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Saleem B, Okogbule-Wonodi AC, Fasano A, Magder LS, Ravel J, Kapoor S, Viscardi RM. Intestinal Barrier Maturation in Very Low Birthweight Infants: Relationship to Feeding and Antibiotic Exposure. J Pediatr 2017; 183:31-36.e1. [PMID: 28159311 PMCID: PMC5367935 DOI: 10.1016/j.jpeds.2017.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/07/2016] [Accepted: 01/04/2017] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To test the hypothesis that feeding and antibiotic exposures affect intestinal barrier maturation in preterm infants, we serially measured intestinal permeability (IP) biomarkers in infants <33 weeks gestation (gestational age [GA]) during the first 2 weeks of life. STUDY DESIGN Eligible infants <33 weeks GA were enrolled within 4 days of birth in a prospective study of IP biomarkers (NCT01756040). Study participants received the nonmetabolized sugars lactulose/rhamnose enterally on study days 1, 8, and 15 and lactulose/rhamnose were measured in urine by high-performance liquid chromatography. Serum zonulin and fecal alpha-1-anti-trypsin, 2 other IP markers, were measured by semiquantitative Western blot and ELISA, respectively. RESULTS In a cohort of 43 subjects, the lactulose/rhamnose ratio was increased on day 1 and decreased over 2 weeks, but remained higher in infants born at ≤28 weeks of gestation compared with IP in infants born at >28 weeks of gestation. Exclusive breastmilk feeding was associated with more rapid maturation in intestinal barrier function. A cluster analysis of 35 subjects who had urine samples from all time points revealed 3 IP patterns (cluster 1, normal maturation: n = 20 [57%]); cluster 2, decreased IP during the first week and subsequent substantial increase: n = 5 [14%]); and cluster 3, delayed maturation: n = 10 [29%]). There were trends toward more prolonged antibiotic exposure (P = .092) and delayed initiation of feeding ≥4 days (P = .064) in infants with abnormal IP patterns. CONCLUSIONS Intestinal barrier maturation in preterm infants is GA and postnatal age dependent, and is influenced by feeding with a maturational effect of breastmilk feeding and possibly by antibiotic exposures. TRIAL REGISTRATION ClinicalTrials.gov: NCT01756040.
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Affiliation(s)
- Bushra Saleem
- Departments of Pediatrics, University of Maryland School of Medicine, Baltimore, MD
| | | | - Alessio Fasano
- MassGeneral Hospital for Children, Center for Celiac Research and Treatment, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA
| | - Laurence S. Magder
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Jacques Ravel
- Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Shiv Kapoor
- Departments of Pediatrics, University of Maryland School of Medicine, Baltimore, MD
| | - Rose M. Viscardi
- Departments of Pediatrics, University of Maryland School of Medicine, Baltimore, MD,Corresponding author (No reprints): Rose M. Viscardi, M.D., University of Maryland School of Medicine, 110 S. Paca Street, 8th Floor, Baltimore, MD 21201, Telephone: (410) 706-1913; Fax: (410) 706-0404;
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152
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Abstract
The advent of fecal microbiota transplantation (FMT) and the prospect of other types of microbiota transplants (MT), e.g. vaginal, skin, oral and nasal, are challenging regulatory agencies. Although FDA is regulating FMT (as a biologic), there is currently no widely accepted or agreed upon scientific or legal definition of FMT or MT. The authors report on discussions regarding a definition of MT that took place among a working group of stakeholders convened under a National Institutes for Allergies and Infectious Diseases grant to address the regulation of MT. In arriving at a definition, the group considered the 1) nature of the material being transplanted; 2) degree of manipulation of the transferred materials prior to implantation; 3) ability to characterize the transplanted product using external techniques; and 4) origin of the stool product (single vs multiple donors).
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Affiliation(s)
- Diane E. Hoffmann
- School of Law, University of Maryland, Baltimore, MD, USA,CONTACT Diane E. Hoffmann School of Law, University of Maryland School of Law, 500 W. Baltimore St., Baltimore, Maryland, United States, 21201
| | - Francis B. Palumbo
- Center for Drugs and Public Policy, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Erik von Rosenvinge
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, VA Maryland Health Care System, Baltimore, MD, USA
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153
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Yu G, Phillips S, Gail MH, Goedert JJ, Humphrys MS, Ravel J, Ren Y, Caporaso NE. The effect of cigarette smoking on the oral and nasal microbiota. Microbiome 2017; 5:3. [PMID: 28095925 PMCID: PMC5240432 DOI: 10.1186/s40168-016-0226-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/25/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From each subject, nine samples including supra and subgingiva plaque scrapes, saliva, swabs from five soft oral tissue sites, and one nasal swab from both the anterior nares were collected. 16S rRNA V3-V4 region was sequenced for microbial profiles. RESULTS We found that alpha diversity was lower in smokers than in nonsmokers in the buccal mucosa, but in other sample sites, microbial diversity and composition were not significantly different by smoking status. Microbial profiles differed significantly among eight oral sites. CONCLUSIONS This study investigates the effect of cigarette smoking on different sites of the oral cavity and shows a potential effect of cigarette smoking on the buccal mucosa microbiota. The marked heterogeneity of the oral microbial ecosystem that we found may contribute to the stability of the oral microbiota in most sites when facing environmental perturbations such as that caused by cigarette smoking.
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Affiliation(s)
- Guoqin Yu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 9609 Medical Center Drive, Room 6E508, Bethesda, MD, 20892-9769, USA.
| | - Stephen Phillips
- Eastman Institute of Oral Health, University of Rochester, Rochester, NY, USA
| | - Mitchell H Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yanfang Ren
- Eastman Institute of Oral Health, University of Rochester, Rochester, NY, USA
| | - Neil E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 9609 Medical Center Drive, Room 6E508, Bethesda, MD, 20892-9769, USA
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154
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Holm J, Gajer P, Ma B, Humphrys M, Ravel J. 8: Detection & implications of lactobacillus iners sub-strain diversity. Am J Obstet Gynecol 2016. [DOI: 10.1016/j.ajog.2016.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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155
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Brotman R, Gajer P, Holm J, Robinson C, Ma B, Humphrys M, Tuddenham S, Ravel J, Ghanem K. 4: Hormonal contraception is associated with stability and lactobacillus-dominance of the vaginal microbiota in a two-year observational study. Am J Obstet Gynecol 2016. [DOI: 10.1016/j.ajog.2016.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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156
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Yu G, Phillips S, Gail MH, Goedert JJ, Humphrys M, Ravel J, Ren Y, Caporaso NE. Evaluation of Buccal Cell Samples for Studies of Oral Microbiota. Cancer Epidemiol Biomarkers Prev 2016; 26:249-253. [DOI: 10.1158/1055-9965.epi-16-0538] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/16/2022] Open
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157
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Abstract
Most of what is known about fungi in the human vagina has come from culture-based studies and phenotypic characterization of single organisms. Though valuable, these approaches have masked the complexity of fungal communities within the vagina. The vaginal mycobiome has become an emerging field of study as genomics tools are increasingly employed and we begin to appreciate the role these fungal communities play in human health and disease. Though vastly outnumbered by its bacterial counterparts, fungi are important constituents of the vaginal ecosystem in many healthy women. Candida albicans, an opportunistic fungal pathogen, colonizes 20% of women without causing any overt symptoms, yet it is one of the leading causes of infectious vaginitis. Understanding its mechanisms of commensalism and patho-genesis are both essential to developing more effective therapies. Describing the interactions between Candida, bacteria (such as Lactobacillus spp.) and other fungi in the vagina is funda-mental to our characterization of the vaginal mycobiome.
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Affiliation(s)
- L. Latéy Bradford
- 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
| | - 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,CONTACT Jacques Ravel Institute for Genome Sciences, 801 W. Baltimore Street, Baltimore, MD 21201, USA
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158
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Van Lent S, De Vos WH, Huot Creasy H, Marques PX, Ravel J, Vanrompay D, Bavoil P, Hsia RC. Analysis of Polymorphic Membrane Protein Expression in Cultured Cells Identifies PmpA and PmpH of Chlamydia psittaci as Candidate Factors in Pathogenesis and Immunity to Infection. PLoS One 2016; 11:e0162392. [PMID: 27631978 PMCID: PMC5025070 DOI: 10.1371/journal.pone.0162392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022] Open
Abstract
The polymorphic membrane protein (Pmp) paralogous families of Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia abortus are putative targets for Chlamydia vaccine development. To determine whether this is also the case for Pmp family members of C. psittaci, we analyzed transcription levels, protein production and localization of several Pmps of C. psittaci. Pmp expression profiles were characterized using quantitative real-time PCR (RT-qPCR), immunofluorescence (IF) and immuno-electron microscopy (IEM) under normal and stress conditions. We found that PmpA was highly produced in all inclusions as early as 12 hpi in all biological replicates. In addition, PmpA and PmpH appeared to be unusually accessible to antibody as determined by both immunofluorescence and immuno-electron microscopy. Our results suggest an important role for these Pmps in the pathogenesis of C. psittaci, and make them promising candidates in vaccine development.
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Affiliation(s)
- Sarah Van Lent
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- * E-mail:
| | - Winnok H. De Vos
- Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Heather Huot Creasy
- Institute for Genome Sciences and Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, Unites States of America
| | - Patricia X. Marques
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, Unites States of America
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, Unites States of America
| | - Daisy Vanrompay
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Patrik Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, Unites States of America
| | - Ru-ching Hsia
- University of Maryland, Baltimore, Electron Microscopy Core Imaging Facility, Maryland, Unites States of America
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159
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Reimers LL, Mehta SD, Massad LS, Burk RD, Xie X, Ravel J, Cohen MH, Palefsky JM, Weber KM, Xue X, Anastos K, Minkoff H, Atrio J, D'Souza G, Ye Q, Colie C, Zolnik CP, Spear GT, Strickler HD. The Cervicovaginal Microbiota and Its Associations With Human Papillomavirus Detection in HIV-Infected and HIV-Uninfected Women. J Infect Dis 2016; 214:1361-1369. [PMID: 27521363 DOI: 10.1093/infdis/jiw374] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is characterized by low abundance of Lactobacillus species, high pH, and immune cell infiltration and has been associated with an increased risk of human papillomavirus (HPV) infection. We molecularly assessed the cervicovaginal microbiota over time in human immunodeficiency virus (HIV)-infected and HIV-uninfected women to more comprehensively study the HPV-microbiota relationship, controlling for immune status. METHODS 16S ribosomal RNA gene amplicon pyrosequencing and HPV DNA testing were conducted annually in serial cervicovaginal lavage specimens obtained over 8-10 years from African American women from Chicago, of whom 22 were HIV uninfected, 22 were HIV infected with a stable CD4+ T-cell count of > 500 cells/mm3, and 20 were HIV infected with progressive immunosuppression. Vaginal pH was serially measured. RESULTS The relative abundances of Lactobacillus crispatus and other Lactobacillus species were inversely associated with vaginal pH (all P < .001). High (vs low) L. crispatus relative abundance was associated with decreased HPV detection (odds ratio, 0.48; 95% confidence interval, .24-.96; Ptrend = .03) after adjustment for repeated observation and multiple covariates, including pH and study group. However, there were no associations between HPV and the relative abundance of Lactobacillus species as a group, nor with Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii individually. CONCLUSIONS L. crispatus may have a beneficial effect on the burden of HPV in both HIV-infected and HIV-uninfected women (independent of pH).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kathleen M Weber
- Cook County Health and Hospitals System/Hektoen Institute of Medicine, Chicago, Illinois
| | | | | | | | | | | | - Qian Ye
- Albert Einstein College of Medicine, Bronx
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160
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Yu G, Gail MH, Consonni D, Carugno M, Humphrys M, Pesatori AC, Caporaso NE, Goedert JJ, Ravel J, Landi MT. Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. Genome Biol 2016; 17:163. [PMID: 27468850 PMCID: PMC4964003 DOI: 10.1186/s13059-016-1021-1] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/07/2016] [Indexed: 12/26/2022] Open
Abstract
Background The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from cancer patients. Results We show that the lung microbiota is distinct from the microbial communities in oral, nasal, stool, skin, and vagina, with Proteobacteria as the dominant phylum (60 %). Microbiota taxonomic alpha diversity increases with environmental exposures, such as air particulates, residence in low to high population density areas, and pack-years of tobacco smoking and decreases in subjects with history of chronic bronchitis. Genus Thermus is more abundant in tissue from advanced stage (IIIB, IV) patients, while Legionella is higher in patients who develop metastases. Moreover, the non-malignant lung tissues have higher microbiota alpha diversity than the paired tumors. Conclusions Our results provide insights into the human lung microbiota composition and function and their link to human lifestyle and clinical outcomes. Studies among subjects without lung cancer are needed to confirm our findings. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1021-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guoqin Yu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Mitchell H Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Milan, Italy
| | - Michele Carugno
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Michael Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Angela C Pesatori
- Epidemiology Unit, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Neil E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria Teresa Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.
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161
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Jones GS, Feigelson HS, Ravel J, Goedert JJ. Abstract 3296: Breast mammographic density and the fecal microbiota. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The microbial population (microbiota) of the distal human gut has multiple functions that modulate cancer risk including digestion of nutrients, deconjugation and enterohepatic circulation of hormones and other bile acids, and regulation of immunity and inflammation. We have previously reported that postmenopausal breast cancer cases, compared to controls, have lower fecal microbiota alpha diversity, independent of age, body mass index, and estrogen levels, and that the cases’ microbiota is compositionally altered. For deeper understanding of these associations with breast cancer, we compared microbiota metrics to a strong cancer risk factor, breast density, among 48 cancer-free, postmenopausal controls in the Breast and Colon Health study (86% non-Hispanic White, mean age 62 years). In routine screening mammograms, they had the following Breast Imaging Reporting and Data System (BI-RADS, 5th ed.) composition: a) almost entirely fatty (N = 4); b) scattered areas of fibroglandular density (N = 14); c) heterogeneously dense (N = 26); and d) extremely dense (N = 4).
As shown in the Table, simple linear regression across these four ordered BI-RADS categories revealed that there was no significant association with fecal microbiota alpha diversity (PD_tree β -0.08, P = 0.56). Breast density in these women also was not associated with microbiota beta diversity (composition) by MiRKAT analysis of un-weighted and weighted UniFrac metrics (P = 0.25 and 0.08, respectively).
We conclude that breast density is unlikely to mediate the association of the gut microbiota with breast cancer in postmenopausal women. Fecal alpha diversity by mammographic density categoryBI-RADS DensityNo.Mean (SD) PD_Whole_TreeAlmost Entirely Fatty436.06 (4.22)Scattered Fibroglandular1438.18 (8.25)Heterogeneously Dense2637.19 (4.88)Extremely Dense438.33 (7.99)
Citation Format: Gieira S. Jones, Heather S. Feigelson, Jacques Ravel, James J. Goedert. Breast mammographic density and the fecal microbiota. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3296.
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Affiliation(s)
| | | | - Jacques Ravel
- 3University of Maryland School of Medicine, Baltimore, MD
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162
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Smith SB, Ravel J. The vaginal microbiota, host defence and reproductive physiology. J Physiol 2016; 595:451-463. [PMID: 27373840 DOI: 10.1113/jp271694] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/28/2016] [Indexed: 02/06/2023] Open
Abstract
The interaction between the human host and the vaginal microbiota is highly dynamic. Major changes in the vaginal physiology and microbiota over a woman's lifetime are largely shaped by transitional periods such as puberty, menopause and pregnancy, while daily fluctuations in microbial composition observed through culture-independent studies are more likely to be the results of daily life activities and behaviours. The vaginal microbiota of reproductive-aged women is largely made up of at least five different community state types. Four of these community state types are dominated by lactic-acid producing Lactobacillus spp. while the fifth is commonly composed of anaerobes and strict anaerobes and is sometimes associated with vaginal symptoms. The production of lactic acid has been associated with contributing to the overall health of the vagina due to its direct and indirect effects on pathogens and host defence. Some species associated with non-Lactobacillus vaginal microbiota may trigger immune responses as well as degrade the host mucosa, processes that ultimately increase susceptibility to infections and contribute to negative reproductive outcomes such as infertility and preterm birth. Further studies are needed to better understand the functional underpinnings of how the vaginal microbiota affect host physiology but also how host physiology affects the vaginal microbiota. Understanding this fine-tuned interaction is key to maintaining women's reproductive health.
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Affiliation(s)
- Steven B Smith
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
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163
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Robinson CK, Brotman RM, Ravel J. Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol 2016; 26:311-21. [PMID: 27180112 PMCID: PMC4892937 DOI: 10.1016/j.annepidem.2016.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/29/2016] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis. METHODS Literature focused on human microbiota research was reviewed and summarized. RESULTS Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes. CONCLUSIONS Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.
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Affiliation(s)
- Courtney K Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore.
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore.
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164
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Abstract
Management, manipulation, and restoration of a robust vaginal microbiota has the potential to vastly improve women’s health and disease prevention. However, a systems level understanding of how the vaginal microbiota is associated with gynecologic and reproductive health is still needed to develop effective interventional strategies.
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Affiliation(s)
- Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Rebecca M Brotman
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
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165
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Crits-Christoph A, Gelsinger DR, Ma B, Wierzchos J, Ravel J, Davila A, Casero MC, DiRuggiero J. Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community. Environ Microbiol 2016; 18:2064-77. [DOI: 10.1111/1462-2920.13259] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | | | - M. Cristina Casero
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
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166
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Crits-Christoph A, Robinson CK, Ma B, Ravel J, Wierzchos J, Ascaso C, Artieda O, Souza-Egipsy V, Casero MC, DiRuggiero J. Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments. Front Microbiol 2016; 7:301. [PMID: 27014224 PMCID: PMC4784552 DOI: 10.3389/fmicb.2016.00301] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/23/2016] [Indexed: 11/13/2022] Open
Abstract
Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic - might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life.
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Affiliation(s)
| | | | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Carmen Ascaso
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | - Virginia Souza-Egipsy
- Instituto de Ciencias Agrarias - Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - M Cristina Casero
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas Madrid, Spain
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167
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Mirmonsef P, Hotton AL, Gilbert D, Burgad D, Landay A, Weber KM, Cohen M, Ravel J, Spear GT. Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH. PLoS One 2015. [PMID: 25033265 DOI: 10.1371/joumal.pone.0102467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
OBJECTIVE Lactobacillus dominates the lower genital tract microbiota of many women, producing a low vaginal pH, and is important for healthy pregnancy outcomes and protection against several sexually transmitted pathogens. Yet, factors that promote Lactobacillus remain poorly understood. We hypothesized that the amount of free glycogen in the lumen of the lower genital tract is an important determinant of Lactobacillus colonization and a low vaginal pH. METHODS Free glycogen in lavage samples was quantified. Pyrosequencing of the 16S rRNA gene was used to identify microbiota from 21 African American women collected over 8-11 years. RESULTS Free glycogen levels varied greatly between women and even in the same woman. Samples with the highest free glycogen had a corresponding median genital pH that was significantly lower (pH 4.4) than those with low glycogen (pH 5.8; p<0.001). The fraction of the microbiota consisting of Lactobacillus was highest in samples with high glycogen versus those with low glycogen (median = 0.97 vs. 0.05, p<0.001). In multivariable analysis, having 1 vs. 0 male sexual partner in the past 6 months was negatively associated, while BMI ≥30 was positively associated with glycogen. High concentrations of glycogen corresponded to higher levels of L. crispatus and L. jensenii, but not L. iners. CONCLUSION These findings show that free glycogen in genital fluid is associated with a genital microbiota dominated by Lactobacillus, suggesting glycogen is important for maintaining genital health. Treatments aimed at increasing genital free glycogen might impact Lactobacillus colonization.
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Affiliation(s)
- Paria Mirmonsef
- Department of Immunology/Microbiology, Rush University, Chicago, Illinois, United States of America
| | - Anna L Hotton
- The CORE Center, Cook County Health & Hospital System, Chicago, Illinois, United States of America
| | - Douglas Gilbert
- Department of Immunology/Microbiology, Rush University, Chicago, Illinois, United States of America
| | - Derick Burgad
- Department of Immunology/Microbiology, Rush University, Chicago, Illinois, United States of America
| | - Alan Landay
- Department of Immunology/Microbiology, Rush University, Chicago, Illinois, United States of America
| | - Kathleen M Weber
- The CORE Center, Cook County Health & Hospital System, Chicago, Illinois, United States of America
| | - Mardge Cohen
- The CORE Center, Cook County Health & Hospital System, Chicago, Illinois, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory T Spear
- Department of Immunology/Microbiology, Rush University, Chicago, Illinois, United States of America
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168
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Breshears LM, Edwards VL, Ravel J, Peterson ML. Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model. BMC Microbiol 2015; 15:276. [PMID: 26652855 PMCID: PMC4675025 DOI: 10.1186/s12866-015-0608-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/30/2015] [Indexed: 02/07/2023] Open
Abstract
Background The vaginal microbiota can impact the susceptibility of women to bacterial vaginosis (BV) and sexually transmitted infections (STIs). BV is characterized by depletion of Lactobacillus spp., an overgrowth of anaerobes (often dominated by Gardnerella vaginalis) and a pH > 4.5. BV is associated with an increased risk of acquiring STIs such as chlamydia and gonorrhea. While these associations have been identified, the molecular mechanism(s) driving the risk of infections are unknown. An ex vivo porcine vaginal mucosal model (PVM) was developed to explore the mechanistic role of Lactobacillus spp. in affecting colonization by G. vaginalis and Neisseria gonorrhoeae. Results The data presented here demonstrate that all organisms tested can colonize and grow on PVM to clinically relevant densities. Additionally, G. vaginalis and N. gonorrhoeae form biofilms on PVM. It was observed that lactic acid, acetic acid, and hydrochloric acid inhibit the growth of G. vaginalis on PVM in a pH-dependent manner. N. gonorrhoeae grows best in the presence of lactic acid at pH 5.5, but did not grow well at this pH in the presence of acetic acid. Finally, a clinical Lactobacillus crispatus isolate (24-9-7) produces lactic acid and inhibits growth of both G. vaginalis and N. gonorrhoeae on PVM. Conclusions These data reveal differences in the effects of pH, various acids and L. crispatus on the growth of G. vaginalis and N. gonorrhoeae on a live vaginal mucosal surface. The PVM is a useful model for studying the interactions of commensal vaginal microbes with pathogens and the mechanisms of biofilm formation on the vaginal mucosa.
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Affiliation(s)
- Laura M Breshears
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, 4-442 McGuire Translational Research Facility, 2001 6th St. SE, Minneapolis, MN, 55455, USA.
| | - Vonetta L Edwards
- Institute for Genome Sciences, University of Maryland, School of Medicine, Bio Park II, 6th Floor, 801 West Baltimore St., Baltimore, MD, 21201, USA.
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland, School of Medicine, Bio Park II, 6th Floor, 801 West Baltimore St., Baltimore, MD, 21201, USA.
| | - Marnie L Peterson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, 4-442 McGuire Translational Research Facility, 2001 6th St. SE, Minneapolis, MN, 55455, USA.
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169
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Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 2015; 64:1732-43. [PMID: 25614621 PMCID: PMC5166700 DOI: 10.1136/gutjnl-2014-308820] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited. DESIGN Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network. RESULTS We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments. CONCLUSIONS In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.
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Affiliation(s)
- Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, Oregon,
USA,Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
| | - Amiran Dzutsev
- Cancer and Inflammation Program, National Cancer Institute/Leidos
Biomedical Research, Inc., Frederick, Maryland, USA
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, Corvallis, Oregon,
USA
| | - Renee L Greer
- College of Veterinary Medicine, Oregon State University, Corvallis,
Oregon, USA
| | - D Joseph Sexton
- Department of Microbiology, Oregon State University, Corvallis,
Oregon, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of
Medicine, Baltimore, Maryland, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis,
Oregon, USA
| | - William Hsiao
- University of British Columbia, Vancouver, British Columbia,
Canada
| | - Polly Matzinger
- Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis,
Oregon, USA,Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
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170
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Nelson TM, Borgogna JLC, Brotman RM, Ravel J, Walk ST, Yeoman CJ. Vaginal biogenic amines: biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis? Front Physiol 2015; 6:253. [PMID: 26483694 PMCID: PMC4586437 DOI: 10.3389/fphys.2015.00253] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/28/2015] [Indexed: 12/12/2022] Open
Abstract
Bacterial vaginosis (BV) is the most common vaginal disorder among reproductive age women. One clinical indicator of BV is a “fishy” odor. This odor has been associated with increases in several biogenic amines (BAs) that may serve as important biomarkers. Within the vagina, BA production has been linked to various vaginal taxa, yet their genetic capability to synthesize BAs is unknown. Using a bioinformatics approach, we show that relatively few vaginal taxa are predicted to be capable of producing BAs. Many of these taxa (Dialister, Prevotella, Parvimonas, Megasphaera, Peptostreptococcus, and Veillonella spp.) are more abundant in the vaginal microbial community state type (CST) IV, which is depleted in lactobacilli. Several of the major Lactobacillus species (L. crispatus, L. jensenii, and L. gasseri) were identified as possessing gene sequences for proteins predicted to be capable of putrescine production. Finally, we show in a small cross sectional study of 37 women that the BAs putrescine, cadaverine and tyramine are significantly higher in CST IV over CSTs I and III. These data support the hypothesis that BA production is conducted by few vaginal taxa and may be important to the outgrowth of BV-associated (vaginal dysbiosis) vaginal bacteria.
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Affiliation(s)
- Tiffanie M Nelson
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA ; Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | | | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA ; Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
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171
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Edwards V, McComb E, Guttman H, Humphrys M, Forney L, Bavoil P, Ravel J. P08.06 Lactic acid isomers differentially reduce chlamydia trachomatisinfection in a ph dependent manner. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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172
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Brotman RM, Gajer P, Robinson CK, Ma B, Humphrys M, Tuddenham S, Ravel J, Ghanem KG. O13.2 Hormonal contraception is associated with stability and lactobacillus-dominance of the vaginal microbiota in a two-year observational study. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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173
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Nelson TM, Borgogna JC, Roberts DW, Michalek RD, Gajer P, Ravel J, Yeoman CJ, Brotman RM. O13.6 Cigarette smoking is associated with an altered metabolic profile in the vaginal tract. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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174
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Ma B, Gajer P, Humphrys M, Yang H, Fu L, Terplan M, Bavoil P, Forney L, Ravel J. P06.06 Azythromycin treatment for chlamydia trachomatisis associated with vaginal microbiota lacking protective lactobacillusspp. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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175
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Tuddenham SA, Rovner AJ, Ma B, Robinson C, Gajer P, Ravel J, Ghanem KG, Brotman RM. O13.5 Association between dietary intake and dysbiotic vaginal microbiota. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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176
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Ravel J. S13.1 The many facets of the vaginal microbiome in health and disease. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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177
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Breshears LM, Edwards VL, Ravel J, Peterson ML. P06.09 Lactobacilluscrispatus inhibits growth of gardnerella vaginalisand neisseria gonorrhoeaeon a porcine vaginal mucosa model. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Background Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. Results In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon’s index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Conclusions Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies.
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Affiliation(s)
- Guoqin Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Doug Fadrosh
- Institute of Genomic Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jacques Ravel
- Institute of Genomic Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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179
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Goedert JJ, Jones G, Hua X, Xu X, Yu G, Flores R, Falk RT, Gail MH, Shi J, Ravel J, Feigelson HS. Investigation of the association between the fecal microbiota and breast cancer in postmenopausal women: a population-based case-control pilot study. J Natl Cancer Inst 2015; 107:djv147. [PMID: 26032724 DOI: 10.1093/jnci/djv147] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/04/2015] [Indexed: 12/13/2022] Open
Abstract
We investigated whether the gut microbiota differed in 48 postmenopausal breast cancer case patients, pretreatment, vs 48 control patients. Microbiota profiles in fecal DNA were determined by Illumina sequencing and taxonomy of 16S rRNA genes. Estrogens were quantified in urine. Case-control comparisons employed linear and unconditional logistic regression of microbiota α-diversity (PD_whole tree) and UniFrac analysis of β-diversity, with two-sided statistical tests. Total estrogens correlated with α-diversity in control patients (Spearman Rho = 0.37, P = .009) but not case patients (Spearman Rho = 0.04, P = .77). Compared with control patients, case patients had statistically significantly altered microbiota composition (β-diversity, P = .006) and lower α-diversity (P = .004). Adjusted for estrogens and other covariates, odds ratio of cancer was 0.50 (95% confidence interval = 0.30 to 0.85) per α-diversity tertile. Differences in specific taxa were not statistically significant when adjusted for multiple comparisons. This pilot study shows that postmenopausal women with breast cancer have altered composition and estrogen-independent low diversity of their gut microbiota. Whether these affect breast cancer risk and prognosis is unknown.
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Affiliation(s)
- James J Goedert
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF).
| | - Gieira Jones
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Xia Xu
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Guoqin Yu
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Roberto Flores
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Roni T Falk
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Mitchell H Gail
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Jacques Ravel
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
| | - Heather Spencer Feigelson
- Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda, MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO (HSF)
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Goedert JJ, Gong Y, Hua X, Zhong H, He Y, Peng P, Yu G, Wang W, Ravel J, Shi J, Zheng Y. Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study. EBioMedicine 2015; 2:597-603. [PMID: 26288821 PMCID: PMC4535156 DOI: 10.1016/j.ebiom.2015.04.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 02/06/2023] Open
Abstract
Background Screening for colorectal cancer (CRC) and precancerous colorectal adenoma (CRA) can detect curable disease. However, participation in colonoscopy and sensitivity of fecal heme for CRA are low. Methods Microbiota metrics were determined by Illumina sequencing of 16S rRNA genes amplified from DNA extracted from feces self-collected in RNAlater. Among fecal immunochemical test-positive (FIT +) participants, colonoscopically-defined normal versus CRA patients were compared by regression, permutation, and random forest plus leave-one-out methods. Findings Of 95 FIT + participants, 61 had successful fecal microbiota profiling and colonoscopy, identifying 24 completely normal patients, 20 CRA patients, 2 CRC patients, and 15 with other conditions. Phylum-level fecal community composition differed significantly between CRA and normal patients (permutation P = 0.02). Rank phylum-level abundance distinguished CRA from normal patients (area under the curve = 0.767, permutation P = 0.006). CRA prevalence was 59% in phylum-level cluster B versus 20% in cluster A (exact P = 0.01). Most of the difference reflected 3-fold higher median relative abundance of Proteobacteria taxa (Wilcoxon signed-rank P = 0.03, positive predictive value = 67%). Antibiotic exposure and other potential confounders did not affect the associations. Interpretation If confirmed in larger, more diverse populations, fecal microbiota analysis might be employed to improve screening for CRA and ultimately to reduce mortality from CRC. Fecal microbiota composition differed for patients with colorectal adenoma compared to normals. Most of the difference reflected 3-fold higher abundance of Proteobacteria in patients with adenoma. Population-wide microbiota screening is feasible and, if validated, could complement established early-detection programs.
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Affiliation(s)
- James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | - Yangming Gong
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | | | | | - Peng Peng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Guoqin Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | - Wenjing Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jacques Ravel
- Institute of Genome Sciences, University of Maryland Medical School, Baltimore MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
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181
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Mojica SA, Hovis KM, Frieman MB, Tran B, Hsia RC, Ravel J, Jenkins-Houk C, Wilson KL, Bavoil PM. SINC, a type III secreted protein of Chlamydia psittaci, targets the inner nuclear membrane of infected cells and uninfected neighbors. Mol Biol Cell 2015; 26:1918-34. [PMID: 25788290 PMCID: PMC4436835 DOI: 10.1091/mbc.e14-11-1530] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/06/2015] [Indexed: 12/31/2022] Open
Abstract
SINC, a new type III secreted protein of the avian and human pathogen Chlamydia psittaci, uniquely targets the nuclear envelope of C. psittaci-infected cells and uninfected neighboring cells. Digitonin-permeabilization studies of SINC-GFP-transfected HeLa cells indicate that SINC targets the inner nuclear membrane. SINC localization at the nuclear envelope was blocked by importazole, confirming SINC import into the nucleus. Candidate partners were identified by proximity to biotin ligase-fused SINC in HEK293 cells and mass spectrometry (BioID). This strategy identified 22 candidates with high confidence, including the nucleoporin ELYS, lamin B1, and four proteins (emerin, MAN1, LAP1, and LBR) of the inner nuclear membrane, suggesting that SINC interacts with host proteins that control nuclear structure, signaling, chromatin organization, and gene silencing. GFP-SINC association with the native LEM-domain protein emerin, a conserved component of nuclear "lamina" structure, or with a complex containing emerin was confirmed by GFP pull down. Our findings identify SINC as a novel bacterial protein that targets the nuclear envelope with the capability of globally altering nuclear envelope functions in the infected host cell and neighboring uninfected cells. These properties may contribute to the aggressive virulence of C. psittaci.
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Affiliation(s)
- Sergio A Mojica
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Kelley M Hovis
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Bao Tran
- Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Ru-ching Hsia
- Core Imaging Facility and Department of Neural and Pain Sciences, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Jacques Ravel
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Clifton Jenkins-Houk
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Patrik M Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
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182
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Mendes-Soares H, Krishnan V, Settles ML, Ravel J, Brown CJ, Forney LJ. Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. Pathog Dis 2015; 73:ftv020. [PMID: 25778779 DOI: 10.1093/femspd/ftv020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 01/29/2023] Open
Abstract
Although vaginal microbial communities of some healthy women have high proportions of Atopobium vaginae, the genus Atopobium is more commonly associated with bacterial vaginosis, a syndrome associated with an increased risk of adverse pregnancy outcomes and the transmission of sexually transmitted diseases. Genetic differences within Atopobium species may explain why single species can be associated with both health and disease. We used 16S rRNA gene sequences from previously published studies to explore the taxonomic diversity of the genus Atopobium in vaginal microbial communities of healthy women. Although A. vaginae was the species most commonly found, we also observed three other Atopobium species in the vaginal microbiota, one of which, A. parvulum, was not previously known to reside in the human vagina. Furthermore, we found several potential novel species of the genus Atopobium and multiple phylogenetic clades of A. vaginae. The diversity of Atopobium found in our study, which focused only on samples from healthy women, is greater than previously recognized, suggesting that analysis of samples from women with BV would yield even more diversity. Classification of microbes only to the genus level may thus obfuscate differences that might be important to better understand health or disease.
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Affiliation(s)
- Helena Mendes-Soares
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow ID 83844, USA
| | - Vandhana Krishnan
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow ID 83844, USA
| | - Matthew L Settles
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow ID 83844, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Celeste J Brown
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow ID 83844, USA
| | - Larry J Forney
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow ID 83844, USA
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Neuendorf E, Gajer P, Bowlin AK, Marques PX, Ma B, Yang H, Fu L, Humphrys MS, Forney LJ, Myers GSA, Bavoil PM, Rank RG, Ravel J. Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota. Pathog Dis 2015; 73:ftv019. [PMID: 25761873 PMCID: PMC4445005 DOI: 10.1093/femspd/ftv019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/09/2023] Open
Abstract
In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection. The vaginal microbiota of the guinea pig differs from that of humans and cannot prevent chlamydial infections efficiently.
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Affiliation(s)
- Elizabeth Neuendorf
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Anne K Bowlin
- Arkansas Children's Hospital Research Institute, Little Rock, AR 72202, USA
| | - Patricia X Marques
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hongqiu Yang
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Li Fu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Larry J Forney
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
| | - Garry S A Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patrik M Bavoil
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
| | - Roger G Rank
- Arkansas Children's Hospital Research Institute, Little Rock, AR 72202, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell 2015; 159:227-30. [PMID: 25303518 DOI: 10.1016/j.cell.2014.09.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology.
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Affiliation(s)
- Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - C Titus Brown
- Department of Microbiology and Molecular Genetics and Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86001, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dirk Gevers
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Health-Related Informatics and Bioimaging, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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185
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evident by the exponential increase in the number of publications describing the composition and structure, and sometimes function, of the microbial communities inhabiting the human body. This rapid evolution of the field has been accompanied by confusion in the vocabulary used to describe different aspects of these communities and their environments. The misuse of terms such as microbiome, microbiota, metabolomic, and metagenome and metagenomics among others has contributed to misunderstanding of many study results by the scientific community and the general public alike. A few review articles have previously defined those terms, but mainly as sidebars, and no clear definitions or use cases have been published. In this editorial, we aim to propose clear definitions of each of these terms, which we would implore scientists in the field to adopt and perfect.
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Affiliation(s)
- Julian R. Marchesi
- />Cardiff School of Biosciences, Division of Microbiology, Cardiff University, Museum Avenue, Cardiff, CF10 3AT United Kingdom
- />Centre for Digestive and Gut Health, Imperial College London, Exhibition Road, London, SW7 2AZ United Kingdom
| | - Jacques Ravel
- />Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201 USA
- />Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201 USA
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187
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Flores R, Shi J, Yu G, Ma B, Ravel J, Goedert JJ, Sinha R. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome 2015; 3:33. [PMID: 26269741 PMCID: PMC4534027 DOI: 10.1186/s40168-015-0092-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/01/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Different bacteria in stool have markedly varied growth and survival when stored at ambient temperature. It is paramount to develop optimal biostabilization of stool samples during collection and assess long-term storage for clinical specimens and epidemiological microbiome studies. We evaluated the effect of collection media and delayed freezing up to 7 days on microbial composition. Ten participants collected triplicate stool samples each into no media as well as RNAlater® with and without kanamycin or ciprofloxacin. For each set of conditions, triplicate samples were frozen on dry ice immediately (time = 0) or frozen at -80 °C after 3-days and 7-days incubation at 25 °C. Microbiota metrics were estimated from Illumina MiSeq sequences of 16S rRNA gene fragments (V3-V4 region). Intraclass correlation coefficients (ICC) across triplicates, collection media, and incubation time were estimated for taxonomy and alpha and beta diversity metrics. RESULTS RNAlater® alone yielded the highest ICCs for diversity metrics at time = 0 [ICC median 0.935 (range 0.89-0.97)], but ICCs varied greatly (range 0.44-1.0) for taxa with relative abundances <1%. The 3- and 7-day freezing delays were generally associated with stable beta diversity for all three media conditions. Freezing delay caused increased variance for Shannon index (median ICC 0.77) and especially for observed species abundance (median ICC 0.47). Variance in observed species abundance and in phylogenetic distance whole tree was similarly increased with a 7-day delay. Antibiotics did not mitigate variance. No media had inferior ICCs at time 0 and differed markedly from any media in microbiome composition (e.g., P =0.01 for relative abundance of Bacteroidetes). CONCLUSION Bacterial community composition was stable for 7 days at room temperature in RNAlater® alone. RNAlater® provides some stability for beta diversity analyses, but analyses of rare taxa will be inaccurate if specimens are not frozen immediately. RNAlater® could be used as collection media with minimal change in the microbiota composition.
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Affiliation(s)
- Roberto Flores
- />Nutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr. RM5E554-MSC9788, Bethesda, MD 20892 USA
| | - Jianxin Shi
- />Biostatistics Branch, Division of Cancer Epidemiology and Genetics, NCI/NIH, Bethesda, MD USA
| | - Guoqin Yu
- />Infections and Immunoepidemiology Branch DCEG/NCI/NIH, Bethesda, MD USA
| | - Bing Ma
- />Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Jacques Ravel
- />Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - James J. Goedert
- />Infections and Immunoepidemiology Branch DCEG/NCI/NIH, Bethesda, MD USA
| | - Rashmi Sinha
- />Nutritional Epidemiology Branch, DCEG/NCI/NIH, Bethesda, MD USA
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Fuhrman BJ, Feigelson HS, Flores R, Gail MH, Xu X, Ravel J, Goedert JJ. Associations of the fecal microbiome with urinary estrogens and estrogen metabolites in postmenopausal women. J Clin Endocrinol Metab 2014; 99:4632-40. [PMID: 25211668 PMCID: PMC4255131 DOI: 10.1210/jc.2014-2222] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
CONTEXT The gut microbiota may influence the risk of breast cancer through effects on endogenous estrogens. OBJECTIVE The objective of the study was to investigate whether urinary estrogens and estrogen metabolites are associated with the diversity and composition of the fecal microbiome. DESIGN AND SETTING This was a cross-sectional study among women enrolled in Kaiser Permanente of Colorado. PARTICIPANTS A total of 60 women drawn from a random sample of healthy postmenopausal women (aged 55-69 y), without current or recent use of antibiotics or hormone therapy and no history of cancer or gastrointestinal disease participated in the study. OUTCOME MEASURES AND METHODS: Creatinine-standardized urinary estrogens (estrone and estradiol) and 13 hydroxylated estrogen metabolites were measured in spot urines by liquid chromatography-tandem mass spectrometry. The fecal microbiome was assessed using pyrosequencing of 16S rRNA amplicons. General linear models were used to test for associations of diversity and composition of the fecal microbiome with parent estrogen (estrone + estradiol), total estrogens, and estrogen metabolites and the ratio of estrogen metabolites to parent estrogen, which has been predictive of postmenopausal breast cancer risk in previous studies. RESULTS The ratio of metabolites to parents was directly associated with whole-tree phylogenetic diversity (R = 0.35, P = .01). Relative abundances of the order Clostridiales (R = 0.32, P = .02) and the genus Bacteroides (R = -0.30, P = .03) were also correlated with the ratio of metabolites to parents. Associations were independent of age, body mass index, and study design factors. CONCLUSIONS Our data suggest that women with a more diverse gut microbiome exhibit an elevated urinary ratio of hydroxylated estrogen metabolites to parent estrogen. Further research is warranted to confirm and relate these findings to clinical disease.
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Affiliation(s)
- Barbara J Fuhrman
- Department of Epidemiology (B.J.F.), Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205; Divisions of Cancer Epidemiology and Genetics (B.J.F., R.F., N.H.G., J.J.G.) and Cancer Prevention (R.F.), National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892-9704; Institute for Health Research (H.S.F.), Kaiser Permanente Colorado, Denver, Colorado 80231; Cancer Research Technology Program (X.X.), Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702; and Institute for Genome Sciences (J.R.), University of Maryland, Baltimore, Maryland 21201
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Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L, Fajans M, Anderson ME, Jaoko W, Kurth AE. An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. AIDS Res Hum Retroviruses 2014; 30:1046-54. [PMID: 25265254 DOI: 10.1089/aid.2013.0251] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Intravaginal practices (IVP) are common among African women and are associated with HIV acquisition. A behavioral intervention to reduce IVP is a potential new HIV risk-reduction strategy. Fifty-eight HIV-1-uninfected Kenyan women reporting IVP and 42 women who denied IVP were followed for 3 months. Women using IVP attended a skill-building, theory-based group intervention occurring weekly for 3 weeks to encourage IVP cessation. Vaginal swabs at each visit were used to detect yeast, to detect bacterial vaginosis, and to characterize the vaginal microbiota. Intravaginal insertion of soapy water (59%) and lemon juice (45%) was most common among 58 IVP women. The group-counseling intervention led to a decrease in IVP from 95% (54/58) at baseline to 0% (0/39) at month 3 (p=0.001). After 3 months of cessation, there was a reduction in yeast on vaginal wet preparation (22% to 7%, p=0.011). Women in the IVP group were more likely to have a Lactobacillus iners-dominated vaginal microbiota at baseline compared to controls [odds ratio (OR), 6.4, p=0.006] without significant change in the microbiota after IVP cessation. The group counseling intervention was effective in reducing IVP for 3 months. Reducing IVP may be important in itself, as well as to support effective use of vaginal microbicides, to prevent HIV acquisition.
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Affiliation(s)
- Sumathi Sivapalasingam
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, New York
| | - R. Scott McClelland
- University of Washington School of Medicine, Seattle, Washington
- University of Nairobi, Nairobi, Kenya
| | - Jacques Ravel
- University of Maryland School of Medicine, Institute for Genomic Sciences, Baltimore, Maryland
| | | | | | - Pawel Gajer
- University of Maryland School of Medicine, Institute for Genomic Sciences, Baltimore, Maryland
| | - Musa Mwamzaka
- University of Maryland School of Medicine, Institute for Genomic Sciences, Baltimore, Maryland
| | | | - Juma Shafi
- Ganjoni Municipal Clinic, Mombasa, Kenya
| | - Linnet Masese
- University of Washington School of Medicine, Seattle, Washington
| | - Mark Fajans
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, New York
| | | | | | - Ann E. Kurth
- College of Nursing, New York University, New York, New York
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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191
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Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PLoS One 2014; 9:e102651. [PMID: 25047912 PMCID: PMC4105404 DOI: 10.1371/journal.pone.0102651] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 06/21/2014] [Indexed: 11/19/2022] Open
Abstract
Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one subclade is only found in the eastern part. This pattern suggests that dispersal into and out of Georgia has been rare and despite historical dispersion within the country, for at least for one lineage, current spread is limited.
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Affiliation(s)
- Ekaterine Khmaladze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Dawn N. Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amber A. Naumann
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Christian B. Hochhalter
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Meagan L. Seymour
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - James Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mikeljon P. Nikolich
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Gvantsa Chanturia
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Ekaterine Zhgenti
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | | | - Lile Malania
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Giorgi Babuadze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | | | | | - Merab Kekelidze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Shota Tsanava
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Holly H. Ganz
- Department Environmental Science Policy and Management, University of California, Berkeley, California, United States of America
| | - Wayne M. Getz
- Department Environmental Science Policy and Management, University of California, Berkeley, California, United States of America
| | - Ofori Pearson
- US Geological Survey, Denver Federal Center, Denver, Colorado, United States of America
| | - Pawel Gajer
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
| | - Mark Eppinger
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
- University of Texas at San Antonio, Texas, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, Baltimore, Maryland, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard T. Okinaka
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
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Ravel J, Blaser MJ, Braun J, Brown E, Bushman FD, Chang EB, Davies J, Dewey KG, Dinan T, Dominguez-Bello M, Erdman SE, Finlay BB, Garrett WS, Huffnagle GB, Huttenhower C, Jansson J, Jeffery IB, Jobin C, Khoruts A, Kong HH, Lampe JW, Ley RE, Littman DR, Mazmanian SK, Mills DA, Neish AS, Petrof E, Relman DA, Rhodes R, Turnbaugh PJ, Young VB, Knight R, White O. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013. Microbiome 2014; 2. [PMCID: PMC4102747 DOI: 10.1186/2049-2618-2-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.
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Affiliation(s)
- Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Martin J Blaser
- Department of Microbiology, Human Microbiome Program, New York University Langone Medical Center, 550 First Avenue, Bellevue CD 689, New York, NY 10016, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Eric Brown
- The Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eugene B Chang
- Knapp Center for Biomedical Discovery, University of Chicago, 900 E. 57th Street, Chicago, IL 60637, USA
| | - Julian Davies
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver BC V6T 1Z3, Canada
| | - Kathryn G Dewey
- Department of Nutrition, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Timothy Dinan
- Department of Psychiatry, GF Unity, Cork University Hospital, Cork, Wilton, Ireland
| | - Maria Dominguez-Bello
- Department of Microbiology, Human Microbiome Program, New York University Langone Medical Center, 550 First Avenue, Bellevue CD 689, New York, NY 10016, USA
| | - Susan E Erdman
- Division of Comparative Medicine, Massachusetts Institute of Technology, One Massachusetts Avenue, Cambridge, MA 02139, USA
| | - B Brett Finlay
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Gary B Huffnagle
- Department of Internal Medicine/Infectious Diseases, Immunology University of Michigan Medical School, 1500 W. Medical Center Drive, Ann Arbor, MI 48109, USA
- Department of Microbiology, Immunology University of Michigan Medical School, 1500 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston MA 02115, USA
| | - Janet Jansson
- Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ian B Jeffery
- Department of Microbiology, The Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Christian Jobin
- Department of Infectious Diseases & Pathology, College of Medicine, University of Florida, 2015 SW 16th Avenue, PO Box 110880, Gainesville, FL 32611, USA
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Florida, 2015 SW 16th Avenue, PO Box 110880, Gainesville, FL 32611, USA
| | - Alexander Khoruts
- Department of Medicine, Center for Immunology, Room 3-184, Medical Biosciences Building, 2101 6th S. E, Minneapolis, MN 55416, USA
| | - Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Johanna W Lampe
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, PO Box 19024, Seattle, WA 98109, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY 14853, USA
| | - Dan R Littman
- Department of Pathology, Molecular Pathogenesis, 540 First Avenue, Skirball Institute, New York, NY 10016, USA
- Department of Microbiology, Molecular Pathogenesis, 540 First Avenue, Skirball Institute, New York, NY 10016, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E. California Bl, Pasadena, CA 91125, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew S Neish
- Department of pathology, Emory University School of Medicine, 105H whitehead bldg., 615 Francis Street, Atlanta, GA 30322, USA
| | - Elaine Petrof
- Department of Medicine/Infectious Diseases, Gastrointestinal Diseases Research Unit, Queens University and Kingston General Hospital, 76 Stuart Street, GIDRU wing, Kingston ON K7L 2V7, Canada
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rosamond Rhodes
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, Box 1076, Annenberg 12-42, New York, NY 10029, USA
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, 52 Oxford St, Cambridge, MA 02138, USA
| | - Vincent B Young
- Department of Internal Medicine/Infectious Diseases, Immunology University of Michigan Medical School, 1500 W. Medical Center Drive, Ann Arbor, MI 48109, USA
- Department of Microbiology, Immunology University of Michigan Medical School, 1500 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, 215 UCB, Boulder, CO 80309, USA
| | - Owen White
- Institute for Genome Sciences, Department of Epidemiology and Public Health, University of Maryland School of Medicine, 660 W. Redwood Street, Baltimore, MD 21201, USA
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Brotman RM, Shardell MD, Gajer P, Tracy JK, Zenilman JM, Ravel J, Gravitt PE. Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. J Infect Dis 2014; 210:1723-33. [PMID: 24943724 DOI: 10.1093/infdis/jiu330] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND We sought to describe the temporal relationship between vaginal microbiota and human papillomavirus (HPV) detection. METHODS Thirty-two reproductive-age women self-collected midvaginal swabs twice weekly for 16 weeks (937 samples). Vaginal bacterial communities were characterized by pyrosequencing of barcoded 16S rRNA genes and clustered into 6 community state types (CSTs). Each swab was tested for 37 HPV types. The effects of CSTs on the rate of transition between HPV-negative and HPV-positive states were assessed using continuous-time Markov models. RESULTS Participants had an average of 29 samples, with HPV point prevalence between 58%-77%. CST was associated with changes in HPV status (P<.001). Lactobacillus gasseri-dominated CSTs had the fastest HPV remission rate, and a low Lactobacillus community with high proportions of the genera Atopobium (CST IV-B) had the slowest rate compared to L. crispatus-dominated CSTs (adjusted transition rate ratio [aTRR], 4.43, 95% confidence interval [CI], 1.11-17.7; aTRR, 0.33, 95% CI, .12-1.19, respectively). The rate ratio of incident HPV for low Lactobacillus CST IV-A was 1.86 (95% CI, .52-6.74). CONCLUSIONS Vaginal microbiota dominated by L. gasseri was associated with increased clearance of detectable HPV. Frequent longitudinal sampling is necessary for evaluation of the association between HPV detection and dynamic microbiota.
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Affiliation(s)
- Rebecca M Brotman
- Department of Epidemiology and Public Health, University of Maryland School of Medicine Institute for Genome Sciences, University of Maryland School of Medicine
| | - Michelle D Shardell
- Department of Epidemiology and Public Health, University of Maryland School of Medicine
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine
| | - J Kathleen Tracy
- Department of Epidemiology and Public Health, University of Maryland School of Medicine
| | - Jonathan M Zenilman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins Medical Institutions, Johns Hopkins Bayview Medical Center
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine Department of Microbiology and Immunology, University of Maryland School of Medicine
| | - Patti E Gravitt
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland
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Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J. Correction: The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2014; 2:10. [PMID: 24735933 PMCID: PMC4022389 DOI: 10.1186/2049-2618-2-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 05/08/2023]
Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Sonia S Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Pawel Gajer
- 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
| | - Adi L Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Douglas W Fadrosh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lorraine Nikita
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Marisa Galuppi
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ronald F Lamont
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynaecology, University of Southern Denmark, Odense, Denmark
- Division of Surgery, University College, Northwick Park Institute for Medical Research Campus, London, UK
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Jezid Miranda
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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195
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Feigelson HS, Bischoff K, Ardini MAE, Ravel J, Gail MH, Flores R, Goedert JJ. Feasibility of self-collection of fecal specimens by randomly sampled women for health-related studies of the gut microbiome. BMC Res Notes 2014; 7:204. [PMID: 24690120 PMCID: PMC3974920 DOI: 10.1186/1756-0500-7-204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/21/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The field of microbiome research is growing rapidly. We developed a method for self-collection of fecal specimens that can be used in population-based studies of the gut microbiome. We conducted a pilot study to test the feasibility of our methods among a random sample of healthy, postmenopausal women who are members of Kaiser Permanente Colorado (KPCO). We aimed to collect questionnaire data, fecal and urine specimens from 60 women, aged 55-69, who recently had a normal screening mammogram. We designed the study such that all questionnaire data and specimens could be collected at home. RESULTS We mailed an invitation packet, consent form and opt-out postcard to 300 women, then recruited by telephone women who did not opt-out. Verbally consented women were mailed an enrollment package including a risk factor questionnaire, link to an online diet questionnaire, specimen collection kit, and instructions for collecting stool and urine. Specimens were shipped overnight to the biorepository. Of the 300 women mailed an invitation packet, 58 (19%) returned the opt-out postcard. Up to 3 attempts were made to telephone the remaining women, of whom 130 (43%) could not be contacted, 23 (8%) refused, and 12 (4%) were ineligible. Enrollment packages were mailed to 77 women, of whom 59 returned the risk factor questionnaire and specimens. We found no statistically significant differences between enrolled women and those who refused participation or could not be contacted. CONCLUSIONS We demonstrated that a representative sample of women can be successfully recruited for a gut microbiome study; however, significant personal contact and carefully timed follow-up from the study personnel are required. The methods employed by our study could successfully be applied to analytic studies of a wide range of clinical conditions that have been postulated to be influenced by the gut microbial population.
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Affiliation(s)
- Heather Spencer Feigelson
- Institute for Health Research, Legacy Highlands, Suite 300, Kaiser Permanente Colorado, P,O, Box 378066, Denver, CO, USA.
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Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PLoS One 2014; 9:e90517. [PMID: 24618773 PMCID: PMC3949686 DOI: 10.1371/journal.pone.0090517] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 02/02/2014] [Indexed: 12/25/2022] Open
Abstract
The bacterial communities of sponges have been studied using molecular techniques as well as culture-based techniques, but the communities described by these two methods are remarkably distinct. Culture-based methods describe communities dominated by Proteobacteria, and Actinomycetes while molecular methods describe communities dominated by predominantly uncultivated groups such as the Chloroflexi, Acidobacteria, and Acidimicrobidae. In this study, we used a wide range of culture media to increase the diversity of cultivable bacteria from the closely related giant barrel sponges, Xestospongia muta collected from the Florida Keys, Atlantic Ocean and Xestospongia testudinaria, collected from Indonesia, Pacific Ocean. Over 400 pure cultures were isolated and identified from X. muta and X. testudinaria and over 90 bacterial species were represented. Over 16,000 pyrosequences were analyzed and assigned to 976 OTUs. We employed both cultured-based methods and pyrosequencing to look for patterns of overlap between the culturable and molecular communities. Only one OTU was found in both the molecular and culturable communities, revealing limitations inherent in both approaches.
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Affiliation(s)
- Naomi F. Montalvo
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jeanette Davis
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jan Vicente
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Raquel Pittiglio
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
- * E-mail:
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197
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Affiliation(s)
- Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
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198
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Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2014; 2:6. [PMID: 24558975 PMCID: PMC3940169 DOI: 10.1186/2049-2618-2-6] [Citation(s) in RCA: 1002] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/16/2014] [Indexed: 05/13/2023]
Abstract
BACKGROUND To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing platforms. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality. RESULTS Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We introduced a 0 to 7 bp "heterogeneity spacer" to the index sequence that allows an equal proportion of samples to be sequenced out of phase. CONCLUSIONS Our approach yields high quality sequence data from 16S rRNA gene amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a flexible and cost-effective sequencing option.
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Affiliation(s)
- Douglas W Fadrosh
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Bing Ma
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Pawel Gajer
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Naomi Sengamalay
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Sandra Ott
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, Department of Epidemiology and Public Health, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore Street, Baltimore, MD 21201, USA
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Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2014; 2:4. [PMID: 24484853 PMCID: PMC3916806 DOI: 10.1186/2049-2618-2-4] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/18/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND This study was undertaken to characterize the vaginal microbiota throughout normal human pregnancy using sequence-based techniques. We compared the vaginal microbial composition of non-pregnant patients with a group of pregnant women who delivered at term. RESULTS A retrospective case-control longitudinal study was designed and included non-pregnant women (n = 32) and pregnant women who delivered at term (38 to 42 weeks) without complications (n = 22). Serial samples of vaginal fluid were collected from both non-pregnant and pregnant patients. A 16S rRNA gene sequence-based survey was conducted using pyrosequencing to characterize the structure and stability of the vaginal microbiota. Linear mixed effects models and generalized estimating equations were used to identify the phylotypes whose relative abundance was different between the two study groups. The vaginal microbiota of normal pregnant women was different from that of non-pregnant women (higher abundance of Lactobacillus vaginalis, L. crispatus, L. gasseri and L. jensenii and lower abundance of 22 other phylotypes in pregnant women). Bacterial community state type (CST) IV-B or CST IV-A characterized by high relative abundance of species of genus Atopobium as well as the presence of Prevotella, Sneathia, Gardnerella, Ruminococcaceae, Parvimonas, Mobiluncus and other taxa previously shown to be associated with bacterial vaginosis were less frequent in normal pregnancy. The stability of the vaginal microbiota of pregnant women was higher than that of non-pregnant women; however, during normal pregnancy, bacterial communities shift almost exclusively from one CST dominated by Lactobacillus spp. to another CST dominated by Lactobacillus spp. CONCLUSION We report the first longitudinal study of the vaginal microbiota in normal pregnancy. Differences in the composition and stability of the microbial community between pregnant and non-pregnant women were observed. Lactobacillus spp. were the predominant members of the microbial community in normal pregnancy. These results can serve as the basis to study the relationship between the vaginal microbiome and adverse pregnancy outcomes.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Sonia S Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Pawel Gajer
- 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
| | - Adi L Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Douglas W Fadrosh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lorraine Nikita
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Marisa Galuppi
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ronald F Lamont
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynaecology, University of Southern Denmark, Odense, Denmark
- Division of Surgery, University College, Northwick Park Institute for Medical Research Campus, London, UK
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Jezid Miranda
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Robinson CK, Wierzchos J, Black C, Crits-Christoph A, Ma B, Ravel J, Ascaso C, Artieda O, Valea S, Roldán M, Gómez-Silva B, DiRuggiero J. Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert. Environ Microbiol 2014; 17:299-315. [PMID: 24372972 DOI: 10.1111/1462-2920.12364] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 12/11/2013] [Accepted: 12/17/2013] [Indexed: 11/26/2022]
Abstract
The Atacama Desert is one of the oldest and driest deserts in the world, and its hyper-arid core is described as 'the most barren region imaginable'. We used a combination of high-throughput sequencing and microscopy methods to characterize the endolithic microbial assemblages of halite pinnacles (salt rocks) collected in several hyper-arid areas of the desert. We found communities dominated by archaea that relied on a single phylotype of Halothece cyanobacteria for primary production. A few other phylotypes of salt-adapted bacteria and archaea, including Salinibacter, Halorhabdus, and Halococcus were major components of the halite communities, indicating specific adaptations to the unique halite environments. Multivariate statistical analyses of diversity metrics clearly separated the halite communities from that of the surrounding soil in the Yungay area. These analyses also revealed distribution patterns of halite communities correlated with atmospheric moisture. Microbial endolithic communities from halites exposed to coastal fogs and high relative humidity were more diverse; their archaeal and bacterial assemblages were accompanied by a novel algae related to oceanic picoplankton of the Mamiellales. In contrast, we did not find any algae in the Yungay pinnacles, suggesting that the environmental conditions in this habitat might be too extreme for eukaryotic photosynthetic life.
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