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Fernández-Edreira D, Liñares-Blanco J, V.-del-Río P, Fernandez-Lozano C. VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria. Comput Struct Biotechnol J 2024; 23:148-156. [PMID: 38144944 PMCID: PMC10749217 DOI: 10.1016/j.csbj.2023.11.050] [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: 09/08/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
This study aimed to develop a robust classification scheme for stratifying patients based on vaginal microbiome. By employing consensus clustering analysis, we identified four distinct clusters using a cohort that includes individuals diagnosed with Bacterial Vaginosis (BV) as well as control participants, each characterized by unique patterns of microbiome species abundances. Notably, the consistent distribution of these clusters was observed across multiple external cohorts, such as SRA022855, SRA051298, PRJNA208535, PRJNA797778, and PRJNA302078 obtained from public repositories, demonstrating the generalizability of our findings. We further trained an elastic net model to predict these clusters, and its performance was evaluated in various external cohorts. Moreover, we developed VIBES, a user-friendly R package that encapsulates the model for convenient implementation and enables easy predictions on new data. Remarkably, we explored the applicability of this new classification scheme in providing valuable insights into disease progression, treatment response, and potential clinical outcomes in BV patients. Specifically, we demonstrated that the combined output of VIBES and VALENCIA scores could effectively predict the response to metronidazole antibiotic treatment in BV patients. Therefore, this study's outcomes contribute to our understanding of BV heterogeneity and lay the groundwork for personalized approaches to BV management and treatment selection.
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Affiliation(s)
- Diego Fernández-Edreira
- Department of Computer Science and Information Technologies, Faculty of Computer Science, CITIC-Research Center of Information and Communication Technologies, Universidade da Coruña, A Coruña, Spain
| | | | - Patricia V.-del-Río
- Servicio de Ginecología, Hospital Universitario Lucus Augusti (HULA). Servizo Galego de Saúde (SERGAS), Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, CITIC-Research Center of Information and Communication Technologies, Universidade da Coruña, A Coruña, Spain
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2
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Plummer EL, Vodstrcil LA, Danielewski JA, Murray GL, Doyle ML, Latimer RL, Fairley CK, Chow EPF, Garland SM, Bradshaw CS. Vaginal anaerobes are associated with cervicitis: A case-control study. J Infect 2024; 89:106210. [PMID: 38944285 DOI: 10.1016/j.jinf.2024.106210] [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: 03/27/2024] [Revised: 05/21/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024]
Abstract
OBJECTIVES Cervicitis is associated with important reproductive sequelae. Primary causes include chlamydia and gonorrhoea, but a known sexually transmitted infection (STI) is not identified in >50% of cases (i.e. STI-negative cervicitis). Bacterial vaginosis (BV) and specific BV-associated bacteria have also been associated with cervicitis, but data are limited. We investigated the association between STI-negative cervicitis and vaginal microbiota composition. METHODS This was a case-control sub-study of the OhMG study conducted at the Melbourne Sexual Health Centre. Cases were women with cervicitis who tested negative for STIs (STI-negative cervicitis, n = 64). Controls were STI-negative asymptomatic women attending for STI-screening (n = 128). The vaginal microbiota was characterised using 16S rRNA gene sequencing. Vaginal community state types were compared between cases and controls using logistic regression. Differential abundance analysis was performed to identify taxa associated with STI-negative cervicitis. RESULTS STI-negative cervicitis cases were more likely than controls to have a Lactobacillus-deficient non-optimal microbiota (adjusted-odds-ratio 2.55, 95% CI 1.18-5.50). Compared to controls, cases had increased abundance of four BV-associated bacteria (Gardnerella, Fannyhessea vaginae, Prevotella bivia, Dialister micraerophilus) and decreased abundance of optimal lactobacilli. CONCLUSIONS We report a positive association between non-optimal vaginal microbiota composition and STI-negative cervicitis. Specific anaerobic BV-associated bacteria may represent infectious causes of cervicitis.
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Affiliation(s)
- Erica L Plummer
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia.
| | - Lenka A Vodstrcil
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia; Melbourne School of Population and Global Health, the University of Melbourne, Parkville, Victoria, Australia.
| | - Jennifer A Danielewski
- Murdoch Children's Research Institute, Parkville, Australia; Women's Centre for Infectious Diseases, the Royal Women's Hospital, Parkville, Australia; Department of Obstetrics and Gynaecology, the University of Melbourne, Parkville, Australia.
| | - Gerald L Murray
- Murdoch Children's Research Institute, Parkville, Australia; Women's Centre for Infectious Diseases, the Royal Women's Hospital, Parkville, Australia; Department of Obstetrics and Gynaecology, the University of Melbourne, Parkville, Australia.
| | - Michelle L Doyle
- Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia.
| | - Rosie L Latimer
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia.
| | - Christopher K Fairley
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia.
| | - Eric P F Chow
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia; Melbourne School of Population and Global Health, the University of Melbourne, Parkville, Victoria, Australia.
| | - Suzanne M Garland
- Murdoch Children's Research Institute, Parkville, Australia; Women's Centre for Infectious Diseases, the Royal Women's Hospital, Parkville, Australia; Department of Obstetrics and Gynaecology, the University of Melbourne, Parkville, Australia.
| | - Catriona S Bradshaw
- School of Translational Medicine, Monash University, Melbourne, Victoria, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Carlton, Victoria, Australia; Melbourne School of Population and Global Health, the University of Melbourne, Parkville, Victoria, Australia.
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3
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Munch MM, Strenk SM, Srinivasan S, Fiedler TL, Proll S, Fredricks DN. Gardnerella Species and Their Association With Bacterial Vaginosis. J Infect Dis 2024; 230:e171-e181. [PMID: 39052736 PMCID: PMC11272073 DOI: 10.1093/infdis/jiae026] [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: 09/22/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a condition marked by high vaginal bacterial diversity. Gardnerella vaginalis has been implicated in BV but is also detected in healthy women. The Gardnerella genus has been expanded to encompass 6 validly named species and several genomospecies. We hypothesized that particular Gardnerella species may be more associated with BV. METHODS Quantitative polymerase chain reaction (PCR) assays were developed targeting the cpn60 gene of species groups including G. vaginalis, G. piotii/pickettii, G. swidsinskii/greenwoodii, and G. leopoldii. These assays were applied to vaginal swabs from individuals with (n = 101) and without BV (n = 150) attending a sexual health clinic in Seattle, Washington. Weekly swabs were collected from 42 participants for up to 12 weeks. RESULTS Concentrations and prevalence of each Gardnerella species group were significantly higher in participants with BV; 91.1% of BV-positive participants had 3 or more Gardnerella species groups detected compared to 32.0% of BV-negative participants (P < .0001). BV-negative participants with 3 or more species groups detected were more likely to develop BV within 100 days versus those with fewer (60.5% vs 3.7%, P < .0001). CONCLUSIONS These results suggest that BV reflects a state of high Gardnerella species diversity. No Gardnerella species group was a specific marker for BV.
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Affiliation(s)
- Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
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4
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McClelland RS, Lokken EM, Kinuthia J, Srinivasan S, Richardson BA, Jaoko W, Lannon S, Pulei A, Fiedler TL, Munch MM, Proll S, John-Stewart G, Fredricks DN. A prospective cohort study examining the association between the periconceptual vaginal microbiota and first-trimester miscarriage in Kenyan women. Paediatr Perinat Epidemiol 2024. [PMID: 38949435 DOI: 10.1111/ppe.13099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/27/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND Studies evaluating the association between the vaginal microbiota and miscarriage have produced variable results. OBJECTIVE This study evaluated the association between periconceptual and first-trimester vaginal microbiota and women's risk for miscarriage. METHODS At monthly preconception visits and at 9-12 weeks gestation, women collected vaginal swabs for molecular characterisation of the vaginal microbiota. Participants who became pregnant were followed to identify miscarriage versus pregnancy continuing to at least 20 weeks gestation. RESULTS Forty-five women experienced miscarriage and 144 had pregnancies continuing to ≥20 weeks. A principal component analysis of periconceptual and first-trimester vaginal bacteria identified by 16S rRNA gene PCR with next-generation sequencing did not identify distinct bacterial communities with miscarriage versus continuing pregnancy. Using taxon-directed quantitative PCR assays, increasing concentrations of Megasphaera hutchinsoni, Mageeibacillus indolicus, Mobiluncus mulieris and Sneathia sanguinegens/vaginalis were not associated with miscarriage. In exploratory analyses, these data were examined as a binary exposure to allow for multivariable modelling. Detection of Mobiluncus mulieris in first-trimester samples was associated with miscarriage (adjusted relative risk [aRR] 2.14, 95% confidence interval [CI] 1.08, 4.22). Additional analyses compared women with early first-trimester miscarriage (range 4.7-7.3 weeks) to women with continuing pregnancies. Mobiluncus mulieris was detected in all eight (100%) first-trimester samples from women with early first-trimester miscarriage compared to 101/192 (52.6%) samples from women with continuing pregnancy (model did not converge). Detection of Mageeibacillus indolicus in first-trimester samples was also associated with early first-trimester miscarriage (aRR 4.10, 95% CI 1.17, 14.31). CONCLUSIONS The primary analyses in this study demonstrated no association between periconceptual or first-trimester vaginal microbiota and miscarriage. Exploratory analyses showing strong associations between first-trimester detection of Mobiluncus mulieris and Mageeibacillus indolicus and early first-trimester miscarriage suggest the need for future studies to determine if these findings are reproducible.
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Affiliation(s)
- R Scott McClelland
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medical Microbiology and Immunology, University of Nairobi, Nairobi, Kenya
| | - Erica M Lokken
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - John Kinuthia
- Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Barbra A Richardson
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Walter Jaoko
- Department of Medical Microbiology and Immunology, University of Nairobi, Nairobi, Kenya
| | - Sophia Lannon
- Northwest Perinatal, Women's Healthcare Associates, Portland, Oregon, USA
| | - Anne Pulei
- Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
- Department of Human Anatomy and Medical Physiology, University of Nairobi, Nairobi, Kenya
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Grace John-Stewart
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - David N Fredricks
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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5
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Javadi K, Ferdosi-Shahandashti E, Rajabnia M, Khaledi M. Vaginal microbiota and gynecological cancers: a complex and evolving relationship. Infect Agent Cancer 2024; 19:27. [PMID: 38877504 PMCID: PMC11179293 DOI: 10.1186/s13027-024-00590-7] [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: 02/17/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
The vagina hosts a community of microorganisms known as the vaginal microbiota. This community is relatively stable and straightforward, with Lactobacillus species being the most dominant members. The vaginal microbiota has various functions that are essential for maintaining human health and balance. For example, it can metabolise dietary nutrients, produce growth factors, communicate with other bacteria, modulate the immune system, and prevent the invasion of harmful pathogens. When the vaginal microbiota is disrupted, it can lead to diseases and infections. The observed disturbance is distinguished by a reduction in the prevalence of Lactobacillus and a concurrent rise in the number of other bacterial species that exhibit a higher tolerance to low oxygen levels. Gynecologic cancers are a group of cancers that affect the female reproductive organs and tissues, such as the ovaries, uterus, cervix, vagina, vulva, and endometrium. These cancers are a major global health problem for women. Understanding the complex interactions between the host and the vaginal microorganisms may provide new insights into the prevention and treatment of gynecologic cancers. This could improve the quality of life and health outcomes for women.
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Affiliation(s)
- Kasra Javadi
- Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Elaheh Ferdosi-Shahandashti
- Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Rajabnia
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Mansoor Khaledi
- Department of Microbiology and Immunology, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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6
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Megli CJ, DePuyt AE, Goff JP, Munyoki SK, Hooven TA, Jašarević E. Diet influences community dynamics following vaginal group B streptococcus colonization. Microbiol Spectr 2024; 12:e0362323. [PMID: 38722155 DOI: 10.1128/spectrum.03623-23] [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: 10/10/2023] [Accepted: 04/22/2024] [Indexed: 06/06/2024] Open
Abstract
The vaginal microbiota plays a pivotal role in reproductive, sexual, and perinatal health and disease. Unlike the well-established connections between diet, metabolism, and the intestinal microbiota, parallel mechanisms influencing the vaginal microbiota and pathogen colonization remain overlooked. In this study, we combine a mouse model of Streptococcus agalactiae strain COH1 [group B Streptococcus (GBS)] vaginal colonization with a mouse model of pubertal-onset obesity to assess diet as a determinant of vaginal microbiota composition and its role in colonization resistance. We leveraged culture-dependent assessment of GBS clearance and culture-independent, sequencing-based reconstruction of the vaginal microbiota in relation to diet, obesity, glucose tolerance, and microbial dynamics across time scales. Our findings demonstrate that excessive body weight gain and glucose intolerance are not associated with vaginal GBS density or timing of clearance. Diets high in fat and low in soluble fiber are associated with vaginal GBS persistence, and changes in vaginal microbiota structure and composition due to diet contribute to GBS clearance patterns in nonpregnant mice. These findings underscore a critical need for studies on diet as a key determinant of vaginal microbiota composition and its relevance to reproductive and perinatal outcomes.IMPORTANCEThis work sheds light on diet as a key determinant influencing the composition of vaginal microbiota and its involvement in group B Streptococcus (GBS) colonization in a mouse model. This study shows that mice fed diets with different nutritional composition display differences in GBS density and timing of clearance in the female reproductive tract. These findings are particularly significant given clear links between GBS and adverse reproductive and neonatal outcomes, advancing our understanding by identifying critical connections between dietary components, factors originating from the intestinal tract, vaginal microbiota, and reproductive outcomes.
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Affiliation(s)
- Christina J Megli
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Maternal-Fetal Medicine, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
- Division of Reproductive Infectious Disease, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Allison E DePuyt
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Julie P Goff
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sarah K Munyoki
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas A Hooven
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Richard King Mellon Institute for Pediatric Research, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eldin Jašarević
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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7
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Chambers LC, Tapia KA, Srinivasan S, Proll S, Morgan JL, Hoffman NG, Lowens MS, Glick SN, Khosropour CM, Golden MR, Hughes JP, Manhart LE, Fredricks DN. The Relationship Between Insertive Oral and Anal Sex and Select Measures of the Composition of the Urethral Microbiota Among Men Who Have Sex With Men. Sex Transm Dis 2024; 51:407-414. [PMID: 38403292 PMCID: PMC11088528 DOI: 10.1097/olq.0000000000001959] [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: 02/27/2024]
Abstract
BACKGROUND Sexual behavior may influence the composition of the male urethral microbiota, but this hypothesis has not been tested in longitudinal studies of men who have sex with men (MSM). METHODS From December 2014 to July 2018, we enrolled MSM with nongonococcal urethritis (NGU) attending a sexual health clinic. Men attended 5 in-clinic visits at 3-week intervals, collected weekly urine specimens at home, and reported daily antibiotics and sexual activity on weekly diaries. We applied broad-range 16S rRNA gene sequencing to urine. We used generalized estimating equations to estimate the association between urethral sexual exposures in the prior 7 days (insertive oral sex [IOS] only, condomless insertive anal intercourse [CIAI] only, IOS with CIAI [IOS + CIAI], or none) and Shannon index, number of species (observed, oral indicator, and rectal indicator), and specific taxa, adjusting for recent antibiotics, age, race/ethnicity, HIV, and preexposure prophylaxis. RESULTS Ninety-six of 108 MSM with NGU attended ≥1 follow-up visit. They contributed 1140 person-weeks of behavioral data and 1006 urine specimens. Compared with those with no urethral sexual exposures, those with IOS only had higher Shannon index ( P = 0.03 ) but similar number of species and presence of specific taxa considered, adjusting for confounders; the exception was an association with Haemophilus parainfluenzae . CIAI only was not associated with measured aspects of the urethral microbiota. IOS + CIAI was only associated with presence of H. parainfluenzae and Haemophilus . CONCLUSIONS Among MSM after NGU, IOS and CIAI did not seem to have a substantial influence on measured aspects of the composition of the urethral microbiota.
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Affiliation(s)
- Laura C. Chambers
- Department of Epidemiology, University of Washington,
Seattle, Washington
| | - Kenneth A. Tapia
- Department of Global Health, University of Washington,
Seattle, Washington
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson
Cancer Center, Seattle, Washington
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson
Cancer Center, Seattle, Washington
| | - Jennifer L. Morgan
- HIV/STI/HCV Program, Public Health – Seattle and
King County, Seattle, Washington
| | - Noah G. Hoffman
- Department of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington
| | - M. Sylvan Lowens
- HIV/STI/HCV Program, Public Health – Seattle and
King County, Seattle, Washington
| | - Sara N. Glick
- Department of Epidemiology, University of Washington,
Seattle, Washington
- HIV/STI/HCV Program, Public Health – Seattle and
King County, Seattle, Washington
- Department of Medicine, University of Washington, Seattle,
Washington
| | | | - Matthew R. Golden
- Department of Epidemiology, University of Washington,
Seattle, Washington
- HIV/STI/HCV Program, Public Health – Seattle and
King County, Seattle, Washington
- Department of Medicine, University of Washington, Seattle,
Washington
| | - James P. Hughes
- Department of Biostatistics, University of Washington,
Seattle, Washington
| | - Lisa E. Manhart
- Department of Epidemiology, University of Washington,
Seattle, Washington
- Department of Global Health, University of Washington,
Seattle, Washington
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson
Cancer Center, Seattle, Washington
- Department of Medicine, University of Washington, Seattle,
Washington
- Department of Microbiology, University of Washington,
Seattle, Washington
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8
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Challa A, Maras JS, Nagpal S, Tripathi G, Taneja B, Kachhawa G, Sood S, Dhawan B, Acharya P, Upadhyay AD, Yadav M, Sharma R, Bajpai M, Gupta S. Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis. J Eur Acad Dermatol Venereol 2024; 38:1152-1165. [PMID: 38284174 DOI: 10.1111/jdv.19805] [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: 10/20/2022] [Accepted: 11/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery. OBJECTIVES The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model. METHODS Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. RESULTS Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model. CONCLUSION Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.
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Affiliation(s)
- A Challa
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - J S Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - B Taneja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Kachhawa
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - S Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - B Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - P Acharya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - A D Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - M Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - R Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M Bajpai
- Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Gupta
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
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9
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Dong W, Wang S, Wang X, Xu G, Liu Q, Li Z, Lv N, Pan Y, Xiong Q, Liu D, Zhu B. Characteristics of Vaginal Microbiota of Women of Reproductive Age with Infections. Microorganisms 2024; 12:1030. [PMID: 38792859 PMCID: PMC11124179 DOI: 10.3390/microorganisms12051030] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The vaginal microbiota can be classified into five major community state types (CSTs) based on the bacterial content. However, the link between different CST subtypes and vaginal infection remains unclear. Here, we analyzed 2017 vaginal microbiota samples from women of a reproductive age with vaginal infections that were published in the last decade. We found that L. iners was the most dominant in 34.8% of the vaginal samples, followed by L. crispatus (21.2%). CST I was common in healthy individuals, whereas CST III and IV were associated with dysbiosis and infection. CST III-B, IV-A, IV-B, and IV-C0 were prevalent in patients with bacterial vaginosis (BV). Based on the relative abundance of bacteria at the (sub)genus level, a random forest classifier was developed to predict vaginal infections with an area under the curve of 0.83. We further identified four modules of co-occurring bacterial taxa: L. crispatus, Gardnerella, Prevotella, and Bacteroides. The functional prediction revealed that nucleotide biosynthesis pathways were upregulated in patients with human papilloma virus, and carbohydrate degradation pathways were downregulated in patients with BV. Overall, our study identified the bacterial signatures of healthy and infected vaginal microbiota, providing unique insights into the clinical diagnosis and health status prediction of women of a reproductive age.
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Affiliation(s)
- Wanting Dong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojin Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Qiuying Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Zheng Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Qian Xiong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
| | - Donglai Liu
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing 100050, China
- NMPA Key Laboratory for Quality Research and Evaluation of Medical Devices, Beijing 100050, China
- NMPA Key Laboratory for Quality Research and Evaluation of In Vitro Diagnostics, Beijing 100050, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (W.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
- Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing 100101, China
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10
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George SD, Van Gerwen OT, Dong C, Sousa LGV, Cerca N, Elnaggar JH, Taylor CM, Muzny CA. The Role of Prevotella Species in Female Genital Tract Infections. Pathogens 2024; 13:364. [PMID: 38787215 PMCID: PMC11123741 DOI: 10.3390/pathogens13050364] [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: 04/04/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Female genital tract infections (FGTIs) include vaginal infections (e.g., bacterial vaginosis [BV]), endometritis, pelvic inflammatory disease [PID], and chorioamnionitis [amniotic fluid infection]. They commonly occur in women of reproductive age and are strongly associated with multiple adverse health outcomes including increased risk of HIV/sexually transmitted infection acquisition and transmission, infertility, and adverse birth outcomes such as preterm birth. These FGTIs are characterized by a disruption of the cervicovaginal microbiota which largely affects host immunity through the loss of protective, lactic acid-producing Lactobacillus spp. and the overgrowth of facultative and strict anaerobic bacteria. Prevotella species (spp.), anaerobic Gram-negative rods, are implicated in the pathogenesis of multiple bacterial FGTIs. Specifically, P. bivia, P. amnii, and P. timonensis have unique virulence factors in this setting, including resistance to antibiotics commonly used in treatment. Additionally, evidence suggests that the presence of Prevotella spp. in untreated BV cases can lead to infections of the upper female genital tract by ascension into the uterus. This narrative review aims to explore the most common Prevotella spp. in FGTIs, highlight their important role in the pathogenesis of FGTIs, and propose future research in this area.
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Affiliation(s)
- Sheridan D. George
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Olivia T. Van Gerwen
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Chaoling Dong
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
| | - Lúcia G. V. Sousa
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (L.G.V.S.); (N.C.)
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (L.G.V.S.); (N.C.)
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (J.H.E.); (C.M.T.)
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (J.H.E.); (C.M.T.)
| | - Christina A. Muzny
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (O.T.V.G.); (C.D.); (C.A.M.)
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11
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Valint D, Fiedler TL, Liu C, Srinivasan S, Fredricks DN. Effect of Metronidazole on Concentrations of Vaginal Bacteria Associated with Risk of HIV Acquisition. RESEARCH SQUARE 2024:rs.3.rs-4219764. [PMID: 38659968 PMCID: PMC11042432 DOI: 10.21203/rs.3.rs-4219764/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Several bacterial vaginosis (BV)-associated bacteria have been associated with elevated risk of HIV acquisition, however susceptibility of these bacteria to antibiotics is poorly understood. Vaginal samples were collected from 22 persons daily for two weeks following BV diagnosis. Metronidazole treatment was prescribed for 5-7 days. Changes in bacterial concentrations were measured with taxon-specific 16S rRNA gene quantitative PCR (qPCR) assays. A culture-based antimicrobial assay confirmed presence of antibiotics in vaginal swab samples. Bacterial DNA concentrations decreased during antibiotic administration for all thirteen bacterial taxa tested. Comparison of bacterial DNA concentrations in samples before administration of antibiotics to samples taken on the last day of antimicrobial assay-confirmed antibiotic presence showed a 2.3-4.5 log10-fold decrease across all taxa. Concentrations were frequently reduced to the qPCR assay's limit of detection, suggesting eradication of bacteria. Mean clearance time varied across taxa (1.2-8.6 days), with several bacteria (e.g., Gemella asaccharolytica, Sneathia spp., Eggerthella-like sp.) taking >7 days to suppress. Metronidazole reduces quantities of bacterial taxa associated with increased HIV acquisition risk. Eradication of high-risk vaginal bacteria using metronidazole is one promising avenue for reducing HIV acquisition risk. A 5-7-day treatment course may not be sufficient to suppress all bacteria.
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Affiliation(s)
- D.J. Valint
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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12
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Stewart LL, Vodstrcil LA, Coombe J, Bradshaw CS, Hocking JS. Bacterial vaginosis after menopause: factors associated and women's experiences: a cross-sectional study of Australian postmenopausal women. Sex Health 2024; 21:SH23094. [PMID: 38626203 DOI: 10.1071/sh23094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 03/21/2024] [Indexed: 04/18/2024]
Abstract
Background Bacterial vaginosis (BV) is the most common cause of vaginal discharge in reproductive age women; however, little is known about it after menopause. We aimed to learn more about BV in Australian postmenopausal women. Methods We conducted an online survey (July-September 2021). Participants were recruited via social media and professional networks and asked about demographic characteristics, sexual history and BV experiences. Outcomes of interest were the proportion who had heard of BV, had BV ever, or had BV after menopause. Factors associated with these outcomes were assessed using logistic regression. Results Of 906 participants, 83% were included in the analysis. Overall, 37.9% had heard of BV, 11.0% reported having a BV diagnosis ever, 6.3% reported having a BV diagnosis after menopause and 4.4% reported having a BV diagnosis only after menopause. Multivariable analysis found that among all women the odds of having a BV diagnosis after menopause were increased for those who had BV before menopause, had douched in the past 12months, or had a previous STI diagnosis. Among those in a sexual relationship, a BV diagnosis after menopause was associated with a BV diagnosis before menopause, or being in a sexual relationship of 5years or less in duration. About half who reported BV after menopause described recurrences, distress, and a detrimental effect on sexual relationships. Conclusions BV in postmenopausal women is associated with sexual activity, and impacts negatively on their lives. Research into BV should not be limited to reproductive age women.
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Affiliation(s)
- Linde L Stewart
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Vic., Australia
| | - Lenka A Vodstrcil
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Vic., Australia; and Melbourne Sexual Health Centre, Alfred Health, Carlton, Vic., Australia; and Central Clinical School, Monash University, The Alfred Centre, Melbourne, Vic., Australia
| | - Jacqueline Coombe
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Vic., Australia
| | - Catriona S Bradshaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Vic., Australia; and Melbourne Sexual Health Centre, Alfred Health, Carlton, Vic., Australia; and Central Clinical School, Monash University, The Alfred Centre, Melbourne, Vic., Australia
| | - Jane S Hocking
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Vic., Australia
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13
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Pedro NA, Mira NP. A molecular view on the interference established between vaginal Lactobacilli and pathogenic Candida species: Challenges and opportunities for the development of new therapies. Microbiol Res 2024; 281:127628. [PMID: 38246122 DOI: 10.1016/j.micres.2024.127628] [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: 10/23/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Vaginal infectious diseases caused by viruses and bacteria have been linked to the occurrence of dysbiosis, that is, a reduction in the abundance of the normally dominating vaginal Lactobacillus species. Mucosal infections in the vagina and/or vulva caused by Candida species, usually known as vulvovaginal candidiasis (or VVC), are among the leading causes of diseases in the vaginal tract. The existence of a clear link between the occurrence of dysbiosis and the development of VVC is still unclear, although multiple observations point in that direction. Based on the idea that vaginal health is linked to a microbiota dominated by lactobacilli, several probiotics have been used in management of VVC, either alone or in combination with antifungals, having obtained different degrees of success. In most cases, the undertaken trials resorted to lactobacilli species other than those indigenous to the vaginal tract, although in vitro these vaginal species were shown to reduce growth, viability and virulence of Candida. In this paper we overview the role of lactobacilli and Candida in the vaginal micro- and myco-biomes, while discussing the results obtained in what concerns the establishment of interference mechanisms in vivo and the environmental factors that could determine that. We also overview the molecular mechanisms by which lactobacilli species have been shown to inhibit pathophysiology of Candida, including the description of the genes and pathways determining their ability to thrive in the presence of each other. In a time where concerns are increasing with the emergence of antifungal resistance and the slow pace of discovery of new antifungals, a thorough understanding of the molecular mechanisms underneath the anti-Candida effect prompted by vaginal lactobacilli is of utmost importance to assure a knowledge-based design of what can be a new generation of pharmaceuticals, eventually focusing therapeutic targets other than the usual ones.
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Affiliation(s)
- Nuno A Pedro
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico - Department of Bioengineering, Universidade de Lisboa, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico - Department of Bioengineering, Universidade de Lisboa, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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14
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Carter KA, France MT, Rutt L, Bilski L, Martinez-Greiwe S, Regan M, Brotman RM, Ravel J. Sexual transmission of urogenital bacteria: whole metagenome sequencing evidence from a sexual network study. mSphere 2024; 9:e0003024. [PMID: 38358269 PMCID: PMC10964427 DOI: 10.1128/msphere.00030-24] [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: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital microbiota is unclear as prior studies largely investigated specific pathogens. We used epidemiologic data and whole metagenome sequencing to characterize urogenital microbiota strain concordance between participants of a sexual network study. Individuals who screened positive for genital Chlamydia trachomatis were enrolled and referred their sexual contacts from the prior 60-180 days. Snowball recruitment of sexual contacts continued for up to four waves. Vaginal swabs and penile urethral swabs were collected for whole metagenome sequencing. We evaluated bacterial strain concordance using inStrain and network analysis. We defined concordance as ≥99.99% average nucleotide identity over ≥50% shared coverage; we defined putative sexual transmission as concordance between sexual contacts with <5 single-nucleotide polymorphisms per megabase. Of 138 participants, 74 (54%) were female; 120 (87%) had genital chlamydia; and 43 (31%) were recruited contacts. We identified 115 strain-concordance events among 54 participants representing 25 bacterial species. Seven events (6%) were between sexual contacts including putative heterosexual transmission of Fannyhessea vaginae, Gardnerella leopoldii, Prevotella amnii, Sneathia sanguinegens, and Sneathia vaginalis (one strain each), and putative sexual transmission of Lactobacillus iners between female contacts. Most concordance events (108, 94%) were between non-contacts, including eight female participants connected through 18 Lactobacillus crispatus and 3 Lactobacillus jensenii concordant strains, and 14 female and 2 male participants densely interconnected through 52 Gardnerella swidsinskii concordance events.IMPORTANCEEpidemiologic evidence consistently indicates bacterial vaginosis (BV) is sexually associated and may be sexually transmitted, though sexual transmission remains subject to debate. This study is not capable of demonstrating BV sexual transmission; however, we do provide strain-level metagenomic evidence that strongly supports heterosexual transmission of BV-associated species. These findings strengthen the evidence base that supports ongoing investigations of concurrent male partner treatment for reducing BV recurrence. Our data suggest that measuring the impact of male partner treatment on F. vaginae, G. leopoldii, P. amnii, S. sanguinegens, and S. vaginalis may provide insight into why a regimen does or does not perform well. We also observed a high degree of strain concordance between non-sexual-contact female participants. We posit that this may reflect limited dispersal capacity of vaginal bacteria coupled with individuals' comembership in regional transmission networks where transmission may occur between parent and child at birth, cohabiting individuals, or sexual contacts.
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Affiliation(s)
- Kayla A. Carter
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lindsay Rutt
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lisa Bilski
- School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | | | - Mary Regan
- School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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15
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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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16
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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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17
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Yu B, Liu C, Proll SC, Manhardt E, Liang S, Srinivasan S, Swisher E, Fredricks DN. Identification of fallopian tube microbiota and its association with ovarian cancer. eLife 2024; 12:RP89830. [PMID: 38451065 PMCID: PMC10942644 DOI: 10.7554/elife.89830] [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: 03/08/2024] Open
Abstract
Investigating the human fallopian tube (FT) microbiota has significant implications for understanding the pathogenesis of ovarian cancer (OC). In this large prospective study, we collected swabs intraoperatively from the FT and other surgical sites as controls to profile the microbiota in the FT and to assess its relationship with OC. Eighty-one OC and 106 non-cancer patients were enrolled and 1001 swabs were processed for 16S rRNA gene PCR and sequencing. We identified 84 bacterial species that may represent the FT microbiota and found a clear shift in the microbiota of the OC patients when compared to the non-cancer patients. Of the top 20 species that were most prevalent in the FT of OC patients, 60% were bacteria that predominantly reside in the gastrointestinal tract, while 30% normally reside in the mouth. Serous carcinoma had higher prevalence of almost all 84 FT bacterial species compared to the other OC subtypes. The clear shift in the FT microbiota in OC patients establishes the scientific foundation for future investigation into the role of these bacteria in the pathogenesis of OC.
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Affiliation(s)
- Bo Yu
- Department of Obstetrics and GynecologyStanfordUnited States
- Stanford Maternal & Child Health Research Institute, Stanford University School of MedicineStanfordUnited States
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Sean C Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Enna Manhardt
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Shuying Liang
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Elizabeth Swisher
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
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18
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Zhu X, Li J, He A, Gurr GM, You M, You S. Developmental Shifts in the Microbiome of a Cosmopolitan Pest: Unraveling the Role of Wolbachia and Dominant Bacteria. INSECTS 2024; 15:132. [PMID: 38392551 PMCID: PMC10888865 DOI: 10.3390/insects15020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Wolbachia bacteria (phylum Proteobacteria) are ubiquitous intracellular parasites of diverse invertebrates. In insects, coevolution has forged mutualistic associations with Wolbachia species, influencing reproduction, immunity, development, pathogen resistance, and overall fitness. However, the impact of Wolbachia on other microbial associates within the insect microbiome, which are crucial for host fitness, remains less explored. The diamondback moth (Plutella xylostella), a major pest of cruciferous vegetables worldwide, harbors the dominant Wolbachia strain plutWB1, known to distort its sex ratio. This study investigated the bacterial community diversity and dynamics across different developmental life stages and Wolbachia infection states in P. xylostella using high-throughput 16S rDNA amplicon sequencing. Proteobacteria and Firmicutes dominated the P. xylostella microbiome regardless of life stage or Wolbachia infection. However, the relative abundance of dominant genera, including an unclassified genus of Enterobacteriaceae, Wolbachia, Carnobacterium, and Delftia tsuruhatensis, displayed significant stage-specific variations. While significant differences in bacterial diversity and composition were observed across life stages, Wolbachia infection had no substantial impact on overall diversity. Nonetheless, relative abundances of specific genera differed between infection states. Notably, Wolbachia exhibited a stable, high relative abundance across all stages and negatively correlated with an unclassified genus of Enterobacteriaceae, Delftia tsuruhatensis, and Carnobacterium. Our findings provide a foundational understanding of the complex interplay between the host, Wolbachia, and the associated microbiome in P. xylostella, paving the way for a deeper understanding of their complex interactions and potential implications for pest control strategies.
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Affiliation(s)
- Xiangyu Zhu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinyang Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ao He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Geoff M Gurr
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Gulbali Institute, Charles Sturt University, Orange, NSW 2800, Australia
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijun You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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19
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Song Z, Li K, Li K. Acute effects of the environmental probiotics Rhodobacter sphaeroides on intestinal bacteria and transcriptome in shrimp Penaeusvannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109316. [PMID: 38142021 DOI: 10.1016/j.fsi.2023.109316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023]
Abstract
In recent years, a substantial number of studies have been dedicated to exploring the potential benefits of probiotics in aquaculture. Rhodobacter sphaeroides can be used in aquaculture-related environmental bioremediation, and its protein is also used as a feed additive in Penaeus vannamei culture. To investigate the effects of releasing R. sphaeroides as environmental probiotics on P. vannamei, we employed 16S rRNA gene and mRNA transcriptome sequencing. Our study focused on assessing alterations in intestinal bacteria and intestinal gene expression in P. vannamei, establishing correlations between them. Our findings revealed a significant increase in the relative abundances of Rhodobacter, Paracoccus, Sulfitobacter, and other bacterial OTUs within the intestinal bacterial community. Additionally, we observed enhanced complexity and stability in the intestinal bacterial correlation network, indicating improved synergy among bacteria and reduced competition. Moreover, the introduction of R. sphaeroides resulted in the down-regulation of certain immune genes and the up-regulation of genes linked to growth and metabolism in the intestinal tissues of P. vannamei. Importantly, we identified a noteworthy correlation between the changes in intestinal bacteria and these alterations in intestinal tissue gene expressions. By conducting analyses of the intestinal bacterial community and intestinal tissue transcriptome, this study revealed the effects of releasing R. sphaeroides as sediment probiotics in P. vannamei culture water. These results serve as vital scientific references for the application of R. sphaeroides in P. vannamei aquaculture.
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Affiliation(s)
- Zule Song
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kui Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China.
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20
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Zhou Z, Feng Y, Xie L, Ma S, Cai Z, Ma Y. Alterations in gut and genital microbiota associated with gynecological diseases: a systematic review and meta-analysis. Reprod Biol Endocrinol 2024; 22:13. [PMID: 38238814 PMCID: PMC10795389 DOI: 10.1186/s12958-024-01184-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Increasing number of studies have demonstrated certain patterns of microbial changes in gynecological diseases; however, the interaction between them remains unclear. To evaluate the consistency or specificity across multiple studies on different gynecological diseases and microbial alterations at different sites of the body (gut and genital tract), we conducted a systematic review and meta-analysis. METHODS We searched PubMed, Embase, Web of Science, and Cochrane Library up to December 5, 2022(PROSPERO: CRD42023400205). Eligible studies focused on gynecological diseases in adult women, applied next-generation sequencing on microbiome, and reported outcomes including alpha or beta diversity or relative abundance. The random-effects model on standardized mean difference (SMD) was conducted using the inverse-variance method for alpha diversity indices. RESULTS Of 3327 unique articles, 87 eligible studies were included. Significant decreases were found in gut microbiome of patients versus controls (observed species SMD=-0.35; 95%CI, -0.62 to -0.09; Shannon index SMD=-0.23; 95%CI, -0.40 to -0.06), whereas significant increases were observed in vaginal microbiome (Chao1 SMD = 1.15; 95%CI, 0.74 to 1.56; Shannon index SMD = 0.51; 95%CI, 0.16 to 0.86). Most studies of different diagnostic categories showed no significant differences in beta diversity. Disease specificity was observed, but almost all the changes were only replicated in three studies, except for the increased Aerococcus in bacterial vaginosis (BV). Patients with major gynecological diseases shared the enrichment of Prevotella and depletion of Lactobacillus, and an overlap in microbes was implied between BV, cervical intraepithelial neoplasia, and cervical cancer. CONCLUSIONS These findings demonstrated an association between alterations in gut and genital microbiota and gynecological diseases. The most observed results were shared alterations across diseases rather than disease-specific alterations. Therefore, further investigation is required to identify specific biomarkers for diagnosis and treatment in the future.
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Affiliation(s)
- Ziwei Zhou
- Obstetrics and Gynecology Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yifei Feng
- Obstetrics and Gynecology Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lishan Xie
- Obstetrics and Gynecology Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Song Ma
- Obstetrics and Gynecology Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhaoxia Cai
- Guangzhou Liwan Maternal and Child Health Hospital, Guangzhou, China
| | - Ying Ma
- Obstetrics and Gynecology Medical Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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21
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Cheng Z, Liu Q, Huang X. Partial Correspondence between Host Plant-Related Differentiation and Symbiotic Bacterial Community in a Polyphagous Insect. Animals (Basel) 2024; 14:283. [PMID: 38254452 PMCID: PMC10812459 DOI: 10.3390/ani14020283] [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: 12/11/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Host plants play a vital role in insect population differentiation, while symbiotic associations between bacteria and insects are ubiquitous in nature. However, existing studies have given limited attention to the connection between host-related differentiation and symbiotic bacterial communities in phytophagous insects. In this study, we collected 58 samples of Aphis odinae from different host plants in southern China and constructed phylogenetic trees to investigate their differentiation in relation to host plants. We also selected aphid samples from the five most preferred host plants and analyzed their symbiotic bacterial composition using Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The phylogeny and symbiotic bacterial community structure of A. odinae populations on different host plants showed that samples from Triadica sebifera (Euphorbiaceae) had a consistent presence of Wolbachia as the predominant secondary symbiont and suggested the possibility of undergoing differentiation. Conversely, although differentiation was observed in samples from Rhus chinensis (Anacardiaceae), no consistent presence of predominant secondary symbionts was found. Additionally, the samples from Heptapleurum heptaphyllum (Araliaceae) consistently carried Serratia, but no host differentiation was evident. In summary, this study reveals a partial correspondence between symbiotic bacterial communities and host-related differentiation in A. odinae. The findings contribute to our understanding of the microevolutionary influencing the macroevolutionary relationships between bacterial symbionts and phytophagous insects. The identification of specific symbionts associated with host-related differentiation provides valuable insights into the intricate dynamics of insect-bacteria interactions.
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Affiliation(s)
| | | | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.C.); (Q.L.)
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22
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Murphy K, Gromisch M, Srinivasan S, Wang T, Wood L, Proll S, Liu C, Fiedler T, Valint DJ, Fredricks DN, Keller MJ, Herold BC. IgA coating of vaginal bacteria is reduced in the setting of bacterial vaginosis (BV) and preferentially targets BV-associated species. Infect Immun 2024; 92:e0037323. [PMID: 38099624 PMCID: PMC10790818 DOI: 10.1128/iai.00373-23] [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: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/17/2024] Open
Abstract
Immunoglobulin (Ig) bacterial coating has been described in the gastrointestinal tract and linked to inflammatory bowel disease; however, little is known about Ig coating of vaginal bacteria and whether it plays a role in vaginal health including bacterial vaginosis (BV). We examined Ig coating in 18 women with symptomatic BV followed longitudinally before, 1 week, and 1 month after oral metronidazole treatment. Immunoglobulin A (IgA) and/or immunoglobulin G (IgG) coating of vaginal bacteria was assessed by flow cytometry, and Ig coated and uncoated bacteria were sorted and characterized using 16S rRNA sequencing. Despite higher levels of IgG compared to IgA in cervicovaginal fluid, the predominant Ig coating the bacteria was IgA. The majority of bacteria were uncoated at all visits, but IgA coating significantly increased after treatment for BV. Despite similar amounts of uncoated and IgA coated majority taxa ( >1% total) across all visits, there was preferential IgA coating of minority taxa (0.2%-1% total) associated with BV including Sneathia, several Prevotella species, and others. At the time of BV, we identified a principal component (PC) driven by proinflammatory mediators that correlated positively with an uncoated BV-associated bacterial community and negatively with an IgA coated protective Lactobacillus bacterial community. The preferential coating of BV-associated species, increase in coating following metronidazole treatment, and positive correlation between uncoated BV-associated species and inflammation suggest that coating may represent a host mechanism designed to limit bacterial diversity and reduce inflammatory responses. Elucidating the role of Ig coating in vaginal mucosal immunity may promote new strategies to prevent recurrent BV.
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Affiliation(s)
- Kerry Murphy
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Matthew Gromisch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lianna Wood
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sean Proll
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Congzhou Liu
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tina Fiedler
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - D. J. Valint
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David N. Fredricks
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Marla J. Keller
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Betsy C. Herold
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
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23
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Bommana S, Hu YJ, Kama M, Wang R, Kodimerla R, Jijakli K, Read TD, Dean D. Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji. mBio 2024; 15:e0306323. [PMID: 38117091 PMCID: PMC10790706 DOI: 10.1128/mbio.03063-23] [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: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of Ct or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E-dominated primarily by Gardnerella vaginalis-to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV. Ct-infected endocervical networks had smaller clusters without interactions with potentially beneficial Lactobacillus spp. Overall, these data suggest that G. vaginalis may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.
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Affiliation(s)
- Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Ruohong Wang
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Reshma Kodimerla
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Kenan Jijakli
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D. Read
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA
- Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA
- University of California San Francisco, Benioff Center for Microbiome Medicine, San Francisco, California, USA
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24
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Ma K, Han X, Li Q, Kong Y, Liu Q, Yan X, Luo Y, Li X, Wen H, Cao Z. Improved anaerobic sludge fermentation mediated by a tryptophan-degrading consortium: Effectiveness assessment and mechanism deciphering. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 350:119623. [PMID: 38029496 DOI: 10.1016/j.jenvman.2023.119623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
The hydrolysis of extracellular polymeric substances (EPS) represents a critical bottleneck in the anaerobic fermentation of waste activated sludge (WAS), while tryptophan is identified as an underestimated constituent of EPS. Herein, we harnessed a tryptophan-degrading microbial consortium (TDC) to enhance the hydrolysis efficiency of WAS. At TDC dosages of 5%, 10%, and 20%, a notable increase in SCOD was observed by factors of 1.13, 1.39, and 1.88, respectively. The introduction of TDC improved both the yield and quality of short chain fatty acids (SCFAs), the maximum SCFA yield increased from 590.6 to 1820.2, 1957.9 and 2194.9 mg COD/L, whilst the acetate ratio within SCFAs was raised from 34.1% to 61.2-70.9%. Furthermore, as TDC dosage increased, the relative activity of protease exhibited significant increments, reaching 116.3%, 168.0%, and 266.1%, respectively. This enhancement facilitated WAS solubilization and the release of organic substances from bound EPS into soluble EPS. Microbial analysis identified Tetrasphaera and Soehngenia as key participants in WAS solubilization and the breakdown of protein fraction. Metabolic analysis revealed that TDC triggered the secretion of enzymes associated with amino acid metabolism and fatty acid biosynthesis, thereby fostering the decomposition of proteins and production of SCFAs.
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Affiliation(s)
- Kaili Ma
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China.
| | - Xinxin Han
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Qiujuan Li
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Yu Kong
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Qiaoli Liu
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Xu Yan
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Yahong Luo
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Xiaopin Li
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Huiyang Wen
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
| | - Zhiguo Cao
- School of Environment, Henan Normal University, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, 453000, China
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25
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Zhang LN, Jiang CH, Si F, Song N, Yang W, Zhu Y, Luo Y, Guo JH. Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota. PLANT DISEASE 2024; 108:94-103. [PMID: 37467122 DOI: 10.1094/pdis-09-22-2196-re] [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: 07/21/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.
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Affiliation(s)
- Li-Na Zhang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng 224002, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Fangjie Si
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Ning Song
- Nanjing Planck Technology and Trade Co., Ltd., Nanjing 210095, China
| | - Wei Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
| | - Yanze Zhu
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huaian 223300, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Engineering Center of Bioresource Pesticide in Jiangsu Province, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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26
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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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27
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Romashchenko N, Linard B, Pardi F, Rivals E. EPIK: precise and scalable evolutionary placement with informative k-mers. Bioinformatics 2023; 39:btad692. [PMID: 37975872 PMCID: PMC10701097 DOI: 10.1093/bioinformatics/btad692] [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: 03/15/2023] [Revised: 09/20/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
MOTIVATION Phylogenetic placement enables phylogenetic analysis of massive collections of newly sequenced DNA, when de novo tree inference is too unreliable or inefficient. Assuming that a high-quality reference tree is available, the idea is to seek the correct placement of the new sequences in that tree. Recently, alignment-free approaches to phylogenetic placement have emerged, both to circumvent the need to align the new sequences and to avoid the calculations that typically follow the alignment step. A promising approach is based on the inference of k-mers that can be potentially related to the reference sequences, also called phylo-k-mers. However, its usage is limited by the time and memory-consuming stage of reference data preprocessing and the large numbers of k-mers to consider. RESULTS We suggest a filtering method for selecting informative phylo-k-mers based on mutual information, which can significantly improve the efficiency of placement, at the cost of a small loss in placement accuracy. This method is implemented in IPK, a new tool for computing phylo-k-mers that significantly outperforms the software previously available. We also present EPIK, a new software for phylogenetic placement, supporting filtered phylo-k-mer databases. Our experiments on real-world data show that EPIK is the fastest phylogenetic placement tool available, when placing hundreds of thousands and millions of queries while still providing accurate placements. AVAILABILITY AND IMPLEMENTATION IPK and EPIK are freely available at https://github.com/phylo42/IPK and https://github.com/phylo42/EPIK. Both are implemented in C++ and Python and supported on Linux and MacOS.
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Affiliation(s)
| | | | - Fabio Pardi
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Eric Rivals
- LIRMM, University of Montpellier, CNRS, Montpellier, France
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Chung Y, Kang SB, Son D, Lee JY, Chung MJ, Lim S. Characterization of the probiotic properties of Lacticaseibacillus rhamnosus LR6 isolated from the vaginas of healthy Korean women against vaginal pathogens. Front Microbiol 2023; 14:1308293. [PMID: 38098667 PMCID: PMC10720895 DOI: 10.3389/fmicb.2023.1308293] [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: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The human microbiome exhibits intricate populations across the body, with the vaginal tract serving as an ecosystem characterized by the prevalence of the genus Lactobacillus. Disruptions in the vaginal microbiota, which are frequently linked to variables such as sexual activity, hormonal fluctuations, and excessive use of antibiotics, can result in vaginal dysbiosis and the development of diseases such as bacterial vaginosis (BV) and candidiasis. Lactobacillus species, owing to their capacity to create an acidic environment through the production of lactic acid, have a key function within this complex microbial community: they inhibit the growth of harmful microorganisms. This study aimed to investigate the genomic characteristics of L. rhamnosus LR6, a newly discovered strain isolated from the vaginal microbiota of 20 healthy women to assess its potential as a vaginal probiotic. We performed a comparative investigation of the genetic traits of L. rhamnosus using 45 publicly available genomes from various sources. We evaluated the genetic characteristics related to carbohydrate utilization, adhesion to host cells, and the presence of bacteriocin clusters. A comprehensive study was conducted by integrating in silico evaluations with experimental techniques to authenticate the physiological characteristics of strain LR6. We further used a rat model to assess the impact of L. rhamnosus LR6 administration on the changes in the gastrointestinal tract and the vaginal microbiome. The assessments revealed a significantly high inhibitory activity against pathogens, enhanced adherence to host cells, and high lactic acid production. Rat experiments revealed changes in both the fecal and vaginal microbiota; in treated rats, Firmicutes increased in both; Lactobacillaceae increased in the fecal samples; and Enterobacteriaceae decreased but Enterococcaceae, Streptococcaceae, and Morganellaceae increased in the vaginal samples. The study results provide evidence of the genetic characteristics and probiotic properties of LR6, and suggest that oral administration of L. rhamnosus LR6 can alter both gut and vaginal microbiome. Collectively, these findings establish L. rhamnosus LR6 as a highly promising candidate for improving vaginal health.
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Affiliation(s)
- Yusook Chung
- R&D Center, Cell Biotech, Co., Ltd., Gimpo-si, Republic of Korea
| | - Seung Beom Kang
- R&D Center, Cell Biotech, Co., Ltd., Gimpo-si, Republic of Korea
| | - Dooheon Son
- R&D Center, Cell Biotech, Co., Ltd., Gimpo-si, Republic of Korea
| | - Ji Young Lee
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Myung Jun Chung
- R&D Center, Cell Biotech, Co., Ltd., Gimpo-si, Republic of Korea
| | - Sanghyun Lim
- R&D Center, Cell Biotech, Co., Ltd., Gimpo-si, Republic of Korea
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29
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Morrill SR, Saha S, Varki AP, Lewis WG, Ram S, Lewis AL. Gardnerella Vaginolysin Potentiates Glycan Molecular Mimicry by Neisseria gonorrhoeae. J Infect Dis 2023; 228:1610-1620. [PMID: 37722688 PMCID: PMC10681867 DOI: 10.1093/infdis/jiad391] [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: 04/14/2023] [Revised: 08/01/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
Bacterial vaginosis (BV) is a dysbiotic condition of the vaginal microbiome associated with higher risk of infection by Neisseria gonorrhoeae-the cause of gonorrhea. Here we test if one known facet of BV-the presence of bacterial cytolysins-leads to mobilization of intracellular contents that enhance gonococcal virulence. We cloned and expressed recombinant vaginolysin (VLY), a cytolysin produced by the BV-associated bacterium Gardnerella, verifying that it liberates contents of cervical epithelial (HeLa) cells, while vector control preparations did not. We tested if VLY mediates a well-known gonococcal virulence mechanism-the molecular mimicry of host glycans. To evade host immunity, N. gonorrhoeae caps its lipooligosaccharide (LOS) with α2-3-linked sialic acid. For this, gonococci must scavenge a metabolite made inside host cells. Flow cytometry-based lectin-binding assays showed that gonococci exposed to vaginolysin-liberated contents of HeLa cells displayed greater sialic acid capping of their LOS. This higher level of bacterial sialylation was accompanied by increased binding of the complement regulatory protein factor H, and greater resistance to complement attack. Together these results suggest that cytolytic activities present during BV may enhance the ability of N. gonorrhoeae to capture intracellular metabolites and evade host immunity via glycan molecular mimicry.
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Affiliation(s)
- Sydney R Morrill
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, California, USA
| | - Sudeshna Saha
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, California, USA
| | - Ajit P Varki
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny, University of California San Diego, La Jolla, California, USA
| | - Warren G Lewis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, California, USA
| | - Sanjay Ram
- Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Amanda L Lewis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, California, USA
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Shi Y, Li H, Wang C, Chen J, Jiang H, Shih YCT, Zhang H, Song Y, Feng Y, Liu L. A flexible quasi-likelihood model for microbiome abundance count data. Stat Med 2023; 42:4632-4643. [PMID: 37607718 PMCID: PMC11045296 DOI: 10.1002/sim.9880] [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: 01/04/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
In this article, we present a flexible model for microbiome count data. We consider a quasi-likelihood framework, in which we do not make any assumptions on the distribution of the microbiome count except that its variance is an unknown but smooth function of the mean. By comparing our model to the negative binomial generalized linear model (GLM) and Poisson GLM in simulation studies, we show that our flexible quasi-likelihood method yields valid inferential results. Using a real microbiome study, we demonstrate the utility of our method by examining the relationship between adenomas and microbiota. We also provide an R package "fql" for the application of our method.
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Affiliation(s)
- Yiming Shi
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri
| | - Huilin Li
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, New York
| | - Chan Wang
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, New York
| | - Jun Chen
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Hongmei Jiang
- Department of Statistics, Northwestern University, Evanston, Illinois
| | - Ya-Chen T. Shih
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, China
| | - Yizhe Song
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri
| | - Yang Feng
- Department of Biostatistics, College of Global Public Health, New York University, New York, New York
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri
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31
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Yu B, Liu C, Proll S, Mannhardt E, Liang S, Srinivasan S, Swisher E, Fredricks DN. Identification of fallopian tube microbiota and its association with ovarian cancer: a prospective study of intraoperative swab collections from 187 patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291999. [PMID: 37425928 PMCID: PMC10327289 DOI: 10.1101/2023.06.28.23291999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Investigating the human fallopian tube (FT) microbiota has significant implications for understanding the pathogenesis of ovarian cancer (OC). In this large prospective study, we collected swabs intraoperatively from the FT and other surgical sites as controls to profile the microbiota in the FT and to assess its relationship with OC. 81 OC and 106 non-cancer patients were enrolled and 1001 swabs were processed for 16S rRNA gene PCR and sequencing. We identified 84 bacterial species that may represent the FT microbiota and found a clear shift in the microbiota of the OC patients when compared to the non-cancer patients. Of the top 20 species that were most prevalent in the FT of OC patients, 60% were bacteria that predominantly reside in the gastrointestinal tract, while 30% normally reside in the mouth. Serous carcinoma had higher prevalence of almost all 84 FT bacterial species compared to the other OC subtypes. The clear shift in the FT microbiota in OC patients establishes the scientific foundation for future investigation into the role of these bacteria in the pathogenesis of ovarian cancer. .
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Zhang G, Bai J, Jia J, Wang W, Wang D, Zhao Q, Wang C, Chen G. Soil microbial communities regulate the threshold effect of salinity stress on SOM decomposition in coastal salt marshes. FUNDAMENTAL RESEARCH 2023; 3:868-879. [PMID: 38933010 PMCID: PMC11197625 DOI: 10.1016/j.fmre.2023.02.024] [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: 05/25/2022] [Revised: 12/23/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Salinity stress is one of the critical environmental drivers of soil organic matter (SOM) decomposition in coastal ecosystems. Although the temperature sensitivity (Q10) of SOM decomposition has been widely applied in Earth system models to forecast carbon processes, the impact of salinity on SOM decomposition by restructuring microbial communities remains uncovered. Here, we conducted a microcosm experiment with soils collected from the coastal salt marsh in the Yellow River Estuary, which is subjected to strong dynamics of salinity due to both tidal flooding and drainage. By setting a gradient of salt solutions, soil salinity was adjusted to simulate salinity stress and soil carbon emission (CO2) rate was measured over the period. Results showed that as salinity increased, the estimated decomposition constants based on first-order kinetics gradually decreased at different temperatures. Below the 20‰ salinity treatments, which doubled the soil salinity, Q10 increased with increasing salinity; but higher salinity constrained the temperature-related response of SOM decomposition by inhibiting microbial growth and carbon metabolisms. Soil bacteria were more sensitive to salinity stress than fungi, which can be inferred from the response of microbial beta-diversity to changing salinity. Among them, the phylotypes assigned to Gammaproteobacteria and Bacilli showed higher salt tolerance, whereas taxa affiliated with Alphaproteobacteria and Bacteroidota were more easily inhibited by the salinity stress. Several fungal taxa belonging to Ascomycota had higher adaptability to the stress. As the substrate was consumed with the incubation, bacterial competition intensified, but the fungal co-occurrence pattern changed weakly during decomposition. Collectively, these findings revealed the threshold effect of salinity on SOM decomposition in coastal salt marshes and emphasized that salt stress plays a key role in carbon sequestration by regulating microbial keystone taxa, metabolisms, and interactions.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dawei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Chen Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Guozhu Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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33
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Jordan SJ, Wilson L, Ren J, Gupta K, Barnes S, Geisler WM. Natural Clearance of Chlamydia trachomatis Infection Is Associated With Distinct Differences in Cervicovaginal Metabolites. J Infect Dis 2023; 228:1119-1126. [PMID: 37163744 PMCID: PMC10582912 DOI: 10.1093/infdis/jiad155] [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: 12/08/2022] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Natural clearance of Chlamydia trachomatis in women occurs in the interval between screening and treatment. In vitro, interferon-γ (IFN-γ)-mediated tryptophan depletion results in C. trachomatis clearance, but whether this mechanism occurs in vivo remains unclear. We previously found that women who naturally cleared C. trachomatis had lower cervicovaginal levels of tryptophan and IFN-γ compared to women with persisting infection, suggesting IFN-γ-independent pathways may promote C. trachomatis clearance. METHODS Cervicovaginal lavages from 34 women who did (n = 17) or did not (n = 17) naturally clear C. trachomatis were subjected to untargeted high-performance liquid chromatography mass-spectrometry to identify metabolites and metabolic pathways associated with natural clearance. RESULTS In total, 375 positively charged metabolites and 149 negatively charged metabolites were annotated. Compared to women with persisting infection, C. trachomatis natural clearance was associated with increased levels of oligosaccharides trehalose, sucrose, melezitose, and maltotriose, and lower levels of indoline and various amino acids. Metabolites were associated with valine, leucine, and isoleucine biosynthesis pathways. CONCLUSIONS The cervicovaginal metabolome in women who did or did not naturally clear C. trachomatis is distinct. In women who cleared C. trachomatis, depletion of various amino acids, especially valine, leucine, and isoleucine, suggests that amino acids other than tryptophan impact C. trachomatis survival in vivo.
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Affiliation(s)
- Stephen J Jordan
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Landon Wilson
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jie Ren
- Department of Biostatics and Health Data Science, Indiana University, Indianapolis, Indiana, USA
| | - Kanupriya Gupta
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Stephen Barnes
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William M Geisler
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Srinivasan S, Austin MN, Fiedler TL, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Beamer MA, Achilles SL, Wiesenfeld HC, Fredricks DN, Hillier SL. Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787404 DOI: 10.1099/ijsem.0.006017] [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: 10/04/2023] Open
Abstract
Four obligately anaerobic Gram-positive bacteria representing one novel genus and two novel species were isolated from the female genital tract. Both novel species, designated UPII 610-JT and KA00274T, and an additional isolate of each species were characterized utilizing biochemical, genotypic and phylogenetic analyses. All strains were non-motile and non-spore forming, asaccharolytic, non-cellulolytic and indole-negative coccobacilli. Fatty acid methyl ester analysis for UPII 610-JT and KA00274T and additional isolates revealed C16 : 0, C18 : 0, C18:1ω9c and C18:2ω6,9c to be the major fatty acids for both species. UPII 610-JT had a 16S rRNA gene sequence similarity of 99.4 % to an uncultured clone sequence (AY724740) designated as Bacterial Vaginosis Associated Bacterium 2 (BVAB2). KA00274T had a 16S rRNA gene sequence similarity of 96.5 % to UPII 610-JT. Whole genomic DNA mol% G+C content was 42.2 and 39.3 % for UPII 610-JT and KA00274T, respectively. Phylogenetic analyses indicate these isolates represent a novel genus and two novel species within the Oscillospiraceae family. We propose the names Amygdalobacter indicium gen. nov., sp. nov., for UPII 610-JT representing the type strain of this species (=DSM 112989T, =ATCC TSD-274T) and Amygdalobacter nucleatus gen. nov., sp. nov., for KA00274T representing the type strain of this species (=DSM 112988T, =ATCC TSD-275T).
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kathy J Agnew
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - May A Beamer
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Sharon L Achilles
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - Harold C Wiesenfeld
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sharon L Hillier
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
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Tsamir-Rimon M, Borenstein E. A Manifold-Based Framework for Studying the Dynamics of the Vaginal Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556518. [PMID: 37732273 PMCID: PMC10508760 DOI: 10.1101/2023.09.06.556518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The vaginal bacterial community plays a crucial role in preventing infections. The composition of this community can be classified into five main groups, termed community state types (CSTs). Four of these CSTs, which are primarily consisted of Lactobacillus species, are considered healthy, while the fifth, which is composed of non-Lactobacillus populations, is considered less protective. This latter CST is often considered to represent a state termed Bacterial vaginosis (BV) - a common disease condition associated with unpleasant symptoms and increased susceptibility to sexually transmitted diseases. However, the exact mechanisms underlying BV development are not yet fully understood, including specifically, the dynamics of the vaginal microbiome in BV, and the possible routes it may take from a healthy to a BV state. This study aims to identify the progression from healthy Lactobacillus-dominant populations to symptomatic BV by analyzing 8,026 vaginal samples and using a manifold-detection framework. This approach is inspired by single-cell analysis and aims to identify low-dimensional trajectories in the high-dimensional composition space. This framework further order samples along these trajectories and assign a score (pseudo-time) to each sample based on its proximity to the BV state. Our results reveal distinct routes of progression between healthy and BV state for each CST, with pseudo-time scores correlating with community diversity and quantifying the health state of each sample. BV indicators, including Nugent score, positive Amsel's test, and several Amsel's criteria, can also be successfully predicted based on pseudo-time scores. Additionally, Gardnerella vaginalis can be identified as a key taxon in BV development using this approach, with increased abundance in samples with high pseudo-time, indicating an unhealthier state across all BV-development routes on the manifold. Taken together, these findings demonstrate how manifold detection can be used to successfully characterizes 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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Lee EM, Srinivasan S, Purvine SO, Fiedler TL, Leiser OP, Proll SC, Minot SS, Deatherage Kaiser BL, Fredricks DN. Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome. mSystems 2023; 8:e0067822. [PMID: 37350639 PMCID: PMC10469846 DOI: 10.1128/msystems.00678-22] [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: 07/25/2022] [Accepted: 04/06/2023] [Indexed: 06/24/2023] Open
Abstract
Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.
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Affiliation(s)
- Elliot M. Lee
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
- University of Washington, Seattle, Washington, DC, USA
| | | | - Samuel O. Purvine
- Pacific Northwest National Laboratory, Richland, Washington, DC, USA
| | - Tina L. Fiedler
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Owen P. Leiser
- Pacific Northwest National Laboratory, Richland, Washington, DC, USA
| | - Sean C. Proll
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Samuel S. Minot
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | | | - David N. Fredricks
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
- University of Washington, Seattle, Washington, DC, USA
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37
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Margolis EB, Maron G, Sun Y, Dallas RH, Allison KJ, Ferrolino J, Ross HS, Davis AE, Jia Q, Turner P, Mackay V, Morin CE, Triplett BM, Klein EJ, Englund JA, Tang L, Hayden RT. Microbiota Predict Infections and Acute Graft-Versus-Host Disease After Pediatric Allogeneic Hematopoietic Stem Cell Transplantation. J Infect Dis 2023; 228:627-636. [PMID: 37249910 PMCID: PMC10469318 DOI: 10.1093/infdis/jiad190] [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: 11/16/2022] [Revised: 04/19/2023] [Accepted: 05/27/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Despite preventive measures, infections continue to pose significant risks to pediatric allogeneic hematopoietic cell transplantation (allo-HCT) recipients. The gut microbiota has been linked to clinical outcomes following adult allo-HCT. This study evaluated whether similar disruptions or differing microbiota patterns were associated with infection risk in pediatric allo-HCT. METHODS In a prospective observational study, fecal samples were obtained from 74 children before conditioning and upon neutrophil recovery. Microbiome signatures identified through sequencing were examined for their associations with infections or acute graft-versus-host disease (aGVHD) in the first-year post-HCT using Cox proportional hazards analysis. RESULTS Microbiome disruption in adults, did not predict infection risk in pediatric allo-HCT. Unique microbiota signatures were associated with different infections or aGVHD. A ratio of strict and facultative anaerobes (eg, Lachnoclostridium, Parabacteroides) prior to conditioning predicted bacteremia risk (Cox hazard ratio [HR], 3.89). A distinct ratio of oral (eg, Rothia, Veillonella) to intestinal anaerobes (eg, Anaerobutyricum, Romboutsia) at neutrophil recovery predicted likelihood of bacterial infections (Cox HR, 1.81) and viral enterocolitis (Cox HR, 1.96). CONCLUSIONS Interactions between medical interventions, pediatric hosts, and microbial communities contribute to microbiota signatures that predict infections. Further multicenter study is necessary to validate the generalizability of these ratios as biomarkers.
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Affiliation(s)
- Elisa B Margolis
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Department of Pediatrics, University of Tennessee Health Sciences Center
| | - Gabriela Maron
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Department of Pediatrics, University of Tennessee Health Sciences Center
| | - Yilun Sun
- Department of Biostatistics, St Jude Children’s Research Hospital
| | - Ronald H Dallas
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Kim J Allison
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Jose Ferrolino
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Hailey S Ross
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Amy E Davis
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis
| | - Qidong Jia
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Paige Turner
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Victoria Mackay
- Department of Infectious Diseases, St Jude Children’s Research Hospital
| | - Cara E Morin
- Division of Radiology and Medical Imaging, Cincinnati Children's Hospital, Ohio
| | - Brandon M Triplett
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, Tennessee
| | | | | | - Li Tang
- Department of Biostatistics, St Jude Children’s Research Hospital
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Mehta SD, Agingu W, Zulaika G, Nyothach E, Bhaumik R, Green SJ, van Eijk AM, Otieno FO, Phillips-Howard PA, Schneider J. Vaginal Microbial Network Analysis Reveals Novel Taxa Relationships among Adolescent and Young Women with Incident Sexually Transmitted Infection Compared with Those Remaining Persistently Negative over a 30-Month Period. Microorganisms 2023; 11:2035. [PMID: 37630595 PMCID: PMC10459434 DOI: 10.3390/microorganisms11082035] [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: 06/07/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus crispatus and is often associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how different groups of bacteria relate to incident STIs, especially among adolescents. In this study, we compared the VMB (measured via 16S ribosomal RNA gene amplicon sequencing) of Kenyan secondary school girls with incident STIs (composite of chlamydia, gonorrhea, and trichomoniasis) to those who remained persistently negative for STIs and BV over 30 months of follow-up. We applied microbial network analysis to identify key taxa (i.e., those with the greatest connectedness in terms of linkages to other taxa), as measured by betweenness and eigenvector centralities, and sub-groups of clustered taxa. VMB networks of those who remained persistently negative reflected greater connectedness compared to the VMB from participants with STI. Taxa with the highest centralities were not correlated with relative abundance and differed between those with and without STI. Subject-level analyses indicated that sociodemographic (e.g., age and socioeconomic status) and behavioral (e.g., sexual activity) factors contribute to microbial network structure and may be of relevance when designing interventions to improve VMB health.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
| | - Walter Agingu
- Nyanza Reproductive Health Society, Kisumu P.O. Box 1764, Kenya
| | - Garazi Zulaika
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | - Runa Bhaumik
- Division of Epidemiology & Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- Division of Infectious Disease Medicine, College of Medicine, Rush University, Chicago, IL 60612, USA
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL 60612, USA
| | - Anna Maria van Eijk
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK (P.A.P.-H.)
| | | | | | - John Schneider
- Departments of Medicine and Public Health Sciences, School of Medicine, University of Chicago, Chicago, IL 60637, USA;
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Koyama M, Hippe DS, Srinivasan S, Proll SC, Miltiadous O, Li N, Zhang P, Ensbey KS, Hoffman NG, Schmidt CR, Yeh AC, Minnie SA, Strenk SM, Fiedler TL, Hattangady N, Kowalsky J, Grady WM, Degli-Esposti MA, Varelias A, Clouston AD, van den Brink MRM, Dey N, Randolph TW, Markey KA, Fredricks DN, Hill GR. Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity. Immunity 2023; 56:1876-1893.e8. [PMID: 37480848 PMCID: PMC10530372 DOI: 10.1016/j.immuni.2023.06.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/11/2023] [Accepted: 06/28/2023] [Indexed: 07/24/2023]
Abstract
Acute graft-versus-host disease (aGVHD) remains a major limitation of allogeneic stem cell transplantation (SCT), and severe intestinal manifestation is the major cause of early mortality. Intestinal microbiota control MHC class II (MHC-II) expression by ileal intestinal epithelial cells (IECs) that promote GVHD. Here, we demonstrated that genetically identical mice of differing vendor origins had markedly different intestinal microbiota and ileal MHC-II expression, resulting in discordant GVHD severity. We utilized cohousing and antibiotic treatment to characterize the bacterial taxa positively and negatively associated with MHC-II expression. A large proportion of bacterial MHC-II inducers were vancomycin sensitive, and peri-transplant oral vancomycin administration attenuated CD4+ T cell-mediated GVHD. We identified a similar relationship between pre-transplant microbes, HLA class II expression, and both GVHD and mortality in a large clinical SCT cohort. These data highlight therapeutically tractable mechanisms by which pre-transplant microbial taxa contribute to GVHD independently of genetic disparity.
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Affiliation(s)
- Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA.
| | - Daniel S Hippe
- Clinical Research Division, FHCC, Seattle, WA 98109, USA
| | | | - Sean C Proll
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Naisi Li
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Kathleen S Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Noah G Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Christine R Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Albert C Yeh
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Simone A Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Namita Hattangady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Jacob Kowalsky
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Willian M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Antiopi Varelias
- Transplantation Immunology Laboratory, Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, University of Queensland, St Lucia, QLD 4067, Australia
| | - Andrew D Clouston
- Molecular and Cellular Pathology, University of Queensland, Brisbane, QLD 4006, Australia
| | - Marcel R M van den Brink
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA; Department of Immunology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Timothy W Randolph
- Clinical Research Division, FHCC, Seattle, WA 98109, USA; Public Health Sciences Division, FHCC, WA 98109, USA
| | - Kate A Markey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Geoffrey R Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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40
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Zinsli KA, Srinivasan S, Balkus JE, Chambers LC, Lowens MS, Morgan J, Rowlinson E, Robinson TS, Romano SS, Munch MM, Manhart LE, Fredricks DN. Bacterial vaginosis-associated bacteria in cisgender men who have sex with women: prevalence, association with non-gonococcal urethritis and natural history. Sex Transm Infect 2023; 99:317-323. [PMID: 36601742 PMCID: PMC10241981 DOI: 10.1136/sextrans-2022-055494] [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: 04/07/2022] [Accepted: 10/18/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Bacterial vaginosis-associated bacterium 2 (BVAB2), Mageeibacillus indolicus and Sneathia spp are highly predictive of bacterial vaginosis (BV) in cisgender women. They have been associated with non-gonococcal urethritis (NGU) in cisgender men in some but not all populations. We evaluated this association in a cross-sectional study of cisgender men who have sex with women only (MSW). METHODS MSW without gonorrhoea attending a sexual health clinic (SHC) from 2014 to 2018 completed a computer-assisted self-interview, clinical interview and examination. NGU was defined as ≥5 polymorphonuclear leucocytes/high-power field in urethral exudates plus either urethral symptoms or visible discharge. Urine was tested for Chlamydia trachomatis and Mycoplasma genitalium using Aptima (Hologic) and for BVAB2, M. indolicus, Sneathia spp, Trichomonas vaginalis, Ureaplasma urealyticum, Haemophilus influenzae, herpes simplex virus and adenovirus using quantitative PCR. RESULTS Of 317 MSW age 17-71, 67 (21.1%) had Sneathia spp, 36 (11.4%) had BVAB2, and 17 (5.4%) had M. indolicus at enrolment. Having ≥3 partners in the past 2 months was the only characteristic that was more common among MSW with than those without these bacteria (BVAB2: 47% vs 23%, M. indolicus: 53% vs 24%, Sneathia spp: 42% vs 22%; p≤0.03 for all). One-hundred seventeen men (37%) were diagnosed with NGU at enrolment. There was no significant association of BVAB2, M. indolicus or Sneathia spp with NGU (adjusted OR=0.59, 95% CI 0.14 to 2.43; aOR=3.40, 95% CI 0.68 to 17.06; aOR=0.46, 95% CI 0.16 to 1.27). Of 109 MSW with monthly samples, 34 (31.2%) had one of the bacteria at one or more follow-up visits, 22 of which were co-colonised with >1. Median persistence over 6 months did not differ significantly (BVAB2=30.5 days, IQR=28-87; M. indolicus=87 days, IQR=60-126; Sneathia spp=70 days, IQR=30-135; p≥0.20 for each comparison). CONCLUSIONS Neither BVAB2, M. indolicus nor Sneathia spp were associated with increased risk of prevalent NGU in MSW attending an SHC.
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Affiliation(s)
- Kaitlin A Zinsli
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer E Balkus
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Laura C Chambers
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - M Sylvan Lowens
- HIV/STD Program, Public Health - Seattle & King County, Seattle, Washington, USA
| | - Jennifer Morgan
- HIV/STD Program, Public Health - Seattle & King County, Seattle, Washington, USA
| | - Emily Rowlinson
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Tashina S Robinson
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Sarah S Romano
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lisa E Manhart
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
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41
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Dass M, Singh Y, Ghai M. A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans. Curr Microbiol 2023; 80:299. [PMID: 37491404 PMCID: PMC10368579 DOI: 10.1007/s00284-023-03413-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 07/27/2023]
Abstract
Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.
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Affiliation(s)
- Mishka Dass
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Yashna Singh
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
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42
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Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN, McClelland RS. Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study. Int J STD AIDS 2023; 34:557-566. [PMID: 36945124 PMCID: PMC11075686 DOI: 10.1177/09564624231160806] [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: 03/23/2023]
Abstract
BACKGROUND The association between vaginal washing and HIV risk may be mediated by vaginal washing-associated changes in vaginal microbiota. METHODS Data from a cohort of HIV-negative US and Kenyan women enrolled in the Preventing Vaginal Infections trial were analyzed. Vaginal fluid samples and vaginal washing data were collected every 2 months for 12 months. Bacterial relative abundances were measured by broad-range 16S rRNA gene polymerase chain reaction with next generation sequencing. Generalized estimating equations were used to evaluate the association between vaginal washing and i) the Shannon Diversity Index (SDI); and ii) mean change in percent bacterial relative abundances, with application of a 10% false discovery rate (FDR). RESULTS Participants (N = 111) contributed 93/630 (14.8%) vaginal washing visits. Mean SDI was 0.74 points higher (95% CI 0.35, 1.14; p < 0.001) at washing visits among US participants (N = 26). Vaginal washing was not associated with SDI in Kenyan participants (N = 85). There were no associations between vaginal washing and vaginal bacterial relative abundances after applying the FDR. CONCLUSIONS The discordant results in Kenyan versus US women suggests the link between vaginal washing and sub-optimal vaginal microbiota may be context specific. Vaginal microbial shifts may not fully explain the association between vaginal washing and HIV acquisition.
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Affiliation(s)
- Michelle C. Sabo
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer E. Balkus
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Joshua Kimani
- Institute for Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Jane Schwebke
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David N. Fredricks
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - R. Scott McClelland
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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Zhu X, Zhang L, Li J, He A, You M, You S. Effects of Antibiotic Treatment on the Development and Bacterial Community of the Wolbachia-Infected Diamondback Moth. Evol Bioinform Online 2023; 19:11769343231175269. [PMID: 37324163 PMCID: PMC10265341 DOI: 10.1177/11769343231175269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
Based on the important role of antibiotic treatment in the research of the interaction between Wolbachia and insect hosts, this study aimed to identify the most suitable antibiotic and concentration for Wolbachia elimination in the P. xylostella, and to investigate the effect of Wolbachia and antibiotic treatment on the bacterial community of P. xylostella. Our results showed that the Wolbachia-infected strain was plutWB1 of supergroup B in the P. xylostella population collected in Nepal in this study; 1 mg/mL rifampicin could remove Wolbachia infection in P. xylostella after 1 generation of feeding treatment and the toxic effect was relatively low; among the 29 samples of adult P. xylostella in our study (10 WU samples, 10 WA samples, and 9 WI samples), 52.5% of the sequences were of Firmicutes and 47.5% were of Proteobacteria, with the dominant genera being mainly Carnobacterium (46.2%), Enterobacter (10.1%), and Enterococcus (6.2%); Moreover, antibiotic removal of Wolbachia infection in P. xylostella and transfer to normal conditions for 10 generations no longer significantly affected the bacterial community of P. xylostella. This study provides a theoretical basis for the elimination method of Wolbachia in the P. xylostella, as well as a reference for the elimination method of Wolbachia in other Wolbachia-infected insect species, and a basis for the study of the extent and duration of the effect of antibiotic treatment on the bacterial community of the P. xylostella.
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Affiliation(s)
- Xiangyu Zhu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
| | - Ling Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
| | - Jinyang Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
| | - Ao He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
| | - Shijun You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
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Asare K, Ngcapu S, Osman F, Vandormael A, Mindel A, Naicker N, Khanyile M, S Abdool Karim S, Tomita A, Garrett N. Incidence, recurrence, and prevalence of bacterial vaginosis from acute to chronic HIV infection in a prospective cohort of women in South Africa. Ann Epidemiol 2023; 82:33-39. [PMID: 37037344 PMCID: PMC10247472 DOI: 10.1016/j.annepidem.2023.04.004] [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: 12/01/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/12/2023]
Abstract
PURPOSE We investigated the incidence, recurrence, prevalence, and risk factors for bacterial vaginosis (BV) diagnosis starting from acute HIV infection among South African women. METHODS The Centre for the AIDS Programme of Research in South Africa 002 study tested and treated women for BV (Nugent score 7-10) once/twice annually from acute to chronic HIV infection (2004-2020). We estimated BV incidence as the number of new cases and recurrence as the number of subsequent diagnoses per 100 person-years (PYs). We fitted Anderson-Gil Cox-proportional-hazard regression models to determine factors associated with BV incidence or recurrence. RESULTS Of 235 participants, the median age at enrollment was 25 years (Inter Quartile Range [IQR] 22-29). BV prevalence at enrollment was 50.6%. BV incidence was 23.9 cases per 100 PYs, and recurrence was 51.3 cases per 100 PYs. BV incidence/recurrence was associated with younger age (<25 years: adjusted hazard ratio [aHR] 1.70, 95% confidence interval [CI] 1.27-2.27), detectable HIV viral load (aHR 1.54, 95% CI 1.27-1.87) and lower CD4 count (<350 cells/μL: aHR 1.33, 95% CI 1.01-1.76). CONCLUSIONS Our findings underscore the need for early antiretroviral treatment initiation with diagnostic BV and sexually transmitted infection care, especially among younger women.
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Affiliation(s)
- Kwabena Asare
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Health Economics and HIV and AIDS Research Division (HEARD), University of KwaZulu-Natal, Durban, South Africa.
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farzana Osman
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Alain Vandormael
- Heidelberg Institute of Global Health, Heidelberg University, Heidelberg, Germany
| | - Adrian Mindel
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nivashnee Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mlungisi Khanyile
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Epidemiology, Columbia University, New York, NY
| | - Andrew Tomita
- Centre for Rural Health, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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Sen K, Bai M, Li J, Ding X, Sen B, Wang G. Spatial Patterns of Planktonic Fungi Indicate Their Potential Contributions to Biological Carbon Pump and Organic Matter Remineralization in the Water Column of South China Sea. J Fungi (Basel) 2023; 9:640. [PMID: 37367576 DOI: 10.3390/jof9060640] [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: 04/22/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi have long been known to be dynamic in coastal water columns with multiple trophic modes. However, little is known about their interactions with abiotic and biotic components, contribution to the biological carbon pump (BCP), and organic matter remineralization in the oceanic water column. In this study, we investigated how fungi vary spatially and how their variations relate to that of bacteria in the water column of the South China Sea (SCS). Fungi were about three orders less prevalent than bacteria, and the main factors influencing their distribution were depth, temperature, and distance from the sites of riverine inputs. The decline in the abundance of fungi with depth was less steep than that of bacteria. Correlation tests revealed a strong positive association between the abundance of fungi and bacteria, especially in the twilight (r = 0.62) and aphotic (r = 0.70) zones. However, the co-occurrence network revealed mutual exclusion between certain members of fungi and bacteria. The majority of fungi in the water column were saprotrophs, which indicated that they were generally involved in the degradation of organic matter, particularly in twilight and aphotic zones. Similar to bacteria, the involvement of fungi in the metabolism of carbohydrates, proteins, and lipids was predicted, pointing to their participation in the turnover of organic carbon and the biogeochemical cycling of carbon, nitrogen, and sulfur. These findings suggest that fungi play a role in BCP and support their inclusion in marine microbial ecosystem models.
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Affiliation(s)
- Kalyani Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Mohan Bai
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiaqian Li
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Xueyan Ding
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China
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Winders TM, Holman DB, Schmidt KN, Luecke SM, Smith DJ, Neville BW, Dahlen CR, Swanson KC, Amat S. Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota. Sci Rep 2023; 13:8121. [PMID: 37208436 DOI: 10.1038/s41598-023-35241-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
A growing number of studies have investigated the feasibility of utilizing hemp by-products as livestock feedstuffs; however, their impact on livestock microbiomes remains unexplored. Here, we evaluated the effects of feeding hempseed cake on the gastrointestinal, respiratory, and reproductive microbiota in beef heifers. Angus-crossbred heifers (19-months old, initial body weight = 494 ± 10 kg [SE]) were fed a corn-based finishing diet containing 20% hempseed cake as a substitute for 20% corn dried distillers' grains with solubles (DM basis; Control; n = 16/group) for 111 days until slaughter. Ruminal fluid and deep nasopharyngeal swabs (days 0, 7, 42, 70 and 98), and vaginal and uterine swabs (at slaughter) were collected, and the microbiota assessed using 16S rRNA gene sequencing. Diet affected the community structure of the ruminal (d 7-98; 0.06 ≤ R2 ≤ 0.12; P < 0.05), nasopharyngeal (d 98; R2 = 0.18; P < 0.001), and vaginal (R2 = 0.06; P < 0.01) microbiota. Heifers fed hempseed cake had increased microbial diversity in the rumen, reduced microbial richness in the vagina, and greater microbial diversity and richness in the uterus. In addition to the distinct microbial communities in the rumen, nasopharynx, vagina and uterus, we identified 28 core taxa that were shared (≥ 60% of all samples) across these sampling locations. Feeding hempseed cake appeared to alter the bovine gut, respiratory and reproductive microbiota. Our results suggest that future research aiming to evaluate the use of hemp by-products in livestock diet should consider their impact on animal microbiome and microbiome mediated animal health and reproductive efficiency. Our findings also highlight the need for research evaluating the impact of hemp-associated food and personal care products on the human microbiome.
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Affiliation(s)
- Thomas M Winders
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Kaycie N Schmidt
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Sarah M Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - David J Smith
- USDA ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Bryan W Neville
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Carl R Dahlen
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
- Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Kendall C Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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Limaye MA, Brubaker S, Randis TM, Ratner AJ. Vaginal carriage of Haemophilus influenzae in a non-pregnant reproductive-age population. BMC Microbiol 2023; 23:141. [PMID: 37208594 PMCID: PMC10197216 DOI: 10.1186/s12866-023-02885-y] [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: 11/12/2022] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Haemophilus influenzae (Hi) is an emerging cause of early onset neonatal sepsis, but mechanisms of transmission are not well understood. We aimed to determine the prevalence of vaginal carriage of Hi in reproductive age women and to examine behavioral and demographic characteristics associated with its carriage. METHODS We performed a secondary analysis of stored vaginal lavage specimens from a prospective cohort study of nonpregnant reproductive-age women. After extraction of bacterial genomic DNA, samples were tested for the presence of the gene encoding Haemophilus protein d (hpd) by quantitative real-time polymerase chain reaction (PCR) using validated primers and probe. PCR for the V3-V4 region of the 16 S rRNA gene (positive control) assessed sample quality. Samples with cycle threshold (CT) value < 35 were defined as positive. Sanger sequencing confirmed the presence of hpd. Behavioral and demographic characteristics associated with vaginal carriage of Hi were examined. RESULTS 415 samples were available. 315 (75.9%) had sufficient bacterial DNA and were included. 14 (4.4%) were positive for hpd. There were no demographic or behavioral differences between the women with Hi vaginal carriage and those without. There was no difference in history of bacterial vaginosis, vaginal microbiome community state type, or presence of Group B Streptococcus in women with and without vaginal carriage of Hi. CONCLUSION Hi was present in vaginal lavage specimens of 4.4% of this cohort. Hi presence was unrelated to clinical or demographic characteristics, though the relatively small number of positive samples may have limited power to detect such differences.
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Affiliation(s)
- Meghana A Limaye
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Sara Brubaker
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, USA
| | - Tara M Randis
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Adam J Ratner
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
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Brown SE, He X, Shardell MD, Ravel J, Ghanem KG, Zenilman JM, Brotman RM. Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Sex Transm Infect 2023; 99:156-161. [PMID: 35636931 PMCID: PMC9708945 DOI: 10.1136/sextrans-2022-055459] [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: 02/15/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Observational studies demonstrate an association between vaginal douching and bacterial vaginosis (BV) characterised by Gram stain. We sought to describe the effect of a douching cessation intervention on the composition and structure of the vaginal microbiota and molecular-BV, a state defined by low levels of Lactobacillus spp evaluated by molecular tools. METHODS 33 women self-collected mid-vaginal swabs twice weekly (982 samples) during a douching observation phase (4 weeks) followed by a douching cessation phase (12 weeks) in a 2005 single crossover pilot study conducted in Baltimore, Maryland. Vaginal microbiota were characterised by 16S rRNA gene amplicon sequencing (V3-V4) and clustered into community state types (CSTs). Conditional logistic regression modelling allowed each participant to serve as their own control. Wilcoxon signed-rank tests were used to evaluate changes in microbiota between phases. Broad-range qPCR assays provided estimates of bacterial absolute abundance per swab in a subsample of seven participants before and after douching. A piecewise linear mixed effects model was used to assess rates of change in bacterial absolute abundance before and after douching. RESULTS There was no statistically significant change in the odds of molecular-BV versus Lactobacillus-dominated CSTs comparing the douching cessation interval to douching observation (adjusted OR 1.77, 95% CI 0.89 to 3.55). Removal of L. iners-dominated CST III from the outcome did not affect the results. There were no significant changes in the relative abundance of four Lactobacillus spp and no meaningful changes in other taxa investigated. There was no significant change in bacterial absolute abundance between a participant's sample collected 3 days prior to and following douching (p=0.46). CONCLUSIONS In this pilot study, douching cessation was not associated with major changes in vaginal microbiota. Douching cessation alone may not durably shift the vaginal microbiota and additional interventions may be needed to restore optimal vaginal microbiota among those who douche.
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Affiliation(s)
- Sarah Elizabeth Brown
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Xin He
- Department of Epidemiology and Biostatistics, University of Maryland at College Park, College Park, Maryland, USA
| | - Michelle D Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Khalil G Ghanem
- Division of Infectious Diseases, Johns Hopkins Medicine School of Medicine, Baltimore, Maryland, USA
| | - Jonathan M Zenilman
- Division of Infectious Diseases, Johns Hopkins Medicine School of Medicine, Baltimore, Maryland, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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49
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Zhao F, Hu X, Ying C. Advances in Research on the Relationship between Vaginal Microbiota and Adverse Pregnancy Outcomes and Gynecological Diseases. Microorganisms 2023; 11:microorganisms11040991. [PMID: 37110417 PMCID: PMC10146011 DOI: 10.3390/microorganisms11040991] [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: 03/06/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The human microbiota inhabiting different parts of the body has been shown to have a significant impact on human health, with the gut microbiota being the most extensively studied in relation to disease. However, the vaginal microbiota is also an essential commensal microbiota in the female body that plays a crucial role in female health. Despite receiving less attention than gut microbiota, its importance in regulating reproductive immunity and its complex dynamic properties have been increasingly recognized in recent years. Advances in research on the relationship between vaginal microbiota and pregnancy outcomes & gynecological diseases in women have shed light on the importance of maintaining a healthy vaginal microbiota. In this review, we aim to compile recent developments in the study of the vaginal microbial ecosystem and its role in female health and reproductive outcomes. We provide a comprehensive account of the normal vaginal microbiota, the association between the vaginal microbiota and pregnancy outcomes, and the impact of the vaginal microbiota on gynecological diseases in women. By reviewing recent research, we hope to contribute to the advancement of academic medicine's understanding of the vaginal microbiota's importance in female health. We also aim to raise awareness among healthcare professionals and the general public of the significance of maintaining a healthy vaginal microbiota for better reproductive health and the prevention of gynecological diseases.
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Affiliation(s)
- Fuju Zhao
- Clinical Laboratory, Huadong Hospital, Fudan University, Shanghai 200031, China
- Clinical Laboratory, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Xianyang Hu
- Huadong Hospital, Fudan University, Shanghai 200031, China
| | - Chunmei Ying
- Clinical Laboratory, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
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Paradoxical Reactions to Anti-TNFα and Anti-IL-17 Treatment in Psoriasis Patients: Are Skin and/or Gut Microbiota Involved? Dermatol Ther (Heidelb) 2023; 13:911-933. [PMID: 36929119 DOI: 10.1007/s13555-023-00904-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
Psoriasis is a chronic, immune-mediated, inflammatory disease primarily affecting the skin. It is currently coming to light that patients with psoriasis have disrupted intestinal barrier and often suffer from comorbidities associated with the gastrointestinal tract. Moreover, there is growing evidence of both cutaneous and intestinal paradoxical reactions during biologic treatment in patients with psoriasis. This review focuses on barrier defects and changes in immune responses in patients with psoriasis, which play an important role in the development of the disease but are also influenced by modern biological treatments targeting IL-17 and TNFα cytokines. Here, we highlight the relationship between the gut-skin axis, microbiota, psoriasis treatment, and the incidence of paradoxical reactions, such as inflammatory bowel disease in patients with psoriasis. A better understanding of the interconnection of these mechanisms could lead to a more personalized therapy and lower the incidence of treatment side effects, thereby improving the quality of life of the affected patients.
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