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Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [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: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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2
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Elnaggar JH, Lammons JW, Taylor CM, Toh E, Ardizzone CM, Dong A, Aaron KJ, Luo M, Tamhane A, Lefkowitz EJ, Quayle AJ, Nelson DE, Muzny CA. Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study. Sex Transm Dis 2023; 50:523-530. [PMID: 37074327 PMCID: PMC10512881 DOI: 10.1097/olq.0000000000001821] [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] [Indexed: 04/20/2023]
Abstract
BACKGROUND Despite more than 60 years of research, the etiology of bacterial vaginosis (BV) remains controversial. In this pilot study, we used shotgun metagenomic sequencing to characterize vaginal microbial community changes before the development of incident BV (iBV). METHODS A cohort of African American women with a baseline healthy vaginal microbiome (no Amsel criteria, Nugent score 0-3 with no Gardnerella vaginalis morphotypes) were followed for 90 days with daily self-collected vaginal specimens for iBV (≥2 consecutive days of a Nugent score of 7-10). Shotgun metagenomic sequencing was performed on select vaginal specimens from 4 women, every other day for 12 days before iBV diagnosis. Sequencing data were analyzed through Kraken2 and bioBakery 3 workflows, and specimens were classified into community state types. Quantitative polymerase chain reaction was performed to compare the correlation of read counts with bacterial abundance. RESULTS Common BV-associated bacteria such as G. vaginalis , Prevotella bivia , and Fannyhessea vaginae were increasingly identified in the participants before iBV. Linear modeling indicated significant increases in G. vaginalis and F . vaginae relative abundance before iBV, whereas the relative abundance of Lactobacillus species declined over time. The Lactobacillus species decline correlated with the presence of Lactobacillus phages. We observed enrichment in bacterial adhesion factor genes on days before iBV. There were also significant correlations between bacterial read counts and abundances measured by quantitative polymerase chain reaction. CONCLUSIONS This pilot study characterizes vaginal community dynamics before iBV and identifies key bacterial taxa and mechanisms potentially involved in the pathogenesis of iBV.
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Affiliation(s)
- Jacob H Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - John W Lammons
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - Evelyn Toh
- Department of Microbiology, Indiana University School of Medicine; Indianapolis, IN, USA
| | - Caleb M Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - Amy Dong
- Department of Microbiology, Indiana University School of Medicine; Indianapolis, IN, USA
| | - Kristal J Aaron
- Division of Infectious Diseases, University of Alabama at Birmingham; Birmingham, AL, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - Ashutosh Tamhane
- Division of Nephrology and 4Center for Clinical and Translational Sciences, University of Alabama at Birmingham; Birmingham, AL, USA
| | - Elliot J Lefkowitz
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham; Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham; Birmingham, AL, USA
| | - Alison J Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center; New Orleans, LA, USA
| | - David E Nelson
- Department of Microbiology, Indiana University School of Medicine; Indianapolis, IN, USA
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham; Birmingham, AL, USA
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3
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Takada K, Melnikov VG, Kobayashi R, Komine-Aizawa S, Tsuji NM, Hayakawa S. Female reproductive tract-organ axes. Front Immunol 2023; 14:1110001. [PMID: 36798125 PMCID: PMC9927230 DOI: 10.3389/fimmu.2023.1110001] [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: 11/28/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023] Open
Abstract
The female reproductive tract (FRT) and remote/versatile organs in the body share bidirectional communication. In this review, we discuss the framework of the "FRT-organ axes." Each axis, namely, the vagina-gut axis, uterus-gut axis, ovary-gut axis, vagina-bladder axis, vagina-oral axis, uterus-oral axis, vagina-brain axis, uterus-brain axis, and vagina-joint axis, is comprehensively discussed separately. Each axis could be involved in the pathogenesis of not only gynecological diseases but also diseases occurring apart from the FRT. Although the microbiota is clearly a key player in the FRT-organ axes, more quantitative insight into the homeostasis of the microbiota could be provided by host function measurements rather than current microbe-centric approaches. Therefore, investigation of the FRT-organ axes would provide us with a multicentric approach, including immune, neural, endocrine, and metabolic aspects, for understanding the homeostatic mechanism of women's bodies. The framework of the FRT-organ axes could also provide insights into finding new therapeutic approaches to maintain women's health.
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Affiliation(s)
- Kazuhide Takada
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,*Correspondence: Kazuhide Takada, ; Satoshi Hayakawa,
| | | | - Ryoki Kobayashi
- Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Microbiology and Immunology, Nihon University, School of Dentistry at Matsudo, Chiba, Japan
| | - Shihoko Komine-Aizawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Noriko M. Tsuji
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Department of Food Science, Jumonji University, Saitama, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,Division of Immune Homeostasis, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,*Correspondence: Kazuhide Takada, ; Satoshi Hayakawa,
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4
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The Vaginal Microbiome in Health and Disease-What Role Do Common Intimate Hygiene Practices Play? Microorganisms 2023; 11:microorganisms11020298. [PMID: 36838262 PMCID: PMC9959050 DOI: 10.3390/microorganisms11020298] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
The vaginal microbiome is a dynamic, sensitive microenvironment. The hallmark of a 'healthy' vaginal microbiome is currently believed to be one dominated by Lactobacillus spp., which acidifies the vaginal environment and help to protect against invading pathogens. However, a 'normal' microbiome is often difficult, if not impossible, to characterise given that it varies in response to numerous variables, including pregnancy, the menstrual cycle, contraceptive use, diet, ethnicity, and stress. A Lactobacillus-depleted microbiome has been linked to a variety of adverse vaginal health outcomes, including preterm birth (PTB), bacterial vaginosis (BV), and increased risk of sexually transmitted infections. The latter two of these have also been associated with feminine intimate hygiene practices, many of which are practised without any evidence of health benefits. The most extensively studied practice is vaginal douching, which is known to cause vaginal dysbiosis, predisposing women to BV, pelvic inflammatory disease, and PTB. However, little is known of the impact that intimate hygiene practices and associated products have on the vaginal microbiome. This review aims to outline the major factors influencing the vaginal microbiome and common vaginal infections, as well as to summarise current research surrounding the impact of hygiene products and practices on the vaginal microbiome.
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Ali A, Jørgensen JS, Lamont RF. The contribution of bacteriophages to the aetiology and treatment of the bacterial vaginosis syndrome. Fac Rev 2022; 11:8. [PMID: 35509673 PMCID: PMC9022730 DOI: 10.12703/r/11-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bacteriophages are obligate intracellular viruses that parasitize bacteria, making use of the host biosynthetic machinery. Bacterial vaginosis (BV) causes serious adverse sequelae, such as sexually transmitted infections, seroconversion to HIV positivity, and preterm birth. The aetiology of BV is multifactorial, and the vaginal microbiota, the response to antibiotics, and the phenotypic outcomes differ between cases. The choice of antibiotics to treat BV depends on the clinician’s personal experience, which contributes to the poor outcome of BV treatment and high recurrence rate. In this review, we classify BV into two subtypes based on whether or not the BV case is sexually associated (potentially phage-related). An appropriate antibiotic can be selected on the basis of this BV-typing to optimise the short- and long-term effects of treatment. Not all Lactobacillus spp. are helpful or protective and some may sequestrate metronidazole, which mitigates its therapeutic efficacy. Phages, used therapeutically, could contribute to eubiosis by sparing beneficial species of Lactobacilli. However, Lactobacilli have an important role in maintaining vaginal eubiosis, so conventional wisdom has been that treatment of BV may benefit from metronidazole that conserves lactobacilli rather than clindamycin, which destroys lactobacilli. Furthermore, if the quality and quantity of vaginal lactobacilli are compromised by phage colonisation, as in the sexually transmitted subtype, eradication of lactobacilli with clindamycin followed by replacement by probiotics may be better therapeutically than metronidazole and reduce recurrence rates. Accordingly, the subtype of BV may provide a more scientific approach to antibiotic selection, which is absent in current clinical guidelines. We provide support for the role of bacteriophages in the aetiology, recurrence or failure to cure BV following treatment, through parasitic colonisation of lactobacilli that may be sexually transmitted and may be enhanced by other risk factors like smoking, a factor associated with BV.
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Affiliation(s)
- Amaan Ali
- St Bartholomew’s and The London School of Medicine and Dentistry, London, UK
| | - Jan Stener Jørgensen
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Odense, Denmark
| | - Ronald F Lamont
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Odense, Denmark
- Division of Surgery, University College London, Northwick Park Institute for Medical Research Campus, London, UK
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In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. Microorganisms 2022; 10:microorganisms10020214. [PMID: 35208669 PMCID: PMC8879116 DOI: 10.3390/microorganisms10020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 01/27/2023] Open
Abstract
While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics.
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Vieira-Baptista P, De Seta F, Verstraelen H, Ventolini G, Lonnee-Hoffmann R, Lev-Sagie A. The Vaginal Microbiome: V. Therapeutic Modalities of Vaginal Microbiome Engineering and Research Challenges. J Low Genit Tract Dis 2022; 26:99-104. [PMID: 34928260 PMCID: PMC8719494 DOI: 10.1097/lgt.0000000000000647] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE This series of articles, titled The Vaginal Microbiome (VMB), written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the recent findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders. MATERIALS AND METHODS A search of PubMed database was performed, using the search terms "vaginal microbiome" with "treatment," "diagnosis," and "research." Full article texts were reviewed. Reference lists were screened for additional articles. RESULTS The currently available approaches for treating vaginitis or attempting to modulate the VMB are often insufficient. It has traditionally relied on the use of antibiotics, antiseptics, and antifungals. The fifth and last article of this series discusses the new and/or alternative therapeutic modalities. It addresses the role of probiotics, prebiotics and symbiotics, activated charcoal, biofilm disrupting agents, acidifying agents, phage therapy, and the concept of vaginal microbiome transplant. The challenges facing the research of VMB, including the clinical impact of microbiome manipulation, classification, and new diagnostic approaches are discussed. CONCLUSIONS Microbiome research has grown dramatically in recent years, motivated by innovations in technology and decrease in analysis costs. This research has yielded huge insight into the nature of microbial communities, their interactions, and effects with their hosts and other microbes. Further understanding of the bacterial, fungal, phage, and viral microbiomes in combination with host genetics, immunologic status, and environmental factors is needed to better understand and provide personalized medical diagnostics and interventions to improve women's health.
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Affiliation(s)
- Pedro Vieira-Baptista
- Hospital Lusíadas Porto, Porto
- Lower Genital Tract Unit, Centro Hospitalar de São João, Porto
- LAP, a Unilabs Company, Porto, Portugal
| | - Francesco De Seta
- Department of Obstetrics and Gynecology, Institute for Maternal and Child Health “IRCCS Burlo Garofolo”, Trieste
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Hans Verstraelen
- Department of Obstetrics & Gynaecology, Ghent University Hospital, Ghent
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Gary Ventolini
- Professor of Obstetrics and Gynecology, Distinguish University Professor, School of Medicine, Texas Tech University Health Sciences Center, Permian Basin, Odessa, Texas, USA
| | - Risa Lonnee-Hoffmann
- Department of Obstetrics and Gynecology, St Olavs University Hospital, Trondheim
- Institute for Clinical and Molekular Medicine, Norwegian University for Science and Technology, Trondheim, Norway
| | - Ahinoam Lev-Sagie
- Faculty of Medicine, Hebrew University of Jerusalem, Israel
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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8
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Happel AU, Balle C, Maust BS, Konstantinus IN, Gill K, Bekker LG, Froissart R, Passmore JA, Karaoz U, Varsani A, Jaspan H. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses 2021; 13:2341. [PMID: 34960611 PMCID: PMC8708031 DOI: 10.3390/v13122341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Brandon S. Maust
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Namibia Institute of Pathology, Hosea Kutako, Windhoek 10005, Namibia
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Rémy Froissart
- CNRS, IRD, Université Montpellier, UMR 5290, MIVEGEC, 34394 Montpellier, France;
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Cape Town 7925, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, 1 Cyclotron Rd., Berkeley, CA 94720, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
- Department of Global Health, University of Washington School of Public Health, 1510 San Juan Road NE, Seattle, WA 98195, USA
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Chopyk J, Bojanowski CM, Shin J, Moshensky A, Fuentes AL, Bonde SS, Chuki D, Pride DT, Crotty Alexander LE. Compositional Differences in the Oral Microbiome of E-cigarette Users. Front Microbiol 2021; 12:599664. [PMID: 34135868 PMCID: PMC8200533 DOI: 10.3389/fmicb.2021.599664] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Electronic (e)-cigarettes have been advocated as a safer alternative to conventional tobacco cigarettes. However, there is a paucity of data regarding the impact of e-cigarette aerosol deposition on the human oral microbiome, a key component in human health and disease. We aimed to fill this knowledge gap through a comparative analysis of the microbial community profiles from e-cigarette users and healthy controls [non-smokers/non-vapers (NSNV)]. Moreover, we sought to determine whether e-cigarette aerosol exposure from vaping induces persistent changes in the oral microbiome. To accomplish this, salivary and buccal mucosa samples were collected from e-cigarette users and NSNV controls, with additional oral samples collected from e-cigarette users after 2 weeks of decreased use. Total DNA was extracted from all samples and subjected to PCR amplification and sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Our analysis revealed several prominent differences associated with vaping, specific to the sample type (i.e., saliva and buccal). In the saliva, e-cigarette users had a significantly higher alpha diversity, observed operational taxonomic units (OTUs) and Faith's phylogenetic diversity (PD) compared to NSNV controls, which declined with decreased vaping. The buccal mucosa swab samples were marked by a significant shift in beta diversity between e-cigarette users and NSNV controls. There were also significant differences in the relative abundance of several bacterial taxa, with a significant increase in Veillonella and Haemophilus in e-cigarette users. In addition, nasal swabs demonstrated a trend toward higher colonization rates with Staphylococcus aureus in e-cigarette users relative to controls (19 vs. 7.1%; p = n.s.). Overall, these data reveal several notable differences in the oral bacterial community composition and diversity in e-cigarette users as compared to NSNV controls.
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Affiliation(s)
- Jessica Chopyk
- Department of Pathology, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Christine M. Bojanowski
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, LA, United States
- Pulmonary Critical Care Section, VA San Diego Healthcare System, La Jolla, CA, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - John Shin
- Pulmonary Critical Care Section, VA San Diego Healthcare System, La Jolla, CA, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Alex Moshensky
- Pulmonary Critical Care Section, VA San Diego Healthcare System, La Jolla, CA, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Ana Lucia Fuentes
- Pulmonary Critical Care Section, VA San Diego Healthcare System, La Jolla, CA, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Saniya S. Bonde
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Dagni Chuki
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - David T. Pride
- Department of Pathology, University of California San Diego (UCSD), La Jolla, CA, United States
- Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Laura E. Crotty Alexander
- Pulmonary Critical Care Section, VA San Diego Healthcare System, La Jolla, CA, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, United States
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10
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Almeida MO, Viana MVC, Cerqueira JC, Aburjaile FF, Junior AAZ, Azevedo V, Carvalho RDO. Novel insights in bacterial vaginosis etiology through genomic approaches. AN ACAD BRAS CIENC 2021; 93:e20200945. [PMID: 33681877 DOI: 10.1590/0001-3765202120200945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/07/2020] [Indexed: 09/02/2023] Open
Abstract
Bacterial vaginosis (BV) has been considered as dysbiosis state whose etiology is not fully understood. This condition affects a large number of women of reproductive age and its study has been highly relevant due to the growing association of BV with and gynecological and obstetric complications and diseases, in addition to a greater susceptibility to sexually transmitted diseases, including HIV. The vaginal microbiota composition presents high variability among different ethnic groups of women, although, generally, the prevalence of lactobacilli species has been reported. Several studies suggest they may play a protective role, especially Lactobacillus crispatus whose population is typically present in low proportions in women with BV. This review article describes the contributions and limitations of genomic approaches in elucidating protective characteristics and mechanisms associated with colonization and persistence of lactobacilli strains. Although some genetic features were associated with resilience of L. crispatus during BV, furher studies are required to uncover their functions.
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Affiliation(s)
- Marcelle O Almeida
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Marcus V C Viana
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil.,Universidade Federal do Pará, Departamento de Genética, Instituto de Ciências Biológicas, Rua Augusto Corrêa, 01, Guamá, 66075-970 Belém, PA, Brazil
| | - JanaÍna C Cerqueira
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Flavia F Aburjaile
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil.,Universidade Federal de Pernambuco, Departamento de Genética, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Andrey A Z Junior
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Bol'shaya Pirogovskaya Ulitsa, 19с1, 119991 Moscow, Russia.,Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Ulitsa Leninskiye Gory, 1с40, 119992 Moscow, Russia
| | - Vasco Azevedo
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Rodrigo D O Carvalho
- Universidade Federal de Minas Gerais, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Av. Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Bol'shaya Pirogovskaya Ulitsa, 19с1, 119991 Moscow, Russia
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11
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Environmental pollutants and the immune response. Nat Immunol 2020; 21:1486-1495. [PMID: 33046888 DOI: 10.1038/s41590-020-0802-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022]
Abstract
Environmental pollution is one of the most serious challenges to health in the modern world. Pollutants alter immune responses and can provoke immunotoxicity. In this Review, we summarize the major environmental pollutants that are attracting wide-ranging concern and the molecular basis underlying their effects on the immune system. Xenobiotic receptors, including the aryl hydrocarbon receptor (AHR), sense and respond to a subset of environmental pollutants by activating the expression of detoxification enzymes to protect the body. However, chronic activation of the AHR leads to immunotoxicity. KEAP1-NRF2 is another important system that protects the body against environmental pollutants. KEAP1 is a sensor protein that detects environmental pollutants, leading to activation of the transcription factor NRF2. NRF2 protects the body from immunotoxicity by inducing the expression of genes involved in detoxification, antioxidant and anti-inflammatory activities. Intervening in these sensor-response systems could protect the body from the devastating immunotoxicity that can be induced by environmental pollutants.
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12
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Characterization of the Vaginal DNA Virome in Health and Dysbiosis. Viruses 2020; 12:v12101143. [PMID: 33050261 PMCID: PMC7600586 DOI: 10.3390/v12101143] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/23/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial vaginosis (BV) is characterized by a reduction in Lactobacillus (L.) spp. abundance and increased abundance of facultative anaerobes, such as Gardnerella spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (q = 0.006, R = 0.26) as well as the presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella spp., and Atopobium vaginae were found (q < 0.002, R > 0.15). The eukaryotic viral community also correlated with BV-status (q = 0.018, R = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.
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13
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da Costa AC, Moron AF, Forney LJ, Linhares IM, Sabino E, Costa SF, Mendes-Correa MC, Witkin SS. Identification of bacteriophages in the vagina of pregnant women: a descriptive study. BJOG 2020; 128:976-982. [PMID: 32970908 DOI: 10.1111/1471-0528.16528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women. DESIGN Descriptive, observational cohort study. SETTING São Paulo, Brazil. POPULATION Pregnant women at 21-24 weeks' gestation. METHODS Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analysed for phages by metagenomic sequencing. MAIN OUTCOME MEASURES Identification of phage families, genera and species. RESULTS Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), three families in 20 women (18.7%), two families in 31 women (29.1%) and one family in 31 women (29.1%). The most common phage species detected were Bacillus phages in 48 (43.6%), Escherichia phages in 45 (40.9%), Staphylococcus phages in 40 (36.4%), Gokushovirus in 33 (30.0%) and Lactobacillus phages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina. CONCLUSIONS Multiple phages are present in the vagina of most mid-trimester pregnant women. TWEETABLE ABSTRACT Bacteriophages are present in the vagina of most pregnant women.
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Affiliation(s)
- A C da Costa
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - A F Moron
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.,Department of Obstetrics, Federal University of São Paulo, São Paulo, Brazil
| | - L J Forney
- Department of Biological Sciences and the Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - I M Linhares
- Department of Gynaecology and Obstetrics, University of São Paulo Medical School, São Paulo, Brazil
| | - E Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - S F Costa
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - M C Mendes-Correa
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - S S Witkin
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
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14
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Miller-Ensminger T, Garretto A, Stark N, Putonti C. Mimicking prophage induction in the body: induction in the lab with pH gradients. PeerJ 2020; 8:e9718. [PMID: 32944418 PMCID: PMC7469935 DOI: 10.7717/peerj.9718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of bacteria within the human body are lysogens, often harboring multiple bacteriophage sequences (prophages) within their genomes. While several different types of environmental stresses can trigger or induce prophages to enter into the lytic cycle, they have yet to be fully explored and understood in the human microbiota. In the laboratory, the most common induction method is the DNA damaging chemical Mitomycin C. Although pH has been listed in the literature as an induction method, it is not widely used. Here, we detail a protocol for prophage induction by culture under different pH conditions. We explored the effects of pH on prophage induction in bacterial isolates from the bladder, where the pH is well documented to vary significantly between individuals as well as between healthy individuals and individuals with urinary tract symptoms or disease. Using this protocol, we successfully induced phages from seven bladder E. coli strains. Testing conditions and stressors appropriate to the environment from which a lysogen is isolated may provide insight into community dynamics of the human microbiota.
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Affiliation(s)
| | - Andrea Garretto
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology & Immunology, University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America
| | - Nicole Stark
- Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Indiana University at Bloomington, Bloomington, IN, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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15
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Federici S, Nobs SP, Elinav E. Phages and their potential to modulate the microbiome and immunity. Cell Mol Immunol 2020; 18:889-904. [PMID: 32901128 DOI: 10.1038/s41423-020-00532-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (hence termed phages) are viruses that target bacteria and have long been considered as potential future treatments against antibiotic-resistant bacterial infection. However, the molecular nature of phage interactions with bacteria and the human host has remained elusive for decades, limiting their therapeutic application. While many phages and their functional repertoires remain unknown, the advent of next-generation sequencing has increasingly enabled researchers to decode new lytic and lysogenic mechanisms by which they attack and destroy bacteria. Furthermore, the last decade has witnessed a renewed interest in the utilization of phages as therapeutic vectors and as a means of targeting pathogenic or commensal bacteria or inducing immunomodulation. Importantly, the narrow host range, immense antibacterial repertoire, and ease of manipulating phages may potentially allow for their use as targeted modulators of pathogenic, commensal and pathobiont members of the microbiome, thereby impacting mammalian physiology and immunity along mucosal surfaces in health and in microbiome-associated diseases. In this review, we aim to highlight recent advances in phage biology and how a mechanistic understanding of phage-bacteria-host interactions may facilitate the development of novel phage-based therapeutics. We provide an overview of the challenges of the therapeutic use of phages and how these could be addressed for future use of phages as specific modulators of the human microbiome in a variety of infectious and noncommunicable human diseases.
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Affiliation(s)
- Sara Federici
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samuel P Nobs
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel. .,Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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16
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The influence of smoking on bacterial resistance after vaccine or antibiotic prophylaxis against recurrent urinary tract infections. Actas Urol Esp 2020; 44:497-504. [PMID: 32595091 DOI: 10.1016/j.acuro.2020.04.002] [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: 08/28/2019] [Revised: 02/20/2020] [Accepted: 04/07/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION The influence of tobacco on the microbiological spectrum, resistance-sensitivity pattern and evolution in patients with recurrent urinary tract infections (RUTI) is analyzed. Evaluation of the effect of polyvalent bacterial vaccine on the prevention of RUTI and smoking status. MATERIAL AND METHODS Retrospective multicenter study of 855 women with RUTI receiving suppressive antibiotic treatment or bacterial vaccine between 2009 and 2013. Group A (GA): Antibiotic (n=495); Subgroups: GA1 non-smoker (n=417), GA2 smoker (n=78). Group B (GB): Vaccine (n=360); Subgroups: GB1 non-smoker (n=263), GB2 smoker (n=97). VARIABLES Age, pre-treatment UTI, disease-free time (DFT), microbial species, sensitivity and resistance. Follow-up at 3, 6 and 12 months with culture and SF-36 questionnaire. RESULTS Mean age 56.51 years (18-75), similar between groups (P=.2257). No difference in the number of pretreatment UTIs (P=.1329) or in the distribution of the bacterial spectrum (P=.7471). DFT was higher in subgroups B compared with A. Urine cultures in GA1: E. coli 62.71% with 8.10% resistance (33% quinolones; 33% cotrimoxazole; 33% quinolones + cotrimoxazole); in GA2 E. coli 61.53% with 75% resistance (16.66% quinolones; 33.33% quinolones + cotrimoxazole; 16.66% amoxicillin-clavulanate; 16.66% erythromycin + phosphomycin + clindamycin) (P=.0133). There were no differences between patients of GA treated with cotrimoxazole and nitrofurantoin (P=.8724). Urine cultures in GB1: E. coli 47.36% with 22.22% resistance (5.55% ciprofloxacin; 5.55% cotrimoxazole; 5.55% ciprofloxacin + cotrimoxazole; 5.55% amoxicillin/clavulanic acid). In GB2 E. coli 70.02% with 61.90% resistances (30.76% quinolones; 30.76% cotrimoxazole; 30.76% quinolones + cotrimoxazole; 17.69% amoxicillin-clavulanic acid) (P=.0144). CONCLUSIONS The development of bacterial resistance is more frequent among women with smoking habits and recurrent urinary infections. This could influence a worse response to preventive treatments, either with antibiotics or vaccines.
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17
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Happel AU, Varsani A, Balle C, Passmore JA, Jaspan H. The Vaginal Virome-Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? Viruses 2020; 12:E832. [PMID: 32751611 PMCID: PMC7472209 DOI: 10.3390/v12080832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Besides bacteria, fungi, protists and archaea, the vaginal ecosystem also contains a range of prokaryote- and eukaryote-infecting viruses, which are collectively referred to as the "virome". Despite its well-described role in the gut and other environmental niches, the vaginal virome remains understudied. With a focus on sexual and reproductive health, we summarize the currently known components of the vaginal virome, its relationship with other constituents of the vaginal microbiota and its association with adverse health outcomes. While a range of eukaryote-infecting viruses has been described to be present in the female genital tract (FGT), few prokaryote-infecting viruses have been described. Literature suggests that various vaginal viruses interact with vaginal bacterial microbiota and host immunity and that any imbalance thereof may contribute to the risk of adverse reproductive health outcomes, including infertility and adverse birth outcomes. Current limitations of vaginal virome research include experimental and analytical constraints. Considering the vaginal virome may represent the missing link in our understanding of the relationship between FGT bacteria, mucosal immunity, and adverse sexual and reproductive health outcomes, future studies evaluating the vaginal microbiome and its population dynamics holistically will be important for understanding the role of the vaginal virome in balancing health and disease.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA;
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
- Department of Pediatrics and Global Health, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA
- Seattle Children’s Research Institute, 307 Westlake Ave N, Seattle, WA 98109, USA
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18
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Boling L, Cuevas DA, Grasis JA, Kang HS, Knowles B, Levi K, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, Rohwer F. Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. Gut Microbes 2020; 11:721-734. [PMID: 31931655 PMCID: PMC7524278 DOI: 10.1080/19490976.2019.1701353] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.
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Affiliation(s)
- Lance Boling
- Department of Biology, San Diego State University, San Diego, CA, USA,CONTACT Lance Boling Department of Biology, San Diego State University, LS301, 5500 Campanile Dr, San Diego, CA92182USA
| | - Daniel A. Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Juris A. Grasis
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Han Suh Kang
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Katelyn McNair
- Department of Biology, San Diego State University, San Diego, CA, USA,Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | | | | | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
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19
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Happel AU, Kullin B, Gamieldien H, Wentzel N, Zauchenberger CZ, Jaspan HB, Dabee S, Barnabas SL, Jaumdally SZ, Dietrich J, Gray G, Bekker LG, Froissart R, Passmore JAS. Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis. PLoS Pathog 2020; 16:e1008559. [PMID: 32497109 PMCID: PMC7271994 DOI: 10.1371/journal.ppat.1008559] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Antibiotics continue to be the standard-of-care for bacterial vaginosis (BV), although recurrence rates are high. Vaginal probiotics may improve durability of BV treatment, although few probiotics for vaginal health contain Lactobacillus spp. that commonly colonize the lower female genital tract. Characteristics of vaginal Lactobacillus strains from South African women were evaluated for their probiotic potential in vitro compared to strains from commercial vaginal products, including growth at varying pHs, ability to lower pH, produce D-/L-lactate and H2O2, influence growth of BV-associated Gardnerella vaginalis and Prevotella bivia, adherence to cervical cells and susceptibility to antibiotics. Fifty-seven Lactobacillus strains were purified from cervico-vaginal fluid, including L. crispatus, L. jensenii, L. gasseri, L. mucosae, and L. vaginalis. L crispatus strains grew better at pHs below 4.5 and lowered pH more effectively than other strains. Production of D-/L-lactate and H2O2 varied between Lactobacillus species and strains. Lactobacillus strains generally inhibited P. bivia more uniformly than G. vaginalis isolates. All vaginal Lactobacillus isolates were resistant to metronidazole while susceptibility to clindamycin varied. Furthermore, vaginal Lactobacillus strains tended to be broadly susceptible to penicillin, amoxicillin, rifampicin and rifabutin. Whole-genome-sequencing of five of the best-performing vaginal Lactobacillus strains confirmed their likely safety, due to antimicrobial resistance elements being largely absent, while putative intact prophages were present in the genomes of two of the five strains. Overall, vaginal Lactobacillus strains largely performed better in these in vitro assays than probiotic strains currently used in probiotics for vaginal health. Including the best-performing vaginal Lactobacillus isolates in a region-specific probiotic for vaginal health may result in improved BV treatment options.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Brian Kullin
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Hoyam Gamieldien
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Nicole Wentzel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Chambrez Z. Zauchenberger
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Seattle Children’s Hospital, Seattle, United States of America
| | - Smritee Dabee
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Seattle Children’s Hospital, Seattle, United States of America
| | - Shaun L. Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Family Centre for Research with Ubuntu (FAMCRU), Stellenbosch University, Tygerberg, South Africa
| | - Shameem Z. Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Janan Dietrich
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Health Systems Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Glenda Gray
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Health Systems Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Linda-Gail Bekker
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Remy Froissart
- UMR MIVEGEC CNRS-IRD-UM, University Montpellier, Montpellier, France
| | - Jo-Ann S. Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- * E-mail:
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20
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Kwak W, Han YH, Seol D, Kim H, Ahn H, Jeong M, Kang J, Kim H, Kim TH. Complete Genome of Lactobacillus iners KY Using Flongle Provides Insight Into the Genetic Background of Optimal Adaption to Vaginal Econiche. Front Microbiol 2020; 11:1048. [PMID: 32528446 PMCID: PMC7264367 DOI: 10.3389/fmicb.2020.01048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/28/2020] [Indexed: 12/02/2022] Open
Abstract
Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited. In this study, the first complete genome of L. iners was constructed using a cost-effective long-read sequencing platform, Flongle from Oxford Nanopore, and comparative genome analysis was conducted using a total of 1,046 strain genomes from 10 vaginal Lactobacillus species. Single-molecule sequencing using Flongle effectively resolved the limitation of the 2nd generation sequencing technologies in dealing with genomic regions of high GC contents, and comparative genome analysis identified three potential core genes (INY, ZnuA, and hsdR) of L. iners which was related to its specific adaption to the vaginal environment. In addition, we performed comparative prophage analysis for 1,046 strain genomes to further identify the species specificity. The number of prophages in L. iners genomes was significantly smaller than other vaginal Lactobacillus species, and one of the specific genes (hsdR) was suggested as the means for defense against bacteriophage. The first complete genome of L. iners and the three specific genes identified in this study will provide useful resources to further expand our knowledge of L. iners and its specific adaption to the vaginal econiche.
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Affiliation(s)
| | - Young-Hyun Han
- Priority Research Center, Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Jaeku Kang
- Priority Research Center, Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea.,Department of Pharmacology, College of Medicine, Konyang University, Daejeon, South Korea
| | - Heebal Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Tae Hyun Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea.,Department of Obstetrics and Gynecology, Konyang University Hospital, Daejeon, South Korea
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21
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Wei B, Peng Z, Huang T, Guan Q, Xie M, Xiong T. Stability of potential prophages in commercial strain Lactobacillus plantarum NCU116 under various stressors. Arch Microbiol 2020; 202:1241-1250. [PMID: 32112122 DOI: 10.1007/s00203-020-01813-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/10/2020] [Accepted: 01/18/2020] [Indexed: 01/21/2023]
Abstract
Genetic stability of bacterium as a starter culture is vital for product quality in fermentation industry. The commercial strain Lactobacillus plantarum NCU116 widely used in fruit and vegetable fermentation was induced with various stressors to investigate the stability of potential prophages. PHAge Search Tool (PHAST) identified three potential prophages in bacterial genome. By spectrophotometric analysis, mitomycin C (MMC), lactic acid, and bile salt were found to inhibit the growth of L. plantarum NCU116 while ethanol and hydrogen peroxide had no notable impacts. Transcriptions of four phage-synthesizing genes (phaR, phacap, phaada, phatail) and four phage-resistant genes (cas116, helR, hsd1, hsd2) under stressors were investigated by quantitative reverse transcription PCR. MMC was found to most significantly upregulated transcriptions of phage-synthesizing genes, followed by lactic acid and bile salt. By transmission electron microscopy, no virus particles from the lysates of strain NCU116 treated by MMC were observed, corresponding to the result that no phage nucleic acids could be extracted from the supernatants of strain NCU116 treated by MMC. This study suggested that no prophages could be induced from L. plantarum NCU116 by strong inducer MMC, indicating its genetic stability, which supports the comprehensive application of strain NCU116 in industry without causing fermentation failure.
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Affiliation(s)
- Benliang Wei
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zhen Peng
- School of Food Science and Technology, Nanchang University, Nanchang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Tao Huang
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Qianqian Guan
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Mingyong Xie
- School of Food Science and Technology, Nanchang University, Nanchang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China
| | - Tao Xiong
- School of Food Science and Technology, Nanchang University, Nanchang, China. .,State Key Laboratory of Food Science and Technology, Nanchang University, 235 East Nanjing Road, Nanchang, 330047, China.
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22
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Gregory AC, Sullivan MB, Segal LN, Keller BC. Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome. Respir Res 2018; 19:174. [PMID: 30208886 PMCID: PMC6136173 DOI: 10.1186/s12931-018-0878-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The role of commensal viruses in humans is poorly understood, and the impact of the virome on lung health and smoking-related disease is particularly understudied. METHODS Genetic material from acellular bronchoalveolar lavage fluid was sequenced to identify and quantify viral members of the lower respiratory tract which were compared against concurrent bronchoalveolar lavage bacterial, metabolite, cytokine and cellular profiles, and clinical data. Twenty smoker and 10 nonsmoker participants with no significant comorbidities were studied. RESULTS Viruses that infect bacteria (phages) represented the vast majority of viruses in the lung. Though bacterial communities were statistically indistinguishable across smokers and nonsmokers as observed in previous studies, lung viromes and metabolic profiles were significantly different between groups. Statistical analyses revealed that changes in viral communities correlate most with changes in levels of arachidonic acid and IL-8, both potentially relevant for chronic obstructive pulmonary disease (COPD) pathogenesis based on prior studies. CONCLUSIONS Our assessment of human lung DNA viral communities reveals that commensal viruses are present in the lower respiratory tract and differ between smokers and nonsmokers. The associations between viral populations and local immune and metabolic tone suggest a significant role for virome-host interaction in smoking related lung disease.
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Affiliation(s)
- Ann C. Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care & Sleep Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Brian C. Keller
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University College of Medicine, 201 Davis Heart & Lung Research Institute, 473 West 12th Avenue, Columbus, OH 43210 USA
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23
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Rascovan N, Duraisamy R, Desnues C. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 2017; 70:125-41. [PMID: 27607550 DOI: 10.1146/annurev-micro-102215-095431] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.
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Affiliation(s)
- Nicolás Rascovan
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Raja Duraisamy
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Christelle Desnues
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
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24
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Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol 2017; 15:397-408. [DOI: 10.1038/nrmicro.2017.30] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Hall B, Wong D, Healy C, Tracy MB, Tracy SK, Rawlinson WD. The presence of vaginal Lactobacillus species does not contribute to a measureable difference in amniotic fluid lactate levels collected from the vaginal tract of laboring women. Acta Obstet Gynecol Scand 2017; 96:487-495. [PMID: 28039853 DOI: 10.1111/aogs.13089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 12/20/2016] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Amniotic fluid lactate research is based on the hypothesis that a relationship exists between fatigued uterine muscles and raised concentrations of the metabolite lactate, which is excreted into the amniotic fluid during labor. To assess potentially confounding effects of lactate-producing organisms on amniotic fluid lactate measurements, we aimed to determine if the presence of vaginal Lactobacillus species was associated with elevated levels of amniotic fluid lactate, measured from the vaginal tract of women in labor. MATERIAL AND METHODS Results from this study contribute to a large prospective longitudinal study of amniotic fluid lactate at a teaching hospital in Sydney, Australia. Amniotic fluid lactate measurement was assessed at the time of routine vaginal examination, after membranes had ruptured, using a hand-held lactate meter StatStripXPress (Nova Biomedical). Vaginal swab samples were collected at the time of the first amniotic fluid lactate measurement and stored for later detection and quantification of Lactobacillus species using a TaqMan real-time PCR assay. Swab sample and amniotic fluid lactate results were paired and analyzed. RESULTS The PCR assay detected Lactobacillus species in 48 of 388 (12%) vaginal swab specimens (8% positive, 4% low positive) collected from women in labor after membranes had ruptured. There was no significant difference in median and mean (respectively) amniotic fluid lactate levels with (8.35 mmol/L; 8.95 mmol/L) or without (8.5 mmol/L; 9.08 mmol/L) Lactobacillus species detected. CONCLUSION There was no association between the presence or level of vaginal Lactobacillus species and the measurement of amniotic fluid lactate collected from the vaginal tract of women during labor.
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Affiliation(s)
- Beverley Hall
- Midwifery and Women's Health Research Unit, Royal Hospital for Women, Randwick, University of Sydney, Sydney, NSW, Australia.,Virology Research, Serology and Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Diana Wong
- Virology Research, Serology and Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Clare Healy
- Midwifery and Women's Health Research Unit, Royal Hospital for Women, Randwick, University of Sydney, Sydney, NSW, Australia
| | - Mark B Tracy
- Center for Newborn Care, Westmead Hospital, Westmead, NSW, Australia.,Department of Paediatrics and Child Health, University of Sydney, Camperdown, NSW, Australia
| | - Sally K Tracy
- Midwifery and Women's Health Research Unit, Royal Hospital for Women, Randwick, University of Sydney, Sydney, NSW, Australia
| | - William D Rawlinson
- Virology Research, Serology and Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, Randwick, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
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26
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Payne MS, Ireland DJ, Watts R, Nathan EA, Furfaro LL, Kemp MW, Keelan JA, Newnham JP. Ureaplasma parvum genotype, combined vaginal colonisation with Candida albicans, and spontaneous preterm birth in an Australian cohort of pregnant women. BMC Pregnancy Childbirth 2016; 16:312. [PMID: 27756249 PMCID: PMC5070304 DOI: 10.1186/s12884-016-1110-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 10/11/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Detection of Ureaplasma, Mycoplasma and Candida spp. in the vagina during pregnancy has previously been associated with preterm birth (PTB). However, the prevalence of these microorganisms and the associated obstetric risks (likely to be population-specific) have not been determined in Australian women; furthermore, in the case of Ureaplasma spp., very few studies have attempted characterisation at the species level and none have examined genotype/serovar status to further refine risk assessment. METHODS In order to address these issues we sampled the vaginal fluid of 191 pregnant Australian women at three time points in pregnancy. Culture methods were used for detection of Ureaplasma spp. and Candida spp., and real-time PCR was used for speciation of U. parvum and U. urealyticum, non-albicans Candida spp., Mycoplasma hominis and Mycoplasma genitalium. High-resolution melt PCR was used to genotype U. parvum. Data on various lifestyle factors (including sex during pregnancy and smoking), antimicrobial use and pregnancy outcome were collected on all participants. Chi-square tests were used to assess the association of vaginal microorganisms with PTB. RESULTS Detection of Ureaplasma spp. was higher among spontaneous PTB cases, specifically in the presence of U. parvum [77 % preterm (95 % confidence interval (CI) 50-100 %) vs. 36 % term (CI: 29-43 %), p = 0.004], but not U. urealyticum. The association with PTB strengthened when U. parvum genotype SV6 was detected (54 % preterm (CI: 22-85 %) vs. 15 % term (CI: 10-20 %), p = 0.002); this genotype was also present in 80 % (4/5) of cases of PTB <34 weeks gestation. When present with Candida albicans in the same sample, the association with PTB remained strong for both U. parvum [46 % preterm (CI: 15-78 %) vs. 13 % term (CI: 8-18 %), p = 0.005] and U. parvum genotype SV6 [39 % preterm (CI: 8-69 %) vs. 7 % term (CI: 3-11 %), p = 0.003]. With the exception of Candida glabrata, vaginal colonisation status for all organisms was stable throughout pregnancy. Smoking significantly increased the likelihood of detection of all target organisms. CONCLUSIONS These data suggest that the presence of different species and serovars of Ureaplasma spp. in the vagina confers an increased risk of spontaneous PTB, findings which may be useful in risk assessment for identifying women who would benefit from antimicrobial treatment.
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Affiliation(s)
- Matthew S. Payne
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Demelza J. Ireland
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Rory Watts
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Elizabeth A. Nathan
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
- Women and Infants Research Foundation, Biostatistics and Research Design Unit, Subiaco, WA 6008 Australia
| | - Lucy L. Furfaro
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Matthew W. Kemp
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Jeffrey A. Keelan
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - John P. Newnham
- School of Women’s and Infants’ Health, University of Western Australia, 2nd Floor, Block A, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
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Affiliation(s)
- Adam Wahida
- Division of Virology, Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Klaus Ritter
- Division of Virology, Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Hans-Peter Horz
- Division of Virology, Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
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28
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Abdelmaksoud AA, Koparde VN, Sheth NU, Serrano MG, Glascock AL, Fettweis JM, Strauss JF, Buck GA, Jefferson KK. Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria. MICROBIOLOGY-SGM 2016; 162:466-475. [PMID: 26747455 DOI: 10.1099/mic.0.000238] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing development of bacterial vaginosis (BV). Amongst the lactobacilli, Lactobacillus crispatus appears to be particularly effective at inhibiting growth of BV-associated bacteria. Nonetheless, some women who are colonized with this species can still develop clinical BV. Therefore, we sought to determine whether strains of L. crispatus that colonize women with lactobacilli-dominated vaginal microbiomes are distinct from strains that colonize women who develop BV. The genomes of L. crispatus isolates from four women with lactobacilli-dominated vaginal microbiomes ( <1% 16S rRNA reads above threshold from genera other than Lactobacillus) and four women with microbiomes containing BV-associated bacteria (>12% 16S rRNA reads from bacterial taxa associated with BV) were sequenced and compared. Lactic acid production by the different strains was quantified. Phage induction in the strains was also analysed. There was considerable genetic diversity between strains, and several genes were exclusive to either the strains from Lactobacillus-dominated microbiomes or those containing BV-associated bacteria. Overall, strains from microbiomes dominated by lactobacilli did not differ from strains from microbiomes containing BV-associated bacteria with respect to lactic acid production. All of the strains contained multiple phage, but there was no clear distinction between the presence or absence of BV-associated bacteria with respect to phage-induced lysis. Genes found to be exclusive to the Lactobacillus-dominated versus BV-associated bacteria-containing microbiomes could play a role in the maintenance of vaginal health and the development of BV, respectively.
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Affiliation(s)
- Abdallah A Abdelmaksoud
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Nihar U Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Abigail L Glascock
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Jennifer M Fettweis
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Kimberly K Jefferson
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
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29
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Mehta SD, Donovan B, Weber KM, Cohen M, Ravel J, Gajer P, Gilbert D, Burgad D, Spear GT. The vaginal microbiota over an 8- to 10-year period in a cohort of HIV-infected and HIV-uninfected women. PLoS One 2015; 10:e0116894. [PMID: 25675346 PMCID: PMC4326357 DOI: 10.1371/journal.pone.0116894] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/16/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND We identified predominant vaginal microbiota communities, changes over time, and how this varied by HIV status and other factors in a cohort of 64 women. METHODS Bacterial DNA was extracted from reposited cervicovaginal lavage samples collected annually over an 8-10 year period from Chicago Women's Interagency HIV Study participants: 22 HIV-negative, 22 HIV-positive with stable infection, 20 HIV-positive with progressive infection. The vaginal microbiota was defined by pyrosequencing of the V1/V2 region of the 16S rRNA gene. Scheduled visits included Bacterial vaginsosis (BV) screening; clinically detected cases were referred for treatment. Hierarchical clustering identified bacterial community state types (CST). Multinomial mixed effects modeling determined trends over time in CST, by HIV status and other factors. RESULTS The median follow-up time was 8.1 years (range 5.5-15.3). Six CSTs were identified. The mean relative abundance (RA) of Lactobacillus spp. by CST (with median number of bacterial taxa) was: CST-1-25.7% (10), CST-2-27.1% (11), CST-3-34.6% (9), CST-4-46.8% (9), CST-5-57.9% (4), CST-6-69.4% (2). The two CSTs representing the highest RA of Lactobacillus and lowest diversity increased with each additional year of follow-up (CST-5, adjusted odds ratio (aOR) = 1.62 [95% CI: 1.34-1.94]; CST-6, aOR = 1.57 [95 CI: 1.31-1.89]), while the two CSTs representing lowest RA of Lactobacillus and higher diversity decreased with each additional year (CST-1, aOR = 0.89 [95% CI: 0.80-1.00]; CST-2, aOR = 0.86 [95% CI: 0.75-0.99]). There was no association between HIV status and CST at baseline or over time. CSTs representing lower RA of Lactobacillus were associated with current cigarette smoking. CONCLUSIONS The vaginal microbial community significantly improved over time in this cohort of women with HIV and at high risk for HIV who had regular detection and treatment referral for BV.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, School of Public Health, Chicago, Illinois, United States of America
- * E-mail:
| | - Brock Donovan
- Department of Bioengineering, University of Illinois at Chicago, College of Medicine, Chicago, Illinois, United States of America
| | - Kathleen M. Weber
- The Core Center at Cook County Health and Hospital System, Chicago, Illinois, United States of America
| | - Mardge Cohen
- The Core Center at Cook County Health and Hospital System, Chicago, Illinois, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland, and Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland, and Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Douglas Gilbert
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Derick Burgad
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Greg T. Spear
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
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Brotman RM, He X, Gajer P, Fadrosh D, Sharma E, Mongodin EF, Ravel J, Glover ED, Rath JM. Association between cigarette smoking and the vaginal microbiota: a pilot study. BMC Infect Dis 2014; 14:471. [PMID: 25169082 PMCID: PMC4161850 DOI: 10.1186/1471-2334-14-471] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 08/18/2014] [Indexed: 12/02/2022] Open
Abstract
Background Smoking has been identified in observational studies as a risk factor for bacterial vaginosis (BV), a condition defined in part by decimation of Lactobacillus spp. The anti-estrogenic effect of smoking and trace amounts of benzo[a]pyrene diol epoxide (BPDE) may predispose women to BV. BPDE increases bacteriophage induction in Lactobacillus spp. and is found in the vaginal secretions of smokers. We compared the vaginal microbiota between smokers and non-smokers and followed microbiota changes in a smoking cessation pilot study. Methods In 2010–2011, 20 smokers and 20 non-smokers were recruited to a cross-sectional study (Phase A) and 9 smokers were enrolled and followed for a 12-week smoking cessation program (Phase B). Phase B included weekly behavioral counseling and nicotine patches to encourage smoking cessation. In both phases, participants self-collected mid-vaginal swabs (daily, Phase B) and completed behavioral surveys. Vaginal bacterial composition was characterized by pyrosequencing of barcoded 16S rRNA genes (V1-V3 regions). Vaginal smears were assigned Nugent Gram stain scores. Smoking status was evaluated (weekly, Phase B) using the semi-quantitative NicAlert® saliva cotinine test and carbon monoxide (CO) exhalation. Results In phase A, there was a significant trend for increasing saliva cotinine and CO exhalation with elevated Nugent scores (P value <0.005). Vaginal microbiota clustered into three community state types (CSTs); two dominated by Lactobacillus (L. iners, L. crispatus), and one lacking significant numbers of Lactobacillus spp. and characterized by anaerobes (termed CST-IV). Women who were observed in the low-Lactobacillus CST-IV state were 25-fold more likely to be smokers than those dominated by L. crispatus (aOR: 25.61, 95 % CI: 1.03-636.61). Four women completed Phase B. One of three who entered smoking cessation with high Nugent scores demonstrated a switch from CST-IV to a L.iners-dominated profile with a concomitant drop in Nugent scores which coincided with completion of nicotine patches. The other two women fluctuated between CST-IV and L. iners-dominated CSTs. The fourth woman had low Nugent scores with L. crispatus-dominated CSTs throughout. Conclusion Smokers had a lower proportion of vaginal Lactobacillus spp. compared to non-smokers. Smoking cessation should be investigated as an adjunct to reducing recurrent BV. Larger studies are needed to confirm these findings. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-471) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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31
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Wang B, Xiao BB, Shang CG, Wang K, Na RS, Nu XX, Liao Q. Molecular analysis of the relationship between specific vaginal bacteria and bacterial vaginosis metronidazole therapy failure. Eur J Clin Microbiol Infect Dis 2014; 33:1749-56. [PMID: 24816815 DOI: 10.1007/s10096-014-2128-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/17/2014] [Indexed: 11/24/2022]
Abstract
Bacterial vaginosis frequently persists, even after treatment. The role of some strains of bacteria associated with bacterial vaginosis treatment failure remains poorly defined. The aim of our study was to define the risk of bacterial vaginosis treatment failure, including pre-treatment detection of specific vaginal bacteria. Bacterial vaginosis is present when the Nugent score is ≥7 and the modified Amsel criteria is positive. Women with bacterial vaginosis were treated with intravaginal metronidazole gel nightly for 5 nights. The 454 pyrosequencing method was used to detect bacteria in vaginal fluid. By univariate analysis, a history of bacterial vaginosis, intrauterine device use and the presence of Facklamia, Corynebacterium and Veillonella were significantly associated with bacterial vaginosis treatment failure. Lactobacillus crispatus, Lactobacillus pentosus and Megasphaera were significantly associated with curing bacterial vaginosis. After logistic regression analysis and detection of these bacteria for test-of-cure, we found that women who had a history of bacterial vaginosis had a higher incidence of bacterial vaginosis treatment failure, whereas women with L. crispatus had a lower incidence of treatment failure. Post-treatment sexual activity was not associated with the treatment effect. Our data suggested that treatment failure may be not caused by drug resistance. Rather, it has a closer relationship with the failed restoration of lactobacilli.
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Affiliation(s)
- B Wang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, 100034, China
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32
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De Paepe M, Leclerc M, Tinsley CR, Petit MA. Bacteriophages: an underestimated role in human and animal health? Front Cell Infect Microbiol 2014; 4:39. [PMID: 24734220 PMCID: PMC3975094 DOI: 10.3389/fcimb.2014.00039] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 01/07/2023] Open
Abstract
Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.
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Affiliation(s)
- Marianne De Paepe
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Marion Leclerc
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Colin R Tinsley
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Marie-Agnès Petit
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
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Brotman RM, Ravel J, Bavoil PM, Gravitt PE, Ghanem KG. Microbiome, sex hormones, and immune responses in the reproductive tract: challenges for vaccine development against sexually transmitted infections. Vaccine 2013; 32:1543-52. [PMID: 24135572 DOI: 10.1016/j.vaccine.2013.10.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 08/05/2013] [Accepted: 10/02/2013] [Indexed: 12/24/2022]
Abstract
The female and male reproductive tracts are complex eco-systems where immune cells, hormones, and microorganisms interact. The characteristics of the reproductive tract mucosa are distinct from other mucosal sites. Reproductive tract mucosal immune responses are compartmentalized, unique, and affected by resident bacterial communities and sex hormones. The female and male genital microbiomes are complex environments that fluctuate in response to external and host-associated stimuli. The female vaginal microbiota play an important role in preventing colonization by pathogenic organisms. Sex hormones and their duration of exposure affect the composition and stability of the microbiome as well as systemic and mucosal immune responses. In addition to the characteristics of the pathogen they are targeting, successful vaccines against sexually transmitted pathogens must take into account the differences between the systemic and mucosal immune responses, the compartmentalization of the mucosal immune responses, the unique characteristics of the reproductive tract mucosa, the role of the mucosal bacterial communities, the impact of sex hormones, and the interactions among all of these factors.
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Affiliation(s)
- Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Patrik M Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA.
| | - Patti E Gravitt
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Khalil G Ghanem
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Ross RP. Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes 2013; 4:4-16. [PMID: 23022738 PMCID: PMC3555884 DOI: 10.4161/gmic.22371] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The human intestinal microbiota is one of the most densely populated ecosystems on Earth, containing up to 10 ( 13) bacteria/g and in some respects can be considered an organ itself given its role in human health. Bacteriophages (phages) are the most abundant replicating entities on the planet and thrive wherever their bacterial hosts exist. They undoubtedly influence the dominant microbial populations in many ecosystems including the human intestine. Within this setting, lysogeny appears to be the preferred life cycle, presumably due to nutrient limitations and lack of suitable hosts protected in biofilms, hence the predator/prey dynamic observed in many ecosystems is absent. On the other hand, free virulent phages in the gut are more common among sufferers of intestinal diseases and have been shown to increase with antibiotic usage. Many of these phages evolve from prophages of intestinal bacteria and emerge under conditions where their bacterial hosts encounter stress suggesting that prophages can significantly alter the microbial community composition. Based on these observations, we propose the "community shuffling" model which hypothesizes that prophage induction contributes to intestinal dysbiosis by altering the ratio of symbionts to pathobionts, enabling pathobiont niche reoccupation. The consequences of the increased phage load on the mammalian immune system are also addressed. While this is an area of intestinal biology which has received little attention, this review assembles evidence from the literature which supports the role of phages as one of the biological drivers behind the composition of the gut microbiota.
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Affiliation(s)
- Susan Mills
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland
| | - Fergus Shanahan
- Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Department of Medicine; University College Cork; National University of Ireland; Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland,Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Department of Microbiology; University College Cork; National University of Ireland; Cork, Ireland
| | - Aidan Coffey
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland,Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Correspondence to: R. Paul Ross,
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Desseauve D, Chantrel J, Fruchart A, Khoshnood B, Brabant G, Ancel PY, Subtil D. Prevalence and risk factors of bacterial vaginosis during the first trimester of pregnancy in a large French population-based study. Eur J Obstet Gynecol Reprod Biol 2012; 163:30-4. [PMID: 22572215 DOI: 10.1016/j.ejogrb.2012.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 12/14/2011] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Bacterial vaginosis is a risk factor for preterm delivery. Its prevalence and risk factors in Europe are not well known. Our objective was to assess both in early pregnancy. STUDY DESIGN As part of the PREMEVA randomized controlled trial, this population-based study included 14,193 women screened before 14 weeks' gestation for bacterial vaginosis in the 160 laboratories of the Nord-Pas-de-Calais region in France. Bacterial vaginosis was defined by a Nugent score ≥ 7. Data were collected about maternal tobacco use, age, education, and history of preterm birth. We estimated the prevalence of bacterial vaginosis and used a multilevel logistic regression model to identify significant risk factors for it. RESULTS Among the 14,193 women assessed before 14 weeks' gestation, the prevalence of bacterial vaginosis was 7.1% (95% CI: 6.6-7.5%). In the multivariate analysis, smoking during pregnancy tobacco (adjusted OR: 1.38; 95% CI: 1.19-1.60), maternal age 18-19 years (adjusted OR: 1.40; 95% CI: 1.01-1.93), and educational level (completed only primary school: adjusted OR: 1.77; 95% CI: 1.35-2.31; completed only secondary school: adjusted OR: 1.27; 95% CI: 1.10-1.48) were independent risk factors for bacterial vaginosis. History of preterm delivery was not an independent risk factor of bacterial vaginosis: adjusted OR: 1.15; 95% CI: 0.90-1.47. CONCLUSION In a large sample of women in their first trimester of pregnancy in France, the prevalence of bacterial vaginosis was lower than rates reported in other countries, but risk factors were similar: young age, low level of education, and tobacco use during pregnancy. These results should be considered in future strategies to reduce preterm delivery.
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Affiliation(s)
- D Desseauve
- INSERM, UMR S953, IFR 69, Unité de Recherche Epidémiologique en Santé Périnatale et Santé des Femmes et des Enfants, Hôpital Tenon, F-75020 Paris, France.
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Abstract
Bacterial vaginosis (BV) is the most common vaginal infection among women of childbearing age. This condition is notorious for causing severe complications related to the reproductive health of women. Five decades of intense research established many risk factors for acquisition of BV; however, because of the complexity of BV and lack of a reliable animal model for this condition, its exact aetiology remains elusive. In this manuscript, we use a historical perspective to critically review the development of major theories on the aetiology of BV, ultimately implicating BV-related pathogens, healthy vaginal microbiota, bacteriophages and the immune response of the host. None of these theories on their own can reliably explain the epidemiological data. Instead, BV is caused by a complex interaction of multiple factors, which include the numerous components of the vaginal microbial ecosystem and their human host. Many of these factors are yet to be characterized because a clear understanding of their relative contribution to the aetiology of BV is pivotal to the formulation of an effective treatment for and prophylaxis of this condition.
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Affiliation(s)
- Y Turovskiy
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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37
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Fleming RI, Harbison S. The use of bacteria for the identification of vaginal secretions. Forensic Sci Int Genet 2010; 4:311-5. [PMID: 20457059 DOI: 10.1016/j.fsigen.2009.11.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 11/27/2009] [Indexed: 10/19/2022]
Abstract
We have used the 16S-23S rRNA intergenic spacer region for identifying vaginal specific bacteria. Lactobacillus crispatus and Lactobacillus gasseri were detected in vaginal secretions but not in semen, blood or saliva. Our data indicated that both L. crispatus and L. gasseri were detected in vaginal secretions from women with different levels of expression of hormonal genes including pregnant, pre- and post-menopausal women, and a woman who has had a hysterectomy. Therefore, we have demonstrated that these Lactobacilli are promising new markers for the forensic identification of vaginal secretions. We have incorporated the Lactobacilli markers into a mRNA multiplex system to produce an 11-plex assay that can identify circulatory blood, menstrual blood, saliva, semen (in the presence and absence of spermatozoa) and vaginal secretions.
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Affiliation(s)
- Rachel I Fleming
- Institute of Environmental Science and Research Ltd., Mt Albert Science Centre, Hampstead Road, Private Bag 92-021, Auckland, New Zealand
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Letarov A, Kulikov E. The bacteriophages in human- and animal body-associated microbial communities. J Appl Microbiol 2009; 107:1-13. [PMID: 19239553 DOI: 10.1111/j.1365-2672.2009.04143.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Felix d'Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro-organism, nevertheless remains quite fragmentary. Analysis of data in various human- and animal body-associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage-bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self-regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. 'killing the winner'). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro-organism. Alternatively, for many systems links between phages and community characteristics have not been established.
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Affiliation(s)
- A Letarov
- Winogradsky Institute of Microbiology RAS, Moscow, Russia.
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Bagaitkar J, Demuth DR, Scott DA. Tobacco use increases susceptibility to bacterial infection. Tob Induc Dis 2008; 4:12. [PMID: 19094204 PMCID: PMC2628337 DOI: 10.1186/1617-9625-4-12] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 12/18/2008] [Indexed: 02/06/2023] Open
Abstract
Active smokers and those exposed to secondhand smoke are at increased risk of bacterial infection. Tobacco smoke exposure increases susceptibility to respiratory tract infections, including tuberculosis, pneumonia and Legionnaires disease; bacterial vaginosis and sexually transmitted diseases, such as chlamydia and gonorrhoea; Helicobacter pylori infection; periodontitis; meningitis; otitis media; and post-surgical and nosocomial infections. Tobacco smoke compromises the anti-bacterial function of leukocytes, including neutrophils, monocytes, T cells and B cells, providing a mechanistic explanation for increased infection risk. Further epidemiological, clinical and mechanistic research into this important area is warranted.
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Affiliation(s)
- Juhi Bagaitkar
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA.
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Abstract
Women are at significant risk of human immunodeficiency virus (HIV) and sexually transmitted infection (STI) acquisition with the genital mucosa serving as the main portal of infection. Exogenously supplied lactobacillus used as a probiotic may prove a cost-effective, female-initiated method to prevent HIV and STI infection in women. A probiotic may act indirectly through treating and preventing recurrent bacterial vaginosis or directly by secreting endogenous (e.g., hydrogen peroxide) and exogenous substances that block HIV and STI transmission. This review summarizes the preclinical and clinical studies that have been conducted so far to test probiotic bacteria for these purposes. Although significant progress has been made in this field, more fundamental research is required to better understand vaginal ecology to maximize probiotic formulations. Once identified, a suitable product will require testing in a well-designed, randomized, placebo-controlled trial to measure its effectiveness in augmenting antibiotic treatment to prevent bacterial vaginosis. If results from such a trial demonstrate efficacy, future studies should be designed to determine whether a probiotic can significantly lower the risk for HIV and STIs in at-risk female populations.
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Smart S, Singal A, Mindel A. Social and sexual risk factors for bacterial vaginosis. Sex Transm Infect 2004; 80:58-62. [PMID: 14755039 PMCID: PMC1758378 DOI: 10.1136/sti.2003.004978] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND A number of sexual and social risk factors for bacterial vaginosis (BV) have been identified. However, many previous studies have used small numbers of patients, or highly selected or convenience samples, or poorly defined populations. This study aims to clarify potential sexual and non-sexual risk factors for BV. METHODS Women attending the Sydney Sexual Health Centre with BV, between March 1991 and July 1999, were included. Controls were randomly selected women without BV. Information on the demographics, clinical findings, and sexual and non-sexual risk behaviours were extracted from the clinic database and analysed using SPSS and SAS. A logistic regression model was used to establish which associations with BV persisted. RESULTS 890 women with BV and 890 controls were studied. Factors that were independently associated with BV were > or =3 male sexual partners in the past 12 months (OR = 1.60, 95% CI: 1.19 to 2.04), at least one female sexual partner in the past 12 months (OR = 2.1, p = 0.003), a past pregnancy (OR = 1.5, p<0.0006), and smoking. In contrast, women with BV were significantly less likely to have used hormonal contraception (OR = 0.60, 95% CI: 0.51 to 0.81) or to have used condoms consistently (OR = 0.5, 95% CI: 0.31 to 0.71) than controls. CONCLUSION Our findings may be important for planning a preventive strategy for BV by discouraging smoking and increasing condom use and hormonal contraception among women.
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Affiliation(s)
- S Smart
- Sexually Transmitted Infections Research Centre, The University of Sydney, Marian Villa, Westmead Hospital, Westmead NSW 2145, Australia
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Kalinka J, Hanke W, Wasiela M, Laudański T. Socioeconomic and environmental risk factors of bacterial vaginosis in early pregnancy. J Perinat Med 2003; 30:467-75. [PMID: 12530102 DOI: 10.1515/jpm.2002.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The main aim of this prospective study was to determine the socioeconomic, demographic and environmental factors that may be associated with the occurrence of bacterial vaginosis at early pregnancy in an indigent population from Central Poland. A group of 196 pregnant women was selected randomly from the patients of 10 district maternity units in the Lodz region, Central Poland. Only singleton pregnancies between 8 and 16 week of gestation were qualified for inclusion in the survey. A standard questionnaire covering medical, socioeconomic, demographic, constitutional and environmental items was administered to every subject and was verified with medical records. Cervico-vaginal swabs were collected from the women under study and tested for bacterial vaginosis (BV) according to Spiegel's criteria. Based on the results of Gram stain, BV was diagnosed in 51 women (28.5%), grade I microflora among 66 (36.9%) and grade II among 62 women (34.6%). In the univariate analysis, only single marital status proved to be an important risk factor associated with BV during pregnancy, this was confirmed in the multivariate analysis. Pregnant women who present risk factors for abnormal cervico-vaginal microflora should be covered by comprehensive prenatal surveillance, which enables early detection and treatment of this pathology. Research that identifies the causal pathways and mechanisms through which social disadvantage leads to a higher risk of preterm birth may help to reduce current socioeconomic and demographic disparities and improve pregnancy outcome.
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Affiliation(s)
- Jarosław Kalinka
- Department of Perinatology, Institute of Gynecology and Obstetrics, Medical University of Lodz.
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Bachrach G, Leizerovici-Zigmond M, Zlotkin A, Naor R, Steinberg D. Bacteriophage isolation from human saliva. Lett Appl Microbiol 2003; 36:50-3. [PMID: 12485342 DOI: 10.1046/j.1472-765x.2003.01262.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To detect bacteriophages for Gram-positive oral pathogens in human saliva. METHODS AND RESULTS Saliva samples from 31 donors were screened for the presence of bacteriophages for Streptococcus sobrinus, Streptococcus mutans, Streptococcus salivarius, Actinomyces viscosus and Enterococcus faecalis. Bacteriophages for Enterococcus faecalis were found in seven samples. Enterococcus faecalis phages were still present in saliva re-collected from one donor one month, and one year after initial saliva collection. CONCLUSIONS The presence and stability of the Enterococcus faecalis bacteriophages in human saliva suggests a possible role of these bacteriophages in the oral ecosystem. SIGNIFICANCE AND IMPACT OF THE STUDY Phage therapy as a way to control oral bacteria might be considered.
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Affiliation(s)
- Gilad Bachrach
- Department of Oral Biology, The Hebrew University - Hadassah School of Dental Medicine, Jerusalem, Israel.
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44
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Abstract
Much of the sophisticated chemistry of life is accomplished by multicomponent complexes, which act as molecular machines. Intrinsic to their accuracy and efficiency is the energy that is supplied by hydrolysis of nucleoside triphosphates. Conditions that deplete energy sources should therefore cause decay and death. But studies on organisms that are exposed to prolonged stress indicate that this fate could be circumvented through the formation of highly ordered intracellular assemblies. In these thermodynamically stable structures, vital components are protected by a physical sequestration that is independent of energy consumption.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Kiliç AO, Pavlova SI, Alpay S, Kiliç SS, Tao L. Comparative study of vaginal Lactobacillus phages isolated from women in the United States and Turkey: prevalence, morphology, host range, and DNA homology. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2001; 8:31-9. [PMID: 11139192 PMCID: PMC96007 DOI: 10.1128/cdli.8.1.31-39.2001] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vaginosis lactobacilli decrease for unknown reasons. Our preliminary study showed that phages could infect vaginal lactobacilli. Therefore, the aim of this study was to analyze the distribution, virulence, and types of vaginal Lactobacillus phages isolated from women of two countries: the United States and Turkey. A total of 209 vaginal lactobacilli were isolated from reproductive-aged women in the United States (n = 107) and Turkey (n = 102). By analysis of 16S rRNA gene sequence and by comparison of protein profiles, most lactobacilli were identified as L. crispatus, L. gasseri, and L. jensenii. After mitomycin C induction, 28% of American lactobacilli and 36% of Turkish lactobacilli released phages. A total of 67 phages were isolated and further characterized by their host range, electron microscopy, and DNA homology. All 67 phages were infective against lactobacilli from both collections. The host ranges of most phages were broad, including multiple Lactobacillus species. Even though the phages were all temperate, they were able to cause lytic infection in various strains. The electron micrographs of these phages showed a hexagon-shaped head and a long tail with or without a contractile tail sheath. Based on their morphology, these phages belonged to Bradley's phage groups A and B, and could be further classified into four morphotypes. All four types were found among American phages, but only three were found among Turkish isolates. DNA hybridization with labeled probes of the four types of phages revealed that additional genetic types existed within each morphotype among these phages. The phage genomic sizes ranged between 34 and 55 kb. Many of the lysogenic Lactobacillus strains released phages spontaneously at a high frequency of 10(-3) to 10(-4) PFU/cell. In conclusion, lysogeny in vaginal lactobacilli is widely spread. Some lysogenic lactobacilli spontaneously release phages with a broad host range, which can be lytic against other vaginal lactobacilli regardless of their geographic origin.
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Affiliation(s)
- A O Kiliç
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Karadeniz Technical University, 61080 Trabzon, Turkey
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46
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Peltonen, RL, Tenovuo, J, Suvanto, O, Loimaranta, V, Peltonen, R, Löfroth, G, Eerola E. Effect of Smoking on Oral and Faecal Microbial Flora Studied by Gas-Liquid Chromatography of Bacterial Cellular Fatty Acids. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2001. [DOI: 10.1080/089106001753341327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Jorma Tenovuo,
- Department of Cariology, Institute of Dentistry, Turku University, Turku, Finl
| | | | | | - Reijo Peltonen,
- Department of Medicine, Turku University Central Hospital, Turku, Finland,
| | - Göran Löfroth,
- Department of Medical Microbiology, Turku University, Turku, Finland
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47
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Abstract
Bacterial vaginosis (BV) is a common cause of vaginal discharge in women of childbearing age. In some individuals, it recurs frequently after treatment, frustrating both the patient and the physician. Standard BV treatment--metronidazole or clindamycin, administered either intravaginally or orally--is followed by relapse in approximately 30% of cases, within one month. Our inability to prevent relapse reflects our lack of understanding of how BV originates. BV has been associated with infectious morbidity in obstetrics and gynecology. Recent studies have found it to be a risk factor for HIV spread. These findings increase the need for us to be able to control recurrent BV and reduce its prevalence in the general population.
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Affiliation(s)
- P Hay
- Department of Genitourinary Medicine, St. George's Hospital Medical School, Cranmer Terrace, London SW17 0QT, UK.
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