal vaginal microbiota and colonisation is not sufficient for BV development. We hypothesise that Gardnerella spp initiate BV biofilm formation, but incident BV (iBV) requires incorporation of other key BVAB (ie, Prevotella bivia, Fannyhessea vaginae) into the biofilm that alter the transcriptome of the polymicrobial consortium. This study will investigate the sequence of microbiologic events preceding iBV. METHODS AND ANALYSIS This study will enrol 150 women aged 18-45 years with normal vaginal microbiota and no sexually transmitted infections at a sexual health research clinic in Birmingham, Alabama. Women will self-collect twice daily vaginal specimens up to 60 days. A combination of 16S rRNA gene sequencing, qPCR for Gardnerella spp, P. bivia and F. vaginae, and broad range 16S rRNA gene qPCR will be performed on twice daily vaginal specimens from women with iBV (Nugent score 7-10 on at least 2 consecutive days) and controls (with comparable age, race, contraceptive method and menstrual cycle days) maintaining normal vaginal microbiota to investigate changes in the vaginal microbiota over time for women with iBV. Participants will complete daily diaries on multiple factors including sexual activity. ETHICS AND DISSEMINATION This protocol is approved by the University of Alabama at Birmingham Institutional Review Board (IRB-300004547) and written informed consent will be obtained from all participants. Findings will be presented at scientific conferences and published in peer-reviewed journals as well as disseminated to providers and patients in communities of interest.
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Affiliation(s)
- Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jacob H Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Lúcia G V Sousa
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Ângela Lima
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Kristal J Aaron
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Isaac C Eastlund
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Keonte J Graves
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chaoling Dong
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olivia T Van Gerwen
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Microbial Genomics Resource Group, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Ashutosh Tamhane
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Dustin Long
- Department of Biostatistics, University of Alabama at Birmingham, School of Public Health, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
- LABBELS-Associate Laboratory, Braga, Guimarães, Portugal
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
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Robbins SJ, Brown SE, Stennett CA, Tuddenham S, Johnston ED, Wnorowski AM, Ravel J, He X, Mark KS, Brotman RM. Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound. PLoS One 2024; 19:e0296346. [PMID: 38315688 PMCID: PMC10843103 DOI: 10.1371/journal.pone.0296346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/11/2023] [Indexed: 02/07/2024] Open
Abstract
Bacterial vaginosis, characterized in part by low levels of vaginal Lactobacillus species, has been associated with pro-inflammatory cytokines which could fuel uterine fibroid development. However, prior work on the associations between uterine fibroids and vaginal bacteria is sparse. Most studies have focused on assessment of individual taxa in a single sample. To address research gaps, we sought to compare short, longitudinal profiles of the vaginal microbiota in uterine fibroid cases versus controls with assessment for hormonal contraceptives (HCs), a possible confounder associated with both protection from fibroid development and increases in Lactobacillus-dominated vaginal microbiota. This is a secondary analysis of 83 reproductive-age cisgender women who presented for transvaginal ultrasound (TVUS) and self-collected mid-vaginal swabs daily for 1-2 weeks before TVUS (Range: 5-16 days, n = 697 samples). Sonography reports detailed uterine fibroid characteristics (N = 21 cases). Vaginal microbiota was assessed by 16S rRNA gene amplicon sequencing and longitudinal microbiota profiles were categorized by hierarchical clustering. We compared longitudinal profiles of the vaginal microbiota among fibroid cases and controls with exact logistic regression. Common indications for TVUS included pelvic mass (34%) and pelvic pain (39%). Fibroid cases tended to be older and report Black race. Cases less often reported HCs versus controls (32% vs. 58%). A larger proportion of cases had low-Lactobacillus longitudinal profiles (48%) than controls (34%). In unadjusted analysis, L. iners-dominated and low-Lactobacillus profiles had higher odds of fibroid case status compared to other Lactobacillus-dominated profiles, however these results were not statistically significant. No association between vaginal microbiota and fibroids was observed after adjusting for race, HC and menstruation. Results were consistent when number of fibroids were considered. There was not a statistically significant association between longitudinal profiles of vaginal microbiota and uterine fibroids after adjustment for common confounders; however, the study was limited by small sample size.
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Affiliation(s)
- Sarah J. Robbins
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Sarah E. Brown
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Christina A. Stennett
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Susan Tuddenham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth D. Johnston
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amelia M. Wnorowski
- Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Xin He
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, Maryland, United States of America
| | - Katrina S. Mark
- Department of Obstetrics and Gynecology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca M. Brotman
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
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Tian Z, Zhao M, Sui X, Li X, Qin L, Chen ZJ, Zhao S, Zhao H. Associations between vaginal microbiota and endometrial polypoid lesions in women of reproductive age: a cross-sectional study. Reprod Biomed Online 2024; 48:103602. [PMID: 38101145 DOI: 10.1016/j.rbmo.2023.103602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 12/17/2023]
Abstract
RESEARCH QUESTION What are the different characteristics of vaginal microbial composition between patients with endometrial polypoid lesions and controls? DESIGN This cohort study compared the pre-operative microbial compositions of vaginal samples in a cohort of 703 women with endometrial polypoid lesions [293 and 410 women diagnosed and not diagnosed with polyps pathologically (polyps group and not-polyps group, respectively] and 703 women in the control group. Bacterial abundance, diversity, differential taxa and microbial network structure were assessed using 16S rRNA gene sequencing. Predictive algorithms were used to determine the functional pathways of vaginal microbiota within the cohort. RESULTS The control group exhibited higher relative abundance of Lactobacillus crispatus in comparison with the polypoid lesions group (P = 0.0427). Beta diversity of vaginal microbiota differed significantly between the groups (P < 0.05). Comparing the polyps group with the not-polyps group, Leptotrichia spp. and Cutibacterium spp. were more abundant in the polyps group, and Fannyhessea spp., Acinetobacter spp. and Achromobacter spp. were more abundant in the not-polyps group. The control group exhibited higher abundance of Bifidobacterium spp., Achromobacter spp. and Escherichia/Shigella spp. (false discovery rate < 0.05). Furthermore, the polyps group and not-polyps group displayed more complex co-occurrence networks compared with the control group. CONCLUSIONS The results of this study provide compelling evidence supporting associations between vaginal microbiota and endometrial polypoid lesions, highlighting the potential relationship between a well-balanced vaginal microbial ecosystem and a healthy intrauterine environment.
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Affiliation(s)
- Zhaomei Tian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Maoning Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xinlei Sui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xiao Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Lang Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China; Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shigang Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Han Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.
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Ziv E, Keller N, Erlich T. Vaginal microflora following the use of a disposable home-use vaginal device and a commercially available ring pessary for pelvic organ prolapse management: a randomized controlled trial. Arch Gynecol Obstet 2024; 309:571-579. [PMID: 37882871 PMCID: PMC10808192 DOI: 10.1007/s00404-023-07260-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023]
Abstract
PURPOSE To investigate whether ProVate, a novel, disposable, self-inserted vaginal device for pelvic organ prolapse management, clinically affects the vaginal microflora, as compared with a commercially available ring pessary, to assess its microbiological safety. METHODS This interventional, prospective, multi-center, open-label, randomized, controlled, statistically powered (noninferiority), home-use, crossover study was conducted at seven sites. Participants were randomized into either group A (using ProVate and then a new reusable commercially available ring pessary [control]) or B (using control device and then ProVate) with a 1:1 ratio. Noninferiority of ProVate over the control was evaluated for the primary endpoint, which was based on meeting one of the failure criteria: significant change in Lactobacillus spp., Gardnerella vaginalis, Candida morphotypes, or Staphylococcus aureus levels compared to the baseline (significant change: Nugent score ≥ 7 or > 1 scale unit increase in S. aureus or Candida morphotype), bothersome vaginal infection symptoms, or symptoms requiring treatment for infection. RESULTS The study included 58 participants (mean age: 64.5 years, 91.4% postmenopausal). There were no significant microfloral changes in terms of the four microorganisms mentioned above, the rate of Nugent score ≥ 7 after use was low and comparable between the two devices, and the rate of patients with a > 1 unit-scale change (increase or decrease) from the baseline to the end-of-use phase in any studied microorganism was comparable between the devices. The failure rate was 15.5% for ProVate and 15.5% for control while using 383 ProVate devices over 1647 days or one control device throughout the study. Two patients had bothersome vaginal complaints and one had overt vaginal infection in the control group, but no such cases were observed in the ProVate group. CONCLUSION The primary endpoint of possible vaginal microbial changes, bothersome vaginal symptoms, or treatment-requiring vaginal complaints while using ProVate was successfully met. Our findings show that the vaginal microflora is comparable when using either ProVate or commercially available ring pessary (control) with a relatively low rate of vaginal infections. Trial registration details: ClinicalTrials.gov; URL: https://www. CLINICALTRIALS gov/ct2/show/NCT03345121?term=NCT03345121&draw=2&rank=1 ; No. NCT03345121; Registration date, November 17, 2017; initial enrollment started on August 20, 2017.
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Affiliation(s)
- Elan Ziv
- ConTIPI Medical Ltd, 2 Alon Ha' Tavor St, Southern Industrial Park, 3088900, Caesarea, Israel.
| | - Nathan Keller
- Ariel University, Ariel, Israel
- Sheba Medical Center, Ramat Gan, Israel
| | - Tsvia Erlich
- ConTIPI Medical Ltd, 2 Alon Ha' Tavor St, Southern Industrial Park, 3088900, Caesarea, Israel
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73
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Asher EE, Bashan A. Model-free prediction of microbiome compositions. MICROBIOME 2024; 12:17. [PMID: 38303006 PMCID: PMC10832217 DOI: 10.1186/s40168-023-01721-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 11/15/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The recent recognition of the importance of the microbiome to the host's health and well-being has yielded efforts to develop therapies that aim to shift the microbiome from a disease-associated state to a healthier one. Direct manipulation techniques of the species' assemblage are currently available, e.g., using probiotics or narrow-spectrum antibiotics to introduce or eliminate specific taxa. However, predicting the species' abundances at the new state remains a challenge, mainly due to the difficulties of deciphering the delicate underlying network of ecological interactions or constructing a predictive model for such complex ecosystems. RESULTS Here, we propose a model-free method to predict the species' abundances at the new steady state based on their presence/absence configuration by utilizing a multi-dimensional k-nearest-neighbors (kNN) regression algorithm. By analyzing data from numeric simulations of ecological dynamics, we show that our predictions, which consider the presence/absence of all species holistically, outperform both the null model that uses the statistics of each species independently and a predictive neural network model. We analyze real metagenomic data of human-associated microbial communities and find that by relying on a small number of "neighboring" samples, i.e., samples with similar species assemblage, the kNN predicts the species abundance better than the whole-cohort average. By studying both real metagenomic and simulated data, we show that the predictability of our method is tightly related to the dissimilarity-overlap relationship of the training data. CONCLUSIONS Our results demonstrate how model-free methods can prove useful in predicting microbial communities and may facilitate the development of microbial-based therapies. Video Abstract.
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Affiliation(s)
- Eitan E Asher
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel
| | - Amir Bashan
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel.
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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75
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Cao W, Fu X, Zhou J, Qi Q, Ye F, Li L, Wang L. The effect of the female genital tract and gut microbiome on reproductive dysfunction. Biosci Trends 2024; 17:458-474. [PMID: 38104979 DOI: 10.5582/bst.2023.01133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Microorganisms are ubiquitous in the human body; they are present in various areas including the gut, mouth, skin, respiratory tract, and reproductive tract. The interaction between the microbiome and reproductive health has become an increasingly compelling area of study. Disruption of the female genital tract microbiome can significantly impact the metabolism of amino acids, carbohydrates, and lipids, increasing susceptibility to reproductive tract diseases such as vaginitis, chronic endometritis, endometrial polyps, endometriosis, and polycystic ovary syndrome. The gut microbiome, considered an endocrine organ, plays a crucial role in the reproductive endocrine system by interacting with hormones like estrogen and androgens. Imbalances in the gut microbiome composition can lead to various diseases and conditions, including polycystic ovary syndrome, endometriosis, and cancer, although research on their mechanisms remains limited. This review highlights the latest advancements in understanding the female genital tract and gut microbiomes in gynecological diseases. It also explores the potential of microbial communities in the treatment of reproductive diseases. Future research should focus on identifying the molecular mechanisms underlying the association between the microbiome and reproductive diseases to develop new and effective strategies for disease prevention, diagnosis, and treatment related to female reproductive organs.
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Affiliation(s)
- Wenli Cao
- Reproductive Medicine Center, Zhoushan Maternal and Child Health Care Hospital, Zhoushan, Zhejiang, China
| | - Xiayan Fu
- Reproductive Medicine Center, Zhoushan Maternal and Child Health Care Hospital, Zhoushan, Zhejiang, China
| | - Jing Zhou
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Qing Qi
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Feijun Ye
- Reproductive Medicine Center, Zhoushan Maternal and Child Health Care Hospital, Zhoushan, Zhejiang, China
| | - Lisha Li
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Ling Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
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Zhang Z, Ma Q, Zhang L, Ma L, Wang D, Yang Y, Jia P, Wu Y, Wang F. Human papillomavirus and cervical cancer in the microbial world: exploring the vaginal microecology. Front Cell Infect Microbiol 2024; 14:1325500. [PMID: 38333037 PMCID: PMC10850380 DOI: 10.3389/fcimb.2024.1325500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
The vaginal microbiota plays a crucial role in female reproductive health and is considered a biomarker for predicting disease outcomes and personalized testing. However, its relationship with human papillomavirus (HPV) infection and cervical cancer is not yet clear. Therefore, this article provides a review of the association between the vaginal microbiota, HPV infection, and cervical cancer. We discuss the composition of the vaginal microbiota, its dysbiosis, and its relationship with HPV infection, as well as potential mechanisms in the development of cervical cancer. In addition, we assess the feasibility of treatment strategies such as probiotics and vaginal microbiota transplantation to modulate the vaginal microbiota for the prevention and treatment of diseases related to HPV infection and cervical cancer. In the future, extensive replication studies are still needed to gain a deeper understanding of the complex relationship between the vaginal microbiota, HPV infection, and cervical cancer, and to clarify the role of the vaginal microbiota as a potential biomarker for predicting disease outcomes, thus providing a theoretical basis for personalized testing.
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Affiliation(s)
- Zhemei Zhang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Qingmei Ma
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Lei Zhang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Li Ma
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Danni Wang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Yongqing Yang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Pengxia Jia
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Yang Wu
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
| | - Fang Wang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Gansu Provincial Clinical Research Center for Laboratory Medicine, Lanzhou, Gansu, China
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Muraoka A, Yokoi A, Kajiyama H. Emerging bacterial factors for understanding pathogenesis of endometriosis. iScience 2024; 27:108739. [PMID: 38269103 PMCID: PMC10805679 DOI: 10.1016/j.isci.2023.108739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
The pathogenesis of endometriosis is a complex process, and recent research has introduced novel hypotheses in this field. This review summarizes recent studies on the pathogenesis of endometriosis. We focused on several classical hypotheses, as well as their interactions with the microenvironment of hormonal dependence and immunosuppression. Furthermore, we highlighted the emergence of bacterial factors associated with endometriosis. Recent advances in next-generation sequencing (NGS) have revealed the presence and detailed distribution of these bacteria as well as the involvement of specific bacteria in pathogenesis. These factors alter the microenvironment in the early stages of endometriosis development, leading to lesion formation. Understanding the mechanisms underlying the early development of endometriosis from a new perspective would be helpful for the development of novel therapeutic agents for endometriosis.
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Affiliation(s)
- Ayako Muraoka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
- Nagoya University Institute for Advanced Research, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency (JST), FOREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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78
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Samarra A, Flores E, Bernabeu M, Cabrera-Rubio R, Bäuerl C, Selma-Royo M, Collado MC. Shaping Microbiota During the First 1000 Days of Life. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1449:1-28. [PMID: 39060728 DOI: 10.1007/978-3-031-58572-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning human reproductive microbiota, and also, the microbial colonization during early life, focusing on the potential impact on infant development and health outcomes. Furthermore, we conclude that some dietary strategies including specific probiotics and other-biotics could become potentially valuable tools to modulate the maternal-neonatal microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Eduard Flores
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Christine Bäuerl
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
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Liu Z, Liu J, Geng J, Wu E, Zhu J, Cong B, Wu R, Sun H. Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study. Forensic Sci Int Genet 2024; 68:102978. [PMID: 37995518 DOI: 10.1016/j.fsigen.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
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Kim DY, Lee SY, Lee JY, Whon TW, Lee JY, Jeon CO, Bae JW. Gut microbiome therapy: fecal microbiota transplantation vs live biotherapeutic products. Gut Microbes 2024; 16:2412376. [PMID: 39377231 PMCID: PMC11469438 DOI: 10.1080/19490976.2024.2412376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 08/28/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024] Open
Abstract
The human intestine hosts a complex ecosystem of various microorganisms, collectively known as the gut microbiome, which significantly impacts human health. Disruptions in the gut microbiome are linked to various disorders, including gastrointestinal diseases, such as Clostridioides difficile infection and inflammatory bowel disease, as well as metabolic, neurological, oncologic conditions. Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as prospective therapeutic procedures to restore microbial and metabolic balance in the gut. This review assesses the latest advancements, challenges, and therapeutic efficacy of FMT and LBPs, highlighting the need for standardization, safety, and long-term evaluation to optimize their clinical application.
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Affiliation(s)
- Do-Yeon Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Korea
| | - So-Yeon Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Korea
| | - Jae-Yun Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Korea
| | - Tae Woong Whon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
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Tsamir-Rimon M, Borenstein E. A manifold-based framework for studying the dynamics of the vaginal microbiome. NPJ Biofilms Microbiomes 2023; 9:102. [PMID: 38102172 PMCID: PMC10724123 DOI: 10.1038/s41522-023-00471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
The vaginal microbiome plays a crucial role in our health. The composition of this community can be classified into five community state types (CSTs), four of which are primarily consisted of Lactobacillus species and considered healthy, while the fifth features non-Lactobacillus populations and signifies a disease state termed Bacterial vaginosis (BV), which is associated with various symptoms and increased susceptibility to diseases. Importantly, however, the exact mechanisms and dynamics underlying BV development are not yet fully understood, including specifically possible routes from a healthy to a BV state. To address this gap, this study set out to characterize the progression from healthy- to BV-associated compositions by analyzing 8026 vaginal samples and using a manifold-detection framework. This approach, inspired by single-cell analysis, aims to identify low-dimensional trajectories in the high-dimensional composition space. It further orders samples along these trajectories and assigns a score (pseudo-time) to each analyzed or new sample based on its proximity to the BV state. Our results reveal distinct routes of progression between healthy and BV states for each CST, with pseudo-time scores correlating with community diversity and quantifying the health state of each sample. Several BV indicators can also be successfully predicted based on pseudo-time scores, and key taxa involved in BV development can be identified using this approach. Taken together, these findings demonstrate how manifold detection can be used to successfully characterize the progression from healthy Lactobacillus-dominant populations to BV and to accurately quantify the health condition of new samples along the route of BV development.
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Affiliation(s)
| | - Elhanan Borenstein
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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82
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Cheddadi R, Yeramilli V, Martin C. From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates. Metabolites 2023; 13:1184. [PMID: 38132866 PMCID: PMC10745069 DOI: 10.3390/metabo13121184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome's onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes.
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Affiliation(s)
- Riadh Cheddadi
- Department of Surgery, Division of Pediatric Surgery, Washington University School of Medicine, Saint Louis, MO 63110, USA (C.M.)
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83
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Du L, Dong X, Song J, Lei T, Liu X, Lan Y, Liu X, Wang J, Yue B, He M, Fan Z, Guo T. Temporal and spatial differences in the vaginal microbiome of Chinese healthy women. PeerJ 2023; 11:e16438. [PMID: 38054020 PMCID: PMC10695111 DOI: 10.7717/peerj.16438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023] Open
Abstract
Background Up the reproductive tract, there are large differences in the composition of vaginal microbes. Throughout the menstrual cycle, the structure of the vaginal microbiome shifts. Few studies have examined both in combination. Our study was designed to explore trends in the microbiome of different parts of the vagina in healthy women over the menstrual cycle. Methods We performed metagenomic sequencing to characterize the microbiome differences between the cervical orifice and mid-vagina throughout the menstrual cycle. Results Our results showed the vaginal microbiome of healthy women in the cervical orifice and the mid-vagina was similar during the periovulatory and luteal phases, with Lactobacillus being the dominant bacteria. In the follicular phase, Acinetobacter was detected in the cervical orifice. From the follicular phase to the luteal phase, the community state types (all five community status types were defined as CSTs) in samples No. 10 and No. 11 changed from CST III to CST I. In addition, the composition of the vaginal microbiome in healthy women from different regions of China was significantly different. We also detected viruses including Human alphaherpesvirus 1 (HSV-1) during periovulatory phase. Conclusion This study is valuable for understanding whether the microbial composition of the vagina is consistent in different parts of the menstrual cycle.
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Affiliation(s)
- Limin Du
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Xue Dong
- Ambulatory Surgery Department, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jiarong Song
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Tingting Lei
- Suining Municipal Hospital of Traditional Chinese Medicine, Suining, Sichuan, China
| | - Xianming Liu
- Mianyang Tumor Hospital, Sichuan Province, Mianyang, China
| | - Yue Lan
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Xu Liu
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Jiao Wang
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Bisong Yue
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Zhenxin Fan
- Sichuan University, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Chengdu, China
| | - Tao Guo
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China
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84
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Hong X, Qin P, Gao L, Huang L, Shi Y, Peng D, Wang B. Change of the vaginal microbiome with oral contraceptive therapy in women with polycystic ovary syndrome: a 6-month longitudinal cohort study. BMC Med 2023; 21:478. [PMID: 38041079 PMCID: PMC10693170 DOI: 10.1186/s12916-023-03196-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The association between the vaginal microbiome and polycystic ovary syndrome (PCOS) is reported, but the longitudinal changes in the vaginal microbiome that accompany oral contraceptive therapy have not been described. METHODS This cohort study included 50 PCOS patients who wanted to make their menstrual periods more regular and accepted only oral contraceptive therapy and lifestyle coaching, then they were successfully followed up for 6 months. Venous blood was collected, and follicle-stimulating hormone (FSH), luteinizing hormone (LH), total testosterone (T), anti-Müllerian hormone (AMH), and estradiol (E2) were assayed at baseline and at months 3 and 6. Vaginal swabs were collected at baseline and at months 3 and 6. 16S rRNA genes were sequenced to identify the microbiota structure. Latent class trajectory models were used to explore the trajectory of the changes in Lactobacillus abundance. RESULTS At 3 months, all patients reported regular periods, and the improvement lasted until 6 months. The body mass index and waist-to-hip ratio decreased with treatment (P < 0.01), and the AMH and T levels showed downward trends. We did not find a statistically significant relationship between hormone levels at the previous time point and the vaginal microbiota at subsequent time points (P > 0.05). The relative abundance of Lactobacillus increased with treatment, and trajectory analysis revealed five classes of Lactobacillus changes. Class 1, stable high level, accounted for 26%; class 2, decrease followed by increase, accounted for 18%; class 3, stable low level, accounted for 10%; class 4, increase, accounted for 20%; class 5, increase followed by decrease, accounted for 26%. Logistic models showed that compared to class 1, a higher baseline T level was associated with a reduced risk of class 2 change (odds ratio (OR) = 0.03, 95% confidence interval (CI):0.01-0.52) and class 4 change (OR = 0.10, 95% CI:0.01-0.93). CONCLUSIONS The abundance of Lactobacilli increased with PCOS treatment; however, the trajectory was inconsistent for each individual. Evidence of the effects of female hormone levels on the vaginal microbiome is insufficient.
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Affiliation(s)
- Xiang Hong
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Pengfei Qin
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, Jiangsu, China
| | - Liting Gao
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Lingling Huang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Yong Shi
- Department of Obstetrics and Gynecology, Zhong Da Hospital, Southeast University, Nanjing, Jiangsu, China
| | - Danhong Peng
- Department of Obstetrics and Gynecology, Zhong Da Hospital, Southeast University, Nanjing, Jiangsu, China
| | - Bei Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, China.
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Boahen A, Chew SY, Neela VK, Than LTL. Limosilactobacillus reuteri 29A Cell-Free Supernatant Antibiofilm and Antagonistic Effects in Murine Model of Vulvovaginal Candidiasis. Probiotics Antimicrob Proteins 2023; 15:1681-1699. [PMID: 36881331 DOI: 10.1007/s12602-023-10050-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 03/08/2023]
Abstract
Vaginal dysbiosis advocates burgeoning of devious human vaginal pathobionts like Candida species that possess multiple virulence properties and metabolic flexibility to cause infections. Inevitably, antifungal resistance may emerge due to their innate nature (e.g., biofilm formation), which assists in their virulence as well as the formation of persister cells after dispersal. In consequence, the phenomenon of biofilm involvement in vulvovaginal candidiasis (VVC) and its recurrence is becoming paramount. Lactic acid bacteria and their derivatives have proven to be hostile to Candida species. Here, we throw more light on the potency of the derivatives, i.e., cell-free supernatant (CFS) produced by an indigenously isolated vaginal Lactobacillus strain, Limosilactobacillus reuteri 29A. In the present study, we investigated the antibiofilm and antagonistic effects of L. reuteri 29A CFS, against biofilms of Candida species and in murine model of vulvovaginal candidiasis. In our in vitro biofilm study, the CFS disrupted and inhibited preformed biofilms of C. albicans and C. glabrata. Scanning electron microscopy displayed the destruction of preformed biofilms and impediment of C. albicans morphogenesis by the CFS. Gas chromatography-mass spectrometry analysis showed multiple key compounds that may act singly or synergistically. In vivo, the CFS showed no collateral damage to uninfected mice; the integrity of infected vaginal tissues was restored by the administration of the CFS as seen from the cytological, histopathological, and electron microscopical analyses. The results of this study document the potential use of CFS as an adjuvant or prophylactic option in addressing vaginal fungal infections.
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Affiliation(s)
- Angela Boahen
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Shu Yih Chew
- Department of Microbiology and Immunology, Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Selangor, 57000, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia.
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, 43400, Malaysia.
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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: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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.
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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.
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Pagan L, Huisman BW, van der Wurff M, Naafs RGC, Schuren FHJ, Sanders IMJG, Smits WK, Zwittink RD, Burggraaf J, Rissmann R, Piek JMJ, Henderickx JGE, van Poelgeest MIE. The vulvar microbiome in lichen sclerosus and high-grade intraepithelial lesions. Front Microbiol 2023; 14:1264768. [PMID: 38094635 PMCID: PMC10716477 DOI: 10.3389/fmicb.2023.1264768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 01/25/2024] Open
Abstract
Background The role of the vulvar microbiome in the development of (pre)malignant vulvar disease is scarcely investigated. The aim of this exploratory study was to analyze vulvar microbiome composition in lichen sclerosus (LS) and vulvar high-grade squamous intraepithelial lesions (HSIL) compared to healthy controls. Methods Women with vulvar lichen sclerosus (n = 10), HSIL (n = 5) and healthy controls (n = 10) were included. Swabs were collected from the vulva, vagina and anal region for microbiome characterization by metagenomic shotgun sequencing. Both lesional and non-lesional sites were examined. Biophysical assessments included trans-epidermal water loss for evaluation of the vulvar skin barrier function and vulvar and vaginal pH measurements. Results Healthy vulvar skin resembled vaginal, anal and skin-like microbiome composition, including the genera Prevotella, Lactobacillus, Gardnerella, Staphylococcus, Cutibacterium, and Corynebacterium. Significant differences were observed in diversity between vulvar skin of healthy controls and LS patients. Compared to the healthy vulvar skin, vulvar microbiome composition of both LS and vulvar HSIL patients was characterized by significantly higher proportions of, respectively, Papillomaviridae (p = 0.045) and Alphapapillomavirus (p = 0.002). In contrast, the Prevotella genus (p = 0.031) and Bacteroidales orders (p = 0.038) were significantly less abundant in LS, as was the Actinobacteria class (p = 0.040) in vulvar HSIL. While bacteria and viruses were most abundant, fungal and archaeal taxa were scarcely observed. Trans-epidermal water loss was higher in vulvar HSIL compared to healthy vulvar skin (p = 0.043). Conclusion This study is the first to examine the vulvar microbiome through metagenomic shotgun sequencing in LS and HSIL patients. Diseased vulvar skin presents a distinct signature compared to healthy vulvar skin with respect to bacterial and viral fractions of the microbiome. Key findings include the presence of papillomaviruses in LS as well as in vulvar HSIL, although LS is generally considered an HPV-independent risk factor for vulvar dysplasia. This exploratory study provides clues to the etiology of vulvar premalignancies and may act as a steppingstone for expanding the knowledge on potential drivers of disease progression.
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Affiliation(s)
- Lisa Pagan
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
| | - Bertine W. Huisman
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Frank H. J. Schuren
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Ingrid M. J. G. Sanders
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Romy D. Zwittink
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Jacobus Burggraaf
- Centre for Human Drug Research, Leiden, Netherlands
- Leiden Amsterdam Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Robert Rissmann
- Centre for Human Drug Research, Leiden, Netherlands
- Leiden Amsterdam Center for Drug Research, Leiden University, Leiden, Netherlands
- Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Jurgen M. J. Piek
- Department of Obstetrics and Gynaecology, Catharina Cancer Institute, Eindhoven, Netherlands
| | - Jannie G. E. Henderickx
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Mariëtte I. E. van Poelgeest
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
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88
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Mejia ME, Mercado-Evans V, Zulk JJ, Ottinger S, Ruiz K, Ballard MB, Fowler SW, Britton RA, Patras KA. Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model. NPJ Biofilms Microbiomes 2023; 9:87. [PMID: 37985659 PMCID: PMC10661851 DOI: 10.1038/s41522-023-00454-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (HMbmice). Like the community structure in conventional mice, HMbmice vaginal microbiota clustered into community state types but, uniquely, HMbmice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, HMbmice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous HMbmouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, HMbmice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.
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Affiliation(s)
- Marlyd E Mejia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Vicki Mercado-Evans
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Ottinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Korinna Ruiz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mallory B Ballard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie W Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Kathryn A Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
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89
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Elovitz M, Anton L, Cristancho A, Ferguson B, Joseph A, Ravel J. Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes. RESEARCH SQUARE 2023:rs.3.rs-3580132. [PMID: 38014044 PMCID: PMC10680926 DOI: 10.21203/rs.3.rs-3580132/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by Lactobacillus spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including Gardnerella vaginalis , have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the in vitro cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that G. vaginalis upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to L. crispatus showed limited transcriptomic changes, while exposure to L. crispatus culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.
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90
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Frąszczak K, Barczyński B, Siwiec R, Kondracka A, Malm A, Kotarski J, Witt E, Korona-Głowniak I. The analysis of Lactobacillus spp. distribution in the vaginal microbiota of Polish women with abnormal Pap smear result. Front Microbiol 2023; 14:1257587. [PMID: 38029074 PMCID: PMC10666048 DOI: 10.3389/fmicb.2023.1257587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction A healthy vaginal microbiota is represented mainly by Lactobacillus spp. and plays a vital role in maintaining the functional balance in the vaginal environment. Scientists have drawn attention to possible correlations between the vaginal microbiome and gynecological neoplasms. Several recent studies have shown a potential link between the vaginal microbiome and the risk of developing cervical cancer from human papillomavirus (HPV) infection. This study aimed to compare the prevalence and abundance of various lactic acid bacteria species (LABs) in vaginal swabs from healthy controls and patients with abnormal Pap smear results. Methods The study included 100 women (79 patients with abnormal cervical Pap smear results and 21 controls) from whom vaginal swabs were collected. Real-time quantitative PCR was used to determine seven lactic acid bacteria (LAB) species and their quantities. Results Most patients were colonized by two Lactobacillus species, primarily Lactobacillus gasseri (93%) and L. crispatus (83%). Patient age and place of residence were associated with the diversity of LAB in the vaginal microbiota. The abundance of L. delbrueckii in the vaginal microbiota increased, whereas the abundance of L. gasseri abundance decreased, with patient age. Lactobacillus acidophilus and Limosilactobacillus fermentum were significantly more often detected in patients living in rural versus urban areas. Statistical analysis did not show any significant differences in LAB between groups of patients with various changes on smear tests. Discussion The degree of dysplastic changes in the endothelium or the presence of a group of atypical cervical stratified epithelial cells was not associated with significant changes in the studied vaginal bacteria.
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Affiliation(s)
- Karolina Frąszczak
- I Department of Oncological Gynaecology and Gynaecology, Medical University in Lublin, Lublin, Poland
| | - Bartłomiej Barczyński
- I Department of Oncological Gynaecology and Gynaecology, Medical University in Lublin, Lublin, Poland
| | - Radosław Siwiec
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University in Lublin, Lublin, Poland
| | - Adrianna Kondracka
- Department of Obstetrics and Pathology of Pregnancy, Medical University in Lublin, Lublin, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University in Lublin, Lublin, Poland
| | - Jan Kotarski
- Independent Laboratory of Cancer Diagnostics and Immunology, Medical University in Lublin, Lublin, Poland
| | - Elzbieta Witt
- Frauenklinik, Marienhospital Witten, Witten, Germany
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University in Lublin, Lublin, Poland
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91
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Ye J, Qi X. Vaginal microecology and its role in human papillomavirus infection and human papillomavirus associated cervical lesions. APMIS 2023. [PMID: 37941500 DOI: 10.1111/apm.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
The vaginal microecology comprises the vaginal microbiome, immune microenvironment, vaginal anatomy, and the cervicovaginal fluid, which is rich in metabolites, enzymes, and cytokines. Investigating its role in the female reproductive system holds paramount significance. The advent of next-generation sequencing enabled a more profound investigation into the structure of the vaginal microbial community in relation to the female reproductive system. Human papillomavirus infection is prevalent among women of reproductive age, and persistent oncogenic HPV infection is widely recognized as a factor associated with cervical cancer. Extensive previous research has demonstrated that dysbiosis of vaginal microbiota characterized by a reduction in Lactobacillus species, heightens susceptivity to HPV infection, consequently contributing to persistent HPV infection and the progression of cervical lesion. Likewise, HPV infection can exacerbate dysbiosis. This review aims to provide a comprehensive summary of current literatures and to elucidate potential mechanisms underlying the interaction between vaginal microecology and HPV infection, with the intention of offering valuable insights for future clinical interventions.
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Affiliation(s)
- Jiatian Ye
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Xiaorong Qi
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
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92
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Sgro M, Ray J, Foster E, Mychasiuk R. Making migraine easier to stomach: the role of the gut-brain-immune axis in headache disorders. Eur J Neurol 2023; 30:3605-3621. [PMID: 37329292 DOI: 10.1111/ene.15934] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND AND PURPOSE Headache disorders place a significant burden on the healthcare system, being the leading cause of disability in those under 50 years. Novel studies have interrogated the relationship between headache disorders and gastrointestinal dysfunction, suggesting a link between the gut-brain-immune (GBI) axis and headache pathogenesis. Although the exact mechanisms driving the complex relationship between the GBI axis and headache disorders remain unclear, there is a growing appreciation that a healthy and diverse microbiome is necessary for optimal brain health. METHODS A literature search was performed through multiple reputable databases in search of Q1 journals within the field of headache disorders and gut microbiome research and were critically and appropriately evaluated to investigate and explore the following; the role of the GBI axis in dietary triggers of headache disorders and the evidence indicating that diet can be used to alleviate headache severity and frequency. The relationship between the GBI axis and post-traumatic headache is then synthesized. Finally, the scarcity of literature regarding paediatric headache disorders and the role that the GBI axis plays in mediating the relationship between sex hormones and headache disorders are highlighted. CONCLUSIONS There is potential for novel therapeutic targets for headache disorders if understanding of the GBI axis in their aetiology, pathogenesis and recovery is increased.
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Affiliation(s)
- Marissa Sgro
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jason Ray
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
- Department of Neurology, Austin Health, Melbourne, Victoria, Australia
| | - Emma Foster
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
- Department of Neurology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Richelle Mychasiuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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93
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Liao L, Sun Y, Huang L, Ye L, Chen L, Shen M. A novel approach for exploring the regional features of vaginal fluids based on microbial relative abundance and alpha diversity. J Forensic Leg Med 2023; 100:102615. [PMID: 37995431 DOI: 10.1016/j.jflm.2023.102615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/14/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023]
Abstract
Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and their characterization is vital to narrow the scope of investigation. Presently, approaches for identifying vaginal fluids in different regions are not only rare but also have certain limitations. However, the microbiome has shown the potential to identify the source of body fluids and reveal the characteristics of individuals. In this study, 16S rRNA gene high-throughput sequencing was used to characterize the vaginal microbial community from three regions, Sichuan, Hainan and Hunan. In addition, data on relative abundance and alpha diversity were used to construct a random forest model. The results revealed that the dominant genera in the three regions were Lactobacillus, followed by Gardnerella. In addition, Ureaplasma, Nitrospira, Nocardiodes, Veillonella and g-norank-f-Vicinamibacteraceae were significantly enriched genera in Sichuan, llumatobacter was enriched in Hainan, and Pseudomonas was enriched in Hunan. The random forest classifier based on combined data on relative abundance and alpha diversity had a good ability to distinguish vaginal fluids with similar dominant microbial compositions in the three regions. The study suggests that combining high-throughput sequencing data with machine learning models has good potential for application in the biogeographic inference of vaginal fluids.
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Affiliation(s)
- Lili Liao
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yunxia Sun
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mei Shen
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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94
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Pouresmaeili F, Alidoost S, Azimirad M, Azizmohammad Looha M, Emami Meibodi A, Abedin-Do A, Shamshiri H, Mohammadi M, Azari I, Fazeli Z, Yadegar A, Hosseinpour TS. Characterization of vaginal Lactobacillus species as a predictor of fertility among Iranian women with unexplained recurrent miscarriage and fertile women without miscarriage history using machine learning modeling. Mol Biol Rep 2023; 50:8785-8797. [PMID: 37644372 DOI: 10.1007/s11033-023-08745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Lactobacillus spp. are the predominant bacteria of the vaginal tract, the alteration of which has been previously linked to miscarriage. Here, we investigated differences between selected vaginal Lactobacillus species of women with a history of recurrent miscarriages and fertile women without a history of miscarriage in Iran. METHODS AND RESULTS Vaginal swabs were taken from 29 fertile and 24 infertile women and quantitative real-time PCR (qPCR) assay was used to determine a selection of vaginal Lactobacillus species in both groups. The logistic regression (LR) model, Naive Bayes (NB) model, support vector machine model (SVM), and neural network model (NN) were developed to predict disease outcome by selected variables. LR analysis was used to construct a nomogram indicating predictions of the risk of miscarriage. The most abundant species among the patients were L. rhamnosus, L. ruminis, and L. acidophilus, while L. gasseri, L. vaginalis, L. fermentum, and L. iners were more abundant in healthy subjects. The distribution of L. ruminis, L. iners, and L. rhamnosus was higher in patients, while L. acidophilus, L. gasseri, and L. fermentum were highly distributed among healthy subjects. Higher AUC in predicting the disease outcome was observed for L. gasseri, L. rhamnosus, L. fermentum, and L. plantarum. CONCLUSION Our findings provide experimental evidence of vaginal Lactobacillus imbalance in infertile women and a suitable predictor for miscarriage based on the AUC algorithms. Further studies with larger sample size and using high-throughput technologies are needed to boost our understanding of the role of lactobacilli in miscarriage.
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Affiliation(s)
- Farkhondeh Pouresmaeili
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeideh Alidoost
- Department of Molecular Genetics, National Institute of Genetics Engineering and Biotechnology (VIGEB), Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Azizmohammad Looha
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armitasadat Emami Meibodi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Abedin-Do
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
- Axe Médecine Régénératrice, Centre de Recherche du CHU de Québec, Département de Chirurgie, Faculté de Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Hourieh Shamshiri
- Department of Community Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahan Mohammadi
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Azari
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Fazeli
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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95
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Lebeer S, Ahannach S, Gehrmann T, Wittouck S, Eilers T, Oerlemans E, Condori S, Dillen J, Spacova I, Vander Donck L, Masquillier C, Allonsius CN, Bron PA, Van Beeck W, De Backer C, Donders G, Verhoeven V. A citizen-science-enabled catalogue of the vaginal microbiome and associated factors. Nat Microbiol 2023; 8:2183-2195. [PMID: 37884815 PMCID: PMC10627828 DOI: 10.1038/s41564-023-01500-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/13/2023] [Indexed: 10/28/2023]
Abstract
Understanding the composition and function of the vaginal microbiome is crucial for reproductive and overall health. Here we established the Isala citizen-science project to analyse the vaginal microbiomes of 3,345 women in Belgium (18-98 years) through self-sampling, 16S amplicon sequencing and extensive questionnaires. The overall vaginal microbiome composition was strongly tied to age, childbirth and menstrual cycle phase. Lactobacillus species dominated 78% of the vaginal samples. Specific bacterial taxa also showed to co-occur in modules based on network correlation analysis. Notably, the module containing Lactobacillus crispatus, Lactobacillus jensenii and Limosilactobacillus taxa was positively linked to oestrogen levels and contraceptive use and negatively linked to childbirth and breastfeeding. Other modules, named after abundant taxa (Gardnerella, Prevotella and Bacteroides), correlated with multiple partners, menopause, menstrual hygiene and contraceptive use. With this resource-rich vaginal microbiome map and associated health, life-course, lifestyle and dietary factors, we provide unique data and insights for follow-up clinical and mechanistic research.
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Affiliation(s)
- Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium.
| | - Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Thies Gehrmann
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Eline Oerlemans
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Sandra Condori
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Jelle Dillen
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Leonore Vander Donck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Caroline Masquillier
- Department of Sociology, Center for Population, Family and Health, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Peter A Bron
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Wannes Van Beeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | | | - Gilbert Donders
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium
- Regional Hospital Heilig Hart, Tienen, Belgium
- Femicare Clinical Research for Women, Tienen, Belgium
| | - Veronique Verhoeven
- Department of Family Medicine and Population Health, University of Antwerp, Antwerp, Belgium
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96
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Zenere G, Wu C, Midkiff CC, Johnson NM, Grice CP, Wimley WC, Kaur A, Braun SE. Extracellular domain, hinge, and transmembrane determinants affecting surface CD4 expression of a novel anti-HIV chimeric antigen receptor (CAR) construct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563930. [PMID: 37961145 PMCID: PMC10634810 DOI: 10.1101/2023.10.25.563930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Chimeric antigen receptor (CAR)-T cells have demonstrated clinical potential, but current receptors still need improvements to be successful against chronic HIV infection. In this study, we address some requirements of CAR motifs for strong surface expression of a novel anti-HIV CAR by evaluating important elements in the extracellular, hinge, and transmembrane (TM) domains. When combining a truncated CD4 extracellular domain and CD8α hinge/TM, the novel CAR did not express extracellularly but was detectable intracellularly. By shortening the CD8α hinge, CD4-CAR surface expression was partially recovered and addition of the LYC motif at the end of the CD8α TM fully recovered both intracellular and extracellular CAR expression. Mutation of LYC to TTA or TTC showed severe abrogation of CAR expression by flow cytometry and confocal microscopy. Additionally, we determined that CD4-CAR surface expression could be maximized by the removal of FQKAS motif at the junction of the extracellular domain and the hinge region. CD4-CAR surface expression also resulted in cytotoxic CAR T cell killing of HIV Env+ target cells. In this study, we identified elements that are crucial for optimal CAR surface expression, highlighting the need for structural analysis studies to establish fundamental guidelines of CAR designs.
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Affiliation(s)
- Giorgio Zenere
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Chengxiang Wu
- Tulane National Primate Research Center, Covington, LA 70433
| | | | - Nathan M. Johnson
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Christopher P. Grice
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
| | - William C. Wimley
- Department of BioChemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Amitinder Kaur
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Stephen E. Braun
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
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97
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Ma Z(S. A new hypothesis on BV etiology: dichotomous and crisscrossing categorization of complex versus simple on healthy versus BV vaginal microbiomes. mSystems 2023; 8:e0004923. [PMID: 37646521 PMCID: PMC10654060 DOI: 10.1128/msystems.00049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/14/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE BV may influence as many as one-third of women, but its etiology remains unclear. A traditional view is that dominance by Lactobacillus is the hallmark of a healthy vaginal microbiome and lack of dominance may make women BV-prone. Recent studies show that the human VMs can be classified into five major types, four of which possess type-specific dominant species of Lactobacillus. The remaining one (type IV) is not dominated by Lactobacillus and contains a handful of strictly anaerobic bacteria. Nevertheless, exceptions to the first hypothesis have been noticed from the very beginning, and there is not a definite relationship, suggested yet, between the five VM types and BV status. Here, we propose and test a novel hypothesis that assumes the existence of four VM types from dichotomous crisscrossing of "complex versus simple (high diversity or low dominance versus low diversity or high dominance)" on "healthy versus BV." Consequently, there are simple BV versus complex BV.
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Affiliation(s)
- Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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98
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Biswas R, Thoma M, Kong X. Functional data analysis to characterize disease patterns in frequent longitudinal data: application to bacterial vaginal microbiota patterns using weekly Nugent scores and identification of pattern-specific risk factors. BMC Med Res Methodol 2023; 23:251. [PMID: 37884907 PMCID: PMC10604810 DOI: 10.1186/s12874-023-02063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Technology advancement has allowed more frequent monitoring of biomarkers. The resulting data structure entails more frequent follow-ups compared to traditional longitudinal studies where the number of follow-up is often small. Such data allow explorations of the role of intra-person variability in understanding disease etiology and characterizing disease processes. A specific example was to characterize pathogenesis of bacterial vaginosis (BV) using weekly vaginal microbiota Nugent assay scores collected over 2 years in post-menarcheeal women from Rakai, Uganda, and to identify risk factors for each vaginal microbiota pattern to inform epidemiological and etiological understanding of the pathogenesis of BV. METHODS We use a fully data-driven approach to characterize the longitudinal patters of vaginal microbiota by considering the densely sampled Nugent scores to be random functions over time and performing dimension reduction by functional principal components. Extending a current functional data clustering method, we use a hierarchical functional clustering framework considering multiple data features to help identify clinically meaningful patterns of vaginal microbiota fluctuations. Additionally, multinomial logistic regression was used to identify risk factors for each vaginal microbiota pattern to inform epidemiological and etiological understanding of the pathogenesis of BV. RESULTS Using weekly Nugent scores over 2 years of 211 sexually active and post-menarcheal women in Rakai, four patterns of vaginal microbiota variation were identified: persistent with a BV state (high Nugent scores), persistent with normal ranged Nugent scores, large fluctuation of Nugent scores which however are predominantly in the BV state; large fluctuation of Nugent scores but predominantly the scores are in the normal state. Higher Nugent score at the start of an interval, younger age group of less than 20 years, unprotected source for bathing water, a woman's partner's being not circumcised, use of injectable/Norplant hormonal contraceptives for family planning were associated with higher odds of persistent BV in women. CONCLUSION The hierarchical functional data clustering method can be used for fully data driven unsupervised clustering of densely sampled longitudinal data to identify clinically informative clusters and risk-factors associated with each cluster.
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Affiliation(s)
| | - Marie Thoma
- University of Maryland, College Park, MD, USA
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99
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Schaefer A, Yang B, Schroeder HA, Harit D, Humphry MS, Ravel J, Lai SK. Broadly neutralizing antibodies consistently trap HIV-1 in fresh cervicovaginal mucus from select individuals. Acta Biomater 2023; 169:387-397. [PMID: 37499728 PMCID: PMC10619885 DOI: 10.1016/j.actbio.2023.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
In addition to direct neutralization and other classical effector functions, IgG possesses a little recognized and thus under-utilized effector function at mucosal surfaces: Fc-mucin bonds enable IgG to trap viruses in mucus. Due to the paucity of envelope glycoproteins that limits the number of IgG that can bind HIV, it remains poorly understood whether IgG-mucin interactions can effectively immobilize HIV in human cervicovaginal mucus (CVM). Here, we obtained 54 fresh, undiluted CVM specimens from 17 different women, and employed high-resolution multiple particle tracking to quantify the mobility of fluorescent HIV virus-like-particles in CVM treated with various HIV-specific IgG. We observed consistent and effective trapping of HIV by broadly neutralizing antibodies (VRC01, PGT121, and 2F5) in a subset of women. While trapping efficacy was not affected by the menstrual cycle, it was positively correlated with appreciable L. Crispatus populations in the microbiome, and negatively correlated with appreciable L. Iners or G. Vaginalis populations. Our work demonstrates for the first time that IgG-mucin crosslinking is capable of reinforcing the mucosal barrier against HIV, and motivates further investigation of passive immunization against vaginal transmission of STIs. STATEMENT OF SIGNIFICANCE: HIV transmission in women primarily occurs vaginally, yet the 3-way interactions between mucins and HIV virions mediated by HIV-binding antibodies in cervicovaginal mucus (CVM) is not well understood. While IgG-Fc possess weak affinity to mucins that trap virus/IgG complexes in mucus, the effectiveness against HIV remains unclear, due to the low number of virion-bound IgG. Here, we discovered that IgG can trap HIV consistently in CVM from select individuals regardless of their birth control status or menstrual cycle phase. IgG-mediated trapping of HIV was moderately associated with microbiome composition. These results suggest that IgG-mucin interactions could potentially reduce HIV transmission and highlight the importance of mucosal secretions in antibody-mediated prevention of HIV and other sexually transmitted infections.
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Affiliation(s)
- Alison Schaefer
- UNC/NCSU Joint Department of Biomedical Engineering, Chapel Hill, NC 27519, USA
| | - Bing Yang
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27519,USA
| | - Holly A Schroeder
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27519,USA
| | - Dimple Harit
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27519,USA
| | - Mike S Humphry
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jacques Ravel
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Samuel K Lai
- UNC/NCSU Joint Department of Biomedical Engineering, Chapel Hill, NC 27519, USA; Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27519,USA; Department of Microbiology & Immunology; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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100
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Martinelli S, Nannini G, Cianchi F, Staderini F, Coratti F, Amedei A. Microbiota Transplant and Gynecological Disorders: The Bridge between Present and Future Treatments. Microorganisms 2023; 11:2407. [PMID: 37894065 PMCID: PMC10609601 DOI: 10.3390/microorganisms11102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a procedure that involves transferring fecal bacteria from a healthy donor to a patients' intestines to restore gut-immunity homeostasis. While FMT was primarily supposed to treat gastrointestinal disorders such as inflammatory bowel disease and irritable bowel syndrome-and especially Clostridium difficile infection (currently the only used as clinical treatment)-recent research has suggested that it may also become a potential treatment for gynecological disorders, including endometriosis and polycystic ovary syndrome (PCOS). On the contrary, vaginal microbiota transplantation (VMT) is a newer and less commonly used procedure than the FMT approach, and its potential applications are still being explored. It involves direct grafting of the entire vaginal microbiota of healthy women into the vaginal tract of patients to easily rebuild the local microbiota environment, restoring vaginal eubiosis and relieving symptoms. Like FMT, VMT is thought to have potential in treating different microbiota-related conditions. In fact, many gynecological disorders, such as bacterial vaginosis and vulvovaginal candidiasis, are thought to be caused by an imbalance in the vaginal microbiota. In this review, we will summarize the development, current challenges, and future perspectives of microbiota transplant, with the aim of exploring new strategies for its employment as a promising avenue for treating a broad range of gynecological diseases.
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Affiliation(s)
- Serena Martinelli
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
| | - Fabio Cianchi
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
| | - Fabio Staderini
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
| | - Francesco Coratti
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, 50139 Florence, Italy; (S.M.); (G.N.); (F.C.); (F.S.); (F.C.)
- SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi (AOUC), 50139 Florence, Italy
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