951
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Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol 2013; 9:666. [PMID: 23670539 PMCID: PMC4039370 DOI: 10.1038/msb.2013.22] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/03/2013] [Indexed: 12/16/2022] Open
Abstract
Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.
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Affiliation(s)
- Nicola Segata
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- Present address: Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Daniela Boernigen
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy L Tickle
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xochitl C Morgan
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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952
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Aldunate M, Tyssen D, Johnson A, Zakir T, Sonza S, Moench T, Cone R, Tachedjian G. Vaginal concentrations of lactic acid potently inactivate HIV. J Antimicrob Chemother 2013; 68:2015-25. [PMID: 23657804 PMCID: PMC3743514 DOI: 10.1093/jac/dkt156] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES When Lactobacillus spp. dominate the vaginal microbiota of women of reproductive age they acidify the vagina to pH <4.0 by producing ∼1% lactic acid in a nearly racemic mixture of d- and l-isomers. We determined the HIV virucidal activity of racemic lactic acid, and its d- and l-isomers, compared with acetic acid and acidity alone (by the addition of HCl). METHODS HIV-1 and HIV-2 were transiently treated with acids in the absence or presence of human genital secretions at 37°C for different time intervals, then immediately neutralized and residual infectivity determined in the TZM-bl reporter cell line. RESULTS l-lactic acid at 0.3% (w/w) was 17-fold more potent than d-lactic acid in inactivating HIVBa-L. Complete inactivation of different HIV-1 subtypes and HIV-2 was achieved with ≥0.4% (w/w) l-lactic acid. At a typical vaginal pH of 3.8, l-lactic acid at 1% (w/w) more potently and rapidly inactivated HIVBa-L and HIV-1 transmitter/founder strains compared with 1% (w/w) acetic acid and with acidity alone, all adjusted to pH 3.8. A final concentration of 1% (w/w) l-lactic acid maximally inactivated HIVBa-L in the presence of cervicovaginal secretions and seminal plasma. The anti-HIV activity of l-lactic acid was pH dependent, being abrogated at neutral pH, indicating that its virucidal activity is mediated by protonated lactic acid and not the lactate anion. CONCLUSIONS l-lactic acid at physiological concentrations demonstrates potent HIV virucidal activity distinct from acidity alone and greater than acetic acid, suggesting a protective role in the sexual transmission of HIV.
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Affiliation(s)
- Muriel Aldunate
- Centre for Virology, Burnet Institute, Melbourne, Victoria 3004, Australia.
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953
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Reigstad CS, Kashyap PC. Beyond phylotyping: understanding the impact of gut microbiota on host biology. Neurogastroenterol Motil 2013; 25:358-72. [PMID: 23594242 PMCID: PMC4524550 DOI: 10.1111/nmo.12134] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 03/19/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Microbial constituents of the gut microbiome interact with each other and the host to alter the luminal environment and impact development, motility, and homeostasis of the gut. Powerful methods are becoming available to investigate connections between the gut microbiome and human health. While high-throughput sequencing of 16S rRNA genes can be used to identify and enumerate microbes in the gut, advances in several techniques (e.g., metagenomics, metatranscriptomics, metabolomics, and metaproteomics) are providing a clearer view as to the specific activities of the microbiota in the context of functional host-microbe interactions. Testing emergent hypotheses regarding microbial effects on host biology, which arise from analyses of 'Big Data' generated from massive parallel high-throughput sequencing technology and spectroscopic techniques, to guide translational research is an important goal for the future. Insights regarding the fundamental operating principles of the gut microbiota should lay the foundation for rational manipulation of the microbiota to promote human health. PURPOSE In this review, we provide an overview of current research on the gut microbiome emphasizing current state-of-the-art technologies, approaches, and directions for improvement of our understanding of the impact of the gut microbiota with specific focus on gastrointestinal motility disorders.
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Affiliation(s)
- Christopher S. Reigstad
- Department of Gastroenterology and Hepatology; Enteric Neuroscience Program; Mayo Clinic; Rochester; MN; USA
| | - Purna C. Kashyap
- Department of Gastroenterology and Hepatology; Enteric Neuroscience Program; Mayo Clinic; Rochester; MN; USA
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954
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Novel PCR-based methods enhance characterization of vaginal microbiota in a bacterial vaginosis patient before and after treatment. Appl Environ Microbiol 2013; 79:4181-5. [PMID: 23624483 DOI: 10.1128/aem.01160-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.
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955
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Bradford LL, Ravel J, Bruno V. Understanding Vulvovaginal Candidiasis Through a Community Genomics Approach. CURRENT FUNGAL INFECTION REPORTS 2013. [DOI: 10.1007/s12281-013-0135-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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956
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Romero R, Korzeniewski SJ. Are infants born by elective cesarean delivery without labor at risk for developing immune disorders later in life? Am J Obstet Gynecol 2013; 208:243-6. [PMID: 23273890 DOI: 10.1016/j.ajog.2012.12.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 12/17/2012] [Indexed: 12/24/2022]
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957
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Gilbert NM, Lewis WG, Lewis AL. Clinical features of bacterial vaginosis in a murine model of vaginal infection with Gardnerella vaginalis. PLoS One 2013; 8:e59539. [PMID: 23527214 PMCID: PMC3602284 DOI: 10.1371/journal.pone.0059539] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/15/2013] [Indexed: 02/03/2023] Open
Abstract
Bacterial vaginosis (BV) is a dysbiosis of the vaginal flora characterized by a shift from a Lactobacillus-dominant environment to a polymicrobial mixture including Actinobacteria and Gram-negative bacilli. BV is a common vaginal condition in women and is associated with increased risk of sexually transmitted infection and adverse pregnancy outcomes such as preterm birth. Gardnerella vaginalis is one of the most frequently isolated bacterial species in BV. However, there has been much debate in the literature concerning the contribution of G. vaginalis to the etiology of BV, since it is also present in a significant proportion of healthy women. Here we present a new murine vaginal infection model with a clinical isolate of G. vaginalis. Our data demonstrate that this model displays key features used clinically to diagnose BV, including the presence of sialidase activity and exfoliated epithelial cells with adherent bacteria (reminiscent of clue cells). G. vaginalis was capable of ascending uterine infection, which correlated with the degree of vaginal infection and level of vaginal sialidase activity. The host response to G. vaginalis infection was characterized by robust vaginal epithelial cell exfoliation in the absence of histological inflammation. Our analyses of clinical specimens from women with BV revealed a measureable epithelial exfoliation response compared to women with normal flora, a phenotype that, to our knowledge, is measured here for the first time. The results of this study demonstrate that G. vaginalis is sufficient to cause BV phenotypes and suggest that this organism may contribute to BV etiology and associated complications. This is the first time vaginal infection by a BV associated bacterium in an animal has been shown to parallel the human disease with regard to clinical diagnostic features. Future studies with this model should facilitate investigation of important questions regarding BV etiology, pathogenesis and associated complications.
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Affiliation(s)
- Nicole M. Gilbert
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Warren G. Lewis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amanda L. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Obstetrics and Gynecology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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958
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Lewis WG, Robinson LS, Gilbert NM, Perry JC, Lewis AL. Degradation, foraging, and depletion of mucus sialoglycans by the vagina-adapted Actinobacterium Gardnerella vaginalis. J Biol Chem 2013; 288:12067-79. [PMID: 23479734 DOI: 10.1074/jbc.m113.453654] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bacterial vaginosis (BV) is a polymicrobial imbalance of the vaginal microbiota associated with reproductive infections, preterm birth, and other adverse health outcomes. Sialidase activity in vaginal fluids is diagnostic of BV and sialic acid-rich components of mucus have protective and immunological roles. However, whereas mucus degradation is believed to be important in the etiology and complications associated with BV, the role(s) of sialidases and the participation of individual bacterial species in the degradation of mucus barriers in BV have not been investigated. Here we demonstrate that the BV-associated bacterium Gardnerella vaginalis uses sialidase to break down and deplete sialic acid-containing mucus components in the vagina. Biochemical evidence using purified sialoglycan substrates supports a model in which 1) G. vaginalis extracellular sialidase hydrolyzes mucosal sialoglycans, 2) liberated sialic acid (N-acetylneuraminic acid) is transported into the bacterium, a process inhibited by excess N-glycolylneuraminic acid, and 3) sialic acid catabolism is initiated by an intracellular aldolase/lyase mechanism. G. vaginalis engaged in sialoglycan foraging in vitro, in the presence of human vaginal mucus, and in vivo, in a murine vaginal model, in each case leading to depletion of sialic acids. Comparison of sialic acid levels in human vaginal specimens also demonstrated significant depletion of mucus sialic acids in women with BV compared with women with a "normal" lactobacilli-dominated microbiota. Taken together, these studies show that G. vaginalis utilizes sialidase to support the degradation, foraging, and depletion of protective host mucus barriers, and that this process of mucus barrier degradation and depletion also occurs in the clinical setting of BV.
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Affiliation(s)
- Warren G Lewis
- Departments of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA.
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959
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Prevalent and incident bacterial vaginosis are associated with sexual and contraceptive behaviours in young Australian women. PLoS One 2013; 8:e57688. [PMID: 23472099 PMCID: PMC3589386 DOI: 10.1371/journal.pone.0057688] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/24/2013] [Indexed: 11/23/2022] Open
Abstract
Background To determine prevalence and incidence of bacterial vaginosis (BV) and risk factors in young sexually-active Australian women. Methods 1093 women aged 16–25 years were recruited from primary-care clinics. Participants completed 3-monthly questionnaires and self-collected vaginal smears 6-monthly for 12-months. The primary endpoint was a Nugent Score = 7–10 (BV) and the secondary endpoint was a NS = 4–10 (abnormal flora [AF]). BV and AF prevalence estimates and 95% confidence intervals (95%CI) were derived, and adjusted odds ratios (AOR) calculated to explore epidemiological associations with prevalent BV and AF. Proportional-hazards regression models were used to examine factors associated with incident BV and AF. Results At baseline 129 women had BV [11.8% (95%CI: 9.4–14.2)] and 188 AF (17.2%; 15.1–19.5). Prevalent BV was associated with having a recent female partner [AOR = 2.1; 1.0–4.4] and lack of tertiary-education [AOR = 1.9; 1.2–3.0]; use of an oestrogen-containing contraceptive (OCC) was associated with reduced risk [AOR = 0.6; 0.4–0.9]. Prevalent AF was associated with the same factors, and additionally with >5 male partners (MSP) in 12-months [AOR = 1.8; 1.2–2.5)], and detection of C.trachomatis or M.genitalium [AOR = 2.1; 1.0–4.5]. There were 82 cases of incident BV (9.4%;7.7–11.7/100 person-years) and 129 with incident AF (14.8%; 12.5–17.6/100 person-years). Incident BV and AF were associated with a new MSP [adjusted rate ratio (ARR) = 1.5; 1.1–2.2 and ARR = 1.5; 1.1–2.0], respectively. OCC-use was associated with reduced risk of incident AF [ARR = 0.7; 0.5–1.0]. Conclusion This paper presents BV and AF prevalence and incidence estimates from a large prospective cohort of young Australian women predominantly recruited from primary-care clinics. These data support the concept that sexual activity is strongly associated with the development of BV and AF and that use of an OCC is associated with reduced risk.
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960
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McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R. From molecules to dynamic biological communities. BIOLOGY & PHILOSOPHY 2013; 28:241-259. [PMID: 23483075 PMCID: PMC3586164 DOI: 10.1007/s10539-013-9364-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/23/2013] [Indexed: 05/22/2023]
Abstract
Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.
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Affiliation(s)
- Daniel McDonald
- Department of Computer Science, University of Colorado at Boulder, Boulder, CO USA
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO USA
| | - Yoshiki Vázquez-Baeza
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO USA
| | - William A. Walters
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO USA
| | - J. Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ USA
- Argonne National Laboratory, Institute for Genomics and Systems Biology, Argonne, IL USA
| | - Rob Knight
- Department of Computer Science, University of Colorado at Boulder, Boulder, CO USA
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO USA
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO USA
- Howard Hughes Medical Institute, Boulder, CO USA
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961
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Reid JNS, Bisanz JE, Monachese M, Burton JP, Reid G. The Rationale for Probiotics Improving Reproductive Health and Pregnancy Outcome. Am J Reprod Immunol 2013; 69:558-66. [DOI: 10.1111/aji.12086] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/07/2013] [Indexed: 12/19/2022] Open
Affiliation(s)
| | | | | | - Jeremy P. Burton
- Human Microbiology and Probiotics; Lawson Health Research Institute; London; ON; Canada
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962
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Hickey RJ, Abdo Z, Zhou X, Nemeth K, Hansmann M, Osborn TW, Wang F, Forney LJ. Effects of tampons and menses on the composition and diversity of vaginal microbial communities over time. BJOG 2013; 120:695-704; discussion 704-6. [DOI: 10.1111/1471-0528.12151] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2012] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | - K Nemeth
- FemCare Product Safety and Regulatory Affairs; The Procter & Gamble Company; Cincinnati; OH; USA
| | - M Hansmann
- FemCare Product Safety and Regulatory Affairs; The Procter & Gamble Company; Cincinnati; OH; USA
| | - TW Osborn
- FemCare Product Development; The Procter & Gamble Company; Cincinnati; OH; USA
| | - F Wang
- FemCare Product Development; The Procter & Gamble Company; Cincinnati; OH; USA
| | - LJ Forney
- Institute for Bioinformatics and Evolutionary Studies; University of Idaho; Moscow; ID; USA
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963
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Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, Väin E, Saarma I, Salumets A, Donders GGG, Metsis M. Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age Estonian women. PLoS One 2013; 8:e54379. [PMID: 23372716 PMCID: PMC3553157 DOI: 10.1371/journal.pone.0054379] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/11/2012] [Indexed: 12/16/2022] Open
Abstract
The application of high-throughput sequencing methods has raised doubt in the concept of the uniform healthy vaginal microbiota consisting predominantly of lactobacilli by revealing the existence of more variable bacterial community composition. As this needs to be analyzed more extensively and there is little straightforward data regarding the vaginal mycobiome of asymptomatic women we aimed to define bacterial and fungal communities in vaginal samples from 494 asymptomatic, reproductive-age Estonian women. The composition of the vaginal microbiota was determined by amplifying bacterial 16S rRNA and fungal internal transcribed spacer-1 (ITS-1) regions and subsequently sequencing them using 454 Life Sciences pyrosequencing. We delineated five major bacterial community groups with distinctive diversity and species composition. Lactobacilli were among the most abundant bacteria in all groups, but also members of genus Gardnerella had high relative abundance in some of the groups. Microbial diversity increased with higher vaginal pH values, and was also higher when a malodorous discharge was present, indicating that some of the women who consider themselves healthy may potentially have asymptomatic bacterial vaginosis (BV). Our study is the first of its kind to analyze the mycobiome that colonizes the healthy vaginal environment using barcoded pyrosequencing technology. We observed 196 fungal operational taxonomic units (OTUs), including 16 OTUs of Candida spp., which is more diverse than previously recognized. However, assessing true fungal diversity was complicated because of the problems regarding the possible air-borne contamination and bioinformatics used for identification of fungal taxons as significant proportion of fungal sequences were assigned to unspecified OTUs.
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MESH Headings
- Adolescent
- Adult
- Asymptomatic Diseases
- Candida/classification
- Candida/genetics
- Candida/isolation & purification
- DNA, Intergenic/classification
- DNA, Intergenic/genetics
- Estonia/epidemiology
- Female
- Gardnerella vaginalis/classification
- Gardnerella vaginalis/genetics
- Gardnerella vaginalis/isolation & purification
- Humans
- Lactobacillus/classification
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Metagenome/genetics
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Vagina/microbiology
- Vaginal Discharge/microbiology
- Vaginosis, Bacterial/diagnosis
- Vaginosis, Bacterial/epidemiology
- Vaginosis, Bacterial/microbiology
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Affiliation(s)
- Tiina Drell
- Centre for Biology of Integrated Systems, Tallinn University of Technology, Tallinn, Estonia.
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964
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Cervantes JL, Hong BY. Role of Next-Generation Sequencing in Understanding the Interactions between Human Papillomavirus and the Cervicovaginal Microbiome. Gynecol Obstet Invest 2013; 76:195-202. [DOI: 10.1159/000351309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/13/2013] [Indexed: 11/19/2022]
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965
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Hoffmann DE, Fortenberry JD, Ravel J. Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2013; 41:454-69. [PMID: 23802897 PMCID: PMC5761648 DOI: 10.1111/jlme.12055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This article examines ways in which research conducted under the Human Microbiome Project, an effort to establish a "reference catalogue" of the micro-organisms present in the human body and determine how changes in those micro-organisms affect health and disease, raise challenging issues for regulation of human subject research. The article focuses on issues related to subject selection and recruitment, group stigma, and informational risks, and explores whether: (1) the Common Rule or proposed changes to the Rule adequately address these issues and (2) the Common Rule is the most appropriate vehicle to provide regulatory oversight and guidance on these topics.
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966
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Spear G, Rothaeulser K, Fritts L, Gillevet PM, Miller CJ. In captive rhesus macaques, cervicovaginal inflammation is common but not associated with the stable polymicrobial microbiome. PLoS One 2012; 7:e52992. [PMID: 23285244 PMCID: PMC3532444 DOI: 10.1371/journal.pone.0052992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/27/2012] [Indexed: 11/18/2022] Open
Abstract
Vaginal inoculation of rhesus macaques (RM) with simian immunodeficiency virus (SIV) has been used to study the biology of HIV transmission. Although the results of vaginal SIV transmission experiments could be affected by vaginal inflammation, studies to date have been conducted without regard to levels of pre-existing genital inflammation present in RM. We collected cevicovaginal secretions (CVS) from 33–36 RM during the mid menstrual cycle (day 10–20) at 2 time points approximately 8 months apart and characterized the mRNA and protein levels of inflammatory cytokines, chemokines and interferon-stimulated genes. There was extreme variability in the levels of inflammatory mediators (IFN-α, IFN-γ, IL-6, TNF, IL-1b, IP-10, MIG, IL-12 and IL-17). In most animals, the mRNA levels of the inflammatory mediators were similar in the 2 CVS samples collected 8 months apart, suggesting that genital inflammation is stable in a subset of captive female RM. At both time points the cervicovaginal microbiota had low levels of Lactobacillus and was relatively diverse with an average of 13 genera in the samples from the first time point (median 13, range 7–21) and an average of 11.5 genera in the samples from the second time point (median 11, range 5–20). Many of the macaques had similar microbiota in the samples collected 8 months apart. However, we found no correlation between specific bacterial genera and the mRNA or protein levels of the inflammatory mediators in the genital tract of RM in this study. It seems likely that results of published vaginal SIV transmission experiments in RM have been influenced by pre-existing inflammation in the animals used for the experiments.
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Affiliation(s)
- Gregory Spear
- Department Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Kristina Rothaeulser
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Linda Fritts
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, United States of America
- Department of Environmental Science and Policy, George Mason University, Manassas, Virginia, United States of America
| | - Christopher J. Miller
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
- * E-mail:
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967
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Abstract
Vaginal HIV microbicides offer great promise in preventing HIV transmission, but failures of phase 3 clinical trials, in which microbicide-treated subjects had an increased risk of HIV transmission, raised concerns about endpoints used to evaluate microbicide safety. A possible explanation for the increased transmission risk is that the agents shifted the vaginal bacterial community, resulting in loss of natural protection and enhanced HIV transmission susceptibility. We characterized vaginal microbiota, using pyrosequencing of bar-coded 16S rRNA gene fragments, in samples from 35 healthy, sexually abstinent female volunteer subjects (ages 18 to 50 years) with regular menses in a repeat phase 1 study of twice-daily application over 13.5 days of 1 of 3 gel products: a hydroxyethylcellulose (HEC)-based “universal” placebo (10 subjects), 6% cellulose sulfate (CS; 13 subjects), and 4% nonoxynol-9 (N-9; 12 subjects). We used mixed effects models inferred using Bayesian Markov chain Monte Carlo methods, which showed that treatment with active agents shifted the microbiota toward a community type lacking significant numbers of Lactobacillus spp. and dominated by strict anaerobes. This state of the vaginal microbiota was associated with a low or intermediate Nugent score and was not identical to bacterial vaginosis, an HIV transmission risk factor. The placebo arm contained a higher proportion of communities dominated by Lactobacillus spp., particularly L. crispatus, throughout treatment. The data suggest that molecular evaluation of microbicide effects on vaginal microbiota may be a critical endpoint that should be incorporated in early clinical assessment of microbicide candidates. Despite large prevention efforts, HIV transmission and acquisition rates remain unacceptably high. In developing countries, transmission mainly occurs through heterosexual intercourse, where women are significantly more vulnerable to infection than men. Vaginal microbicides are considered to be one of the most promising female-controlled products, in that women themselves insert the microbicides into the vagina to prevent HIV transmission during sexual intercourse. The failure of several microbicides in clinical trials has raised questions concerning the low in vivo efficacy of such anti-HIV molecules. This study was designed to gain insights into the failures of two microbicides by testing the hypothesis that the microbicides negatively affect a critical line of defense against HIV, the vaginal microbiota. The results suggest that in the early assessment of candidate microbicides, culture-independent evaluation of their effect on the vaginal microbiota should be considered and may constitute a critical endpoint.
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968
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Conrad MD, Bradic M, Warring SD, Gorman AW, Carlton JM. Getting trichy: tools and approaches to interrogating Trichomonas vaginalis in a post-genome world. Trends Parasitol 2012; 29:17-25. [PMID: 23219217 DOI: 10.1016/j.pt.2012.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/29/2012] [Accepted: 10/29/2012] [Indexed: 11/28/2022]
Abstract
Trichomonas vaginalis is a parasite of the urogenital tract in men and women, with a worldwide presence and significant implications for global public health. T. vaginalis research entered the age of genomics with the publication of the first genome sequence in 2007, but subsequent utilization of other 'omics' technologies and methods has been slow. Here, we review some of the tools and approaches available to interrogate T. vaginalis biology, with an emphasis on recent advances and current limitations, and draw attention to areas where further efforts are needed to examine effectively the complex and intriguing biology of the parasite.
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Affiliation(s)
- Melissa D Conrad
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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969
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970
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Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet 2012; 29:51-8. [PMID: 23140990 DOI: 10.1016/j.tig.2012.09.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 12/14/2022]
Abstract
Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe-microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools.
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Affiliation(s)
- Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
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971
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Abstract
The vaginal microbiome in healthy women changes over short periods of time, differs among individuals, and varies in its response to sexual intercourse.
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Affiliation(s)
- Steven S Witkin
- Division of Immunology and Infectious Diseases, Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY 10065, USA.
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972
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Abstract
Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host-microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host-microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host-microbe interaction to reduce the risk of disease in the child.
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973
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Santiago GLDS, Tency I, Verstraelen H, Verhelst R, Trog M, Temmerman M, Vancoillie L, Decat E, Cools P, Vaneechoutte M. Longitudinal qPCR study of the dynamics of L. crispatus, L. iners, A. vaginae, (sialidase positive) G. vaginalis, and P. bivia in the vagina. PLoS One 2012; 7:e45281. [PMID: 23028904 PMCID: PMC3448655 DOI: 10.1371/journal.pone.0045281] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 08/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To obtain more detailed understanding of the causes of disturbance of the vaginal microflora (VMF), a longitudinal study was carried out for 17 women during two menstrual cycles. METHODS Vaginal swabs were obtained daily from 17 non-pregnant, menarchal volunteers. For each woman, Gram stains were scored, the quantitative changes of 5 key vaginal species, i.e. Atopobium vaginae, Lactobacillus crispatus, L. iners, (sialidase positive) Gardnerella vaginalis and Prevotella bivia were quantified with qPCR and hydrogen-peroxide production was assessed on TMB+ agar. RESULTS Women could be divided in 9 subjects with predominantly normal VMF (grades Ia, Ib and Iab, group N) and 8 with predominantly disturbed VMF (grades I-like, II, III and IV, group D). VMF was variable between women, but overall stable for most of the women. Menses were the strongest disturbing factor of the VMF. L. crispatus was present at log7-9 cells/ml in grade Ia, Iab and II VMF, but concentrations declined 100-fold during menses. L. crispatus below log7 cells/ml corresponded with poor H(2)O(2)-production. L. iners was present at log 10 cells/ml in grade Ib, II and III VMF. Sialidase negative G. vaginalis strains (average log5 cells/ml) were detected in grade I, I-like and IV VMF. In grade II VMF, predominantly a mixture of both sialidase negative and positive G. vaginalis strains (average log9 cells/ml) were present, and predominantly sialidase positive strains in grade III VMF. The presence of A. vaginae (average log9 cells/ml) coincided with grade II and III VMF. P. bivia (log4-8 cells/ml) was mostly present in grade III vaginal microflora. L. iners, G. vaginalis, A. vaginae and P. bivia all increased around menses for group N women, and as such L. iners was considered a member of disturbed VMF. CONCLUSIONS This qPCR-based study confirms largely the results of previous culture-based, microscopy-based and pyrosequencing-based studies.
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Affiliation(s)
- Guido Lopes dos Santos Santiago
- Laboratory for Bacteriology Research, Department of Clinical Chemistry, Microbiology, and Immunology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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974
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Smith BC, McAndrew T, Chen Z, Harari A, Barris DM, Viswanathan S, Rodriguez AC, Castle P, Herrero R, Schiffman M, Burk RD. The cervical microbiome over 7 years and a comparison of methodologies for its characterization. PLoS One 2012; 7:e40425. [PMID: 22792313 PMCID: PMC3392218 DOI: 10.1371/journal.pone.0040425] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/06/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The rapidly expanding field of microbiome studies offers investigators a large choice of methods for each step in the process of determining the microorganisms in a sample. The human cervicovaginal microbiome affects female reproductive health, susceptibility to and natural history of many sexually transmitted infections, including human papillomavirus (HPV). At present, long-term behavior of the cervical microbiome in early sexual life is poorly understood. METHODS The V6 and V6-V9 regions of the 16S ribosomal RNA gene were amplified from DNA isolated from exfoliated cervical cells. Specimens from 10 women participating in the Natural History Study of HPV in Guanacaste, Costa Rica were sampled successively over a period of 5-7 years. We sequenced amplicons using 3 different platforms (Sanger, Roche 454, and Illumina HiSeq 2000) and analyzed sequences using pipelines based on 3 different classification algorithms (usearch, RDP Classifier, and pplacer). RESULTS Usearch and pplacer provided consistent microbiome classifications for all sequencing methods, whereas RDP Classifier deviated significantly when characterizing Illumina reads. Comparing across sequencing platforms indicated 7%-41% of the reads were reclassified, while comparing across software pipelines reclassified up to 32% of the reads. Variability in classification was shown not to be due to a difference in read lengths. Six cervical microbiome community types were observed and are characterized by a predominance of either G. vaginalis or Lactobacillus spp. Over the 5-7 year period, subjects displayed fluctuation between community types. A PERMANOVA analysis on pairwise Kantorovich-Rubinstein distances between the microbiota of all samples yielded an F-test ratio of 2.86 (p<0.01), indicating a significant difference comparing within and between subjects' microbiota. CONCLUSIONS Amplification and sequencing methods affected the characterization of the microbiome more than classification algorithms. Pplacer and usearch performed consistently with all sequencing methods. The analyses identified 6 community types consistent with those previously reported. The long-term behavior of the cervical microbiome indicated that fluctuations were subject dependent.
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Affiliation(s)
- Benjamin C. Smith
- Department of Pediatrics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | - Thomas McAndrew
- Department of Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | - Ariana Harari
- Department of Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | - David M. Barris
- Department of Pediatrics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | - Shankar Viswanathan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
| | | | - Phillip Castle
- American Society of Clinical Pathology (ASCP) Institute, Washington, D.C., United States of America
| | - Rolando Herrero
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
- Department of Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, United States of America
- * E-mail:
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975
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Abstract
Vaginal microbiota form a mutually beneficial relationship with their host and have a major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others are composed of a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal condition and is vaguely characterized as the disruption of the equilibrium of the normal vaginal microbiota. A better understanding of normal and healthy vaginal ecosystems that is based on their true function and not simply on their composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.
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Affiliation(s)
- Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201, USA.
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976
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Costello EK, Stagaman K, Dethlefsen L, Bohannan BJM, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science 2012; 336:1255-62. [PMID: 22674335 DOI: 10.1126/science.1224203] [Citation(s) in RCA: 917] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like "patch" of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts. We explore three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representing assembly after disturbance; and invasion by pathogens, representing assembly in the context of invasive species. Judicious application of ecological theory may lead to improved strategies for restoring and maintaining the microbiota and the crucial health-associated ecosystem services that it provides.
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Affiliation(s)
- Elizabeth K Costello
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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977
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Macklaim JM, Cohen CR, Donders G, Gloor GB, Hill JE, Parham GP, Ravel J, Spear G, van de Wijgert J, Reid G. Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease. Reprod Sci 2012; 19:1154-62. [PMID: 22614624 DOI: 10.1177/1933719112446075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Urogenital diseases, especially infection and cancer, are major causes of death and morbidity in females. Yet, millions of women in the developing world have no access to basic urogynecological care, and the diagnosis and treatment of widespread aberrant bacterial conditions (bacterial vaginosis [BV] and aerobic vaginitis [AV]) remain suboptimal the world over. Samples from women living in resource-disadvantaged and developed countries have been analyzed by high-throughput sequencing to reveal the diversity of bacteria in the vagina, how rapidly the bacterial population fluctuates over time, and how rapidly the switch occurs between healthy and aberrant conditions. Unfortunately, clinical diagnostic methods are inefficient and too often outdated therapies are administered. The net result is suboptimal care and recurrent disease that adversely affects the quality of life. This viewpoint outlines a scientific and translational road map designed to improve the cervicovaginal health and treatment of disease. This comprises (1) improving education of women and physicians on the vaginal microbiota; (2) having agencies target funding for research to improve diagnosis and test new therapies; and (3) making sure that new approaches are accessible in developing countries, empowering to women, and are acceptable and appropriate for different populations.
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Affiliation(s)
- Jean M Macklaim
- Department of Biochemistry, The University of Western Ontario, London, Canada
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