251
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Kumbhare SV, Patangia DVV, Patil RH, Shouche YS, Patil NP. Factors influencing the gut microbiome in children: from infancy to childhood. J Biosci 2019; 44:49. [PMID: 31180062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The human microbiota plays a crucial role in educating the immune system and influencing host health right since birth. Various maternal factors along with the vertical microbial transfer from the mother, as well as the horizontal environmental transmission and internal factors relating to the infant, play a crucial role in modulating the gut microbiota. The early life microflora is highly unstable and undergoes dynamic changes during the first few years, converging towards a more stabilized adult microbiota by co-evolving with the host by the age of 3-4 years. Microbiota studies have underlined the role of dysbiosis in developing several metabolic disorders like obesity, diabetes and immune-related disorders like asthma, to name a few. Thus, understanding early life microbial composition and various factors affecting the microbial community will provide a platform for developing strategies/techniques to maintain host health by restoring gut microbial flora. This review focuses on the factors that affect the microbial composition of the foetus in utero, during birth, infancy through childhood.
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Affiliation(s)
- Shreyas V Kumbhare
- National Centre for Cell Science, Savitribai Phule University of Pune Campus, Pune, Maharashtra 411007, India
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252
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Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy. Nat Med 2019; 25:1001-1011. [PMID: 31142850 DOI: 10.1038/s41591-019-0465-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/24/2019] [Indexed: 12/11/2022]
Abstract
The microbiome of the female reproductive tract has implications for women's reproductive health. We examined the vaginal microbiome in two cohorts of women who experienced normal term births: a cross-sectionally sampled cohort of 613 pregnant and 1,969 non-pregnant women, focusing on 300 pregnant and 300 non-pregnant women of African, Hispanic or European ancestry case-matched for race, gestational age and household income; and a longitudinally sampled cohort of 90 pregnant women of African or non-African ancestry. In these women, the vaginal microbiome shifted during pregnancy toward Lactobacillus-dominated profiles at the expense of taxa often associated with vaginal dysbiosis. The shifts occurred early in pregnancy, followed predictable patterns, were associated with simplification of the metabolic capacity of the microbiome and were significant only in women of African or Hispanic ancestry. Both genomic and environmental factors are likely contributors to these trends, with socioeconomic status as a likely environmental influence.
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253
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Fettweis JM, Serrano MG, Brooks JP, Edwards DJ, Girerd PH, Parikh HI, Huang B, Arodz TJ, Edupuganti L, Glascock AL, Xu J, Jimenez NR, Vivadelli SC, Fong SS, Sheth NU, Jean S, Lee V, Bokhari YA, Lara AM, Mistry SD, Duckworth RA, Bradley SP, Koparde VN, Orenda XV, Milton SH, Rozycki SK, Matveyev AV, Wright ML, Huzurbazar SV, Jackson EM, Smirnova E, Korlach J, Tsai YC, Dickinson MR, Brooks JL, Drake JI, Chaffin DO, Sexton AL, Gravett MG, Rubens CE, Wijesooriya NR, Hendricks-Muñoz KD, Jefferson KK, Strauss JF, Buck GA. The vaginal microbiome and preterm birth. Nat Med 2019; 25:1012-1021. [PMID: 31142849 PMCID: PMC6750801 DOI: 10.1038/s41591-019-0450-2] [Citation(s) in RCA: 506] [Impact Index Per Article: 101.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 12/15/2022]
Abstract
The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes ‘omics’ data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth. As part of the second phase of Human Microbiome Project, the Multi-Omic Microbiome Study: Pregnancy Initiative presents a community resource to help better understand how microbiome and host profiles change throughout pregnancy as well as to identify new opportunities for assessment of the risk of preterm birth.
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Affiliation(s)
- Jennifer M Fettweis
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - J Paul Brooks
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Supply Chain Management and Analytics, School of Business, Virginia Commonwealth University, Richmond, VA, USA
| | - David J Edwards
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Statistical Sciences and Operations Research, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Philippe H Girerd
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Hardik I Parikh
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Huang
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Tom J Arodz
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Laahirie Edupuganti
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Jie Xu
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Division of Neonatal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Nicole R Jimenez
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephany C Vivadelli
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephen S Fong
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Chemical and Life Science Engineering, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Nihar U Sheth
- Center for the Study of Biological Complexity, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Sophonie Jean
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Lee
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Yahya A Bokhari
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Ana M Lara
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Shreni D Mistry
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Robert A Duckworth
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Steven P Bradley
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - X Valentine Orenda
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah H Milton
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah K Rozycki
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrey V Matveyev
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Michelle L Wright
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA.,Department of Women's Health, Dell School of Medicine, University of Texas at Austin, Austin, TX, USA.,School of Nursing, University of Texas at Austin, Austin, TX, USA
| | - Snehalata V Huzurbazar
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, WV, USA
| | - Eugenie M Jackson
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, WV, USA
| | - Ekaterina Smirnova
- Department of Mathematical Sciences, University of Montana, Missoula, MT, USA.,Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | | | - Molly R Dickinson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jamie L Brooks
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jennifer I Drake
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Donald O Chaffin
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - Amber L Sexton
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - Michael G Gravett
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA.,Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Craig E Rubens
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - N Romesh Wijesooriya
- Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Karen D Hendricks-Muñoz
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Division of Neonatal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Kimberly K Jefferson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA. .,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA.
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254
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Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR, MacIntyre DA. Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes. Transl Res 2019; 207:30-43. [PMID: 30633889 PMCID: PMC6489901 DOI: 10.1016/j.trsl.2018.12.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 10/31/2022]
Abstract
Vaginal bacterial community composition influences pregnancy outcome. Preterm prelabor rupture of the fetal membranes (PPROM), which precedes 30% of all spontaneous preterm births, is associated with high vaginal bacterial diversity prior to rupture. The point at which vaginal bacterial diversity is established before PPROM is unknown. In this study, we use metataxonomics to longitudinally characterize the vaginal bacterial composition from as early as 6 weeks of gestation in women at high (n = 38) and low (n = 22) risk of preterm birth who subsequently experience PPROM and in women delivering at term without complications (n = 36). Reduced Lactobacillus spp. abundance and high diversity was observed prior to PPROM in 20% and 26% of women at low and high risk of preterm births respectively, but in only 3% of women who delivered at term. PPROM was associated with instability of bacterial community structure during pregnancy and a shift toward higher diversity predominately occurring during the second trimester. This was characterized by increased relative abundance of potentially pathogenic species including Prevotella, Peptoniphilus, Streptococcus, and Dialister. This study identifies reduced Lactobacillus spp. abundance and increasing vaginal bacterial diversity as an early risk factor for PPROM and highlights the need for interventional studies designed to assess the impact of modifying vaginal bacterial composition for the prevention of preterm birth.
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Key Words
- bmi, body mass index
- dna, deoxyribonucleic acid
- ena, european nucleotide archive
- ga, gestational age
- hca, hierarchical cluster analysis
- lda, latent discriminatory analysis
- mr, membrane rupture
- nhs, national health service
- nice, national institute for health and care excellence
- pcr, polymerase chain reaction
- pprom, preterm prelabor rupture of the fetal membranes
- ptb, preterm birth
- rdp, ribosomal database project
- sra, sequence read archive
- stamp, statistical analysis of metagenomic profiles
- sop, standard operating procedure
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Affiliation(s)
- Richard G Brown
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Maya Al-Memar
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Julian R Marchesi
- March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK; Centre for Digestive and Gut Health, Imperial College London, London, UK; School of Biosciences, Cardiff University, Cardiff, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - Ann Smith
- School of Medicine, Cardiff University, Cardiff, UK
| | - Denise Chan
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Holly Lewis
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Lindsay Kindinger
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Vasso Terzidou
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK; Chelsea & Westminster Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Tom Bourne
- March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK.
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255
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256
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Greenbaum S, Greenbaum G, Moran-Gilad J, Weintraub AY. Ecological dynamics of the vaginal microbiome in relation to health and disease. Am J Obstet Gynecol 2019; 220:324-335. [PMID: 30447213 DOI: 10.1016/j.ajog.2018.11.1089] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
The bacterial composition of the vaginal microbiome is thought to be related to health and disease states of women. This microbiome is particularly dynamic, with compositional changes related to pregnancy, menstruation, and disease states such as bacterial vaginosis. In order to understand these dynamics and their impact on health and disease, ecological theories have been introduced to study the complex interactions between the many taxa in the vaginal bacterial ecosystem. The goal of this review is to introduce the ecological principles that are used in the study of the vaginal microbiome and its dynamics, and to review the application of ecology to vaginal microbial communities with respect to health and disease. Although applications of vaginal microbiome analysis and modulation have not yet been introduced into the routine clinical setting, a deeper understanding of its dynamics has the potential to facilitate development of future practices, for example in the context of postmenopausal vaginal symptoms, stratifying risk for obstetric complications, and controlling sexually transmitted infections.
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Affiliation(s)
- Shirley Greenbaum
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA; Department of Obstetrics and Gynecology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Gili Greenbaum
- Department of Biology, Stanford University, Stanford, CA
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Adi Y Weintraub
- Department of Obstetrics and Gynecology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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257
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Identification of Factors Affecting Bacterial Abundance and Community Structures in a Full-Scale Chlorinated Drinking Water Distribution System. WATER 2019. [DOI: 10.3390/w11030627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Disentangling factors influencing suspended bacterial community structure across distribution system and building plumbing provides insight into microbial control strategies from source to tap. Water quality parameters (residence time, chlorine, and total cells) and bacterial community structure were investigated across a full-scale chlorinated drinking water distribution system. Sampling was conducted in treated water, in different areas of the distribution system and in hospital building plumbing. Bacterial community was evaluated using 16S rRNA gene sequencing. Bacterial community structure clearly differed between treated, distributed, and premise plumbing water samples. While Proteobacteria (60%), Planctomycetes (20%), and Bacteroidetes (10%) were the most abundant phyla in treated water, Proteobacteria largely dominated distribution system sites (98%) and taps (91%). Distributed and tap water differed in their Proteobacteria profile: Alphaproteobacteria was dominant in distributed water (92% vs. 65% in tap waters), whereas Betaproteobacteria was most abundant in tap water (18% vs. 2% in the distribution system). Finally, clustering of bacterial community profiles was largely explained by differences in chlorine residual concentration, total bacterial count, and water residence time. Residual disinfectant and hydraulic residence time were determinant factors of the community structure in main pipes and building plumbing, rather than treated water bacterial communities.
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258
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Brown RG, Chan D, Terzidou V, Lee YS, Smith A, Marchesi JR, MacIntyre DA, Bennett PR. Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage. BJOG 2019; 126:916-925. [PMID: 30854760 PMCID: PMC6750128 DOI: 10.1111/1471-0528.15600] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/01/2022]
Abstract
OBJECTIVE To investigate the relation between vaginal microbiota composition and outcome of rescue cervical cerclage. DESIGN Prospective observational study. SETTING Queen Charlotte's and Chelsea Hospital, London. POPULATION Twenty singleton pregnancies undergoing a rescue cervical cerclage. METHODS Vaginal microbiota composition was analysed in women presenting with a dilated cervix and exposed fetal membranes before and 10 days following rescue cervical cerclage and was correlated with clinical outcomes. MAIN OUTCOME MEASURES Composition of vaginal bacteria was characterised by culture-independent next generation sequencing. Successful cerclage was defined as that resulting in the birth of a neonate discharged from hospital without morbidity. Unsuccessful cerclage was defined as procedures culminating in miscarriage, intrauterine death, neonatal death or significant neonatal morbidity. RESULTS Reduced Lactobacillus spp. relative abundance was observed in 40% of cases prior to rescue cerclage compared with 10% of gestation age-matched controls (8/20, 40% versus 3/30, 10%, P = 0.017). Gardnerella vaginalis was over-represented in women presenting with symptoms (3/7, 43% versus 0/13, 0%, P = 0.03, linear discriminant analysis, LDA (log 10) and cases culminating in miscarriage (3/6, 50% versus 0/14, 0%, P = 0.017). In the majority of cases (10/14, 71%) bacterial composition was unchanged following cerclage insertion and perioperative interventions. CONCLUSIONS Reduced relative abundance of Lactobacillus spp. is associated with premature cervical dilation, whereas high levels of G. vaginalis are associated with unsuccessful rescue cerclage cases. The insertion of a rescue cerclage does not affect the underlying bacterial composition in the majority of cases. TWEETABLE ABSTRACT Preterm cervical dilatation associates with reduced Lactobacillus spp. Presence of Gardnerella vaginalis predicts rescue cerclage failure.
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Affiliation(s)
- R G Brown
- Queen Charlotte's & Chelsea Hospital, Imperial College Healthcare National Health Service Trust, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - D Chan
- Queen Charlotte's & Chelsea Hospital, Imperial College Healthcare National Health Service Trust, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - V Terzidou
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Chelsea & Westminster Hospital, Chelsea & Westminster National Health Service Foundation Trust, London, UK
| | - Y S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - A Smith
- School of Biosciences, Cardiff University, Cardiff, UK
| | - J R Marchesi
- School of Biosciences, Cardiff University, Cardiff, UK.,Centre for Digestive and Gut Health, Imperial College London, London, UK
| | - D A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - P R Bennett
- Queen Charlotte's & Chelsea Hospital, Imperial College Healthcare National Health Service Trust, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
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259
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Kroon SJ, Ravel J, Huston WM. Cervicovaginal microbiota, women's health, and reproductive outcomes. Fertil Steril 2019; 110:327-336. [PMID: 30098679 DOI: 10.1016/j.fertnstert.2018.06.036] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 02/08/2023]
Abstract
The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.
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Affiliation(s)
- Samuel J Kroon
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia.
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260
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Bayigga L, Kateete DP, Anderson DJ, Sekikubo M, Nakanjako D. Diversity of vaginal microbiota in sub-Saharan Africa and its effects on HIV transmission and prevention. Am J Obstet Gynecol 2019; 220:155-166. [PMID: 30321529 PMCID: PMC10715630 DOI: 10.1016/j.ajog.2018.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/27/2018] [Accepted: 10/07/2018] [Indexed: 01/23/2023]
Abstract
The vaginal microbial community ("microbiota") is a key component of the reproductive health of women, providing protection against urogenital infections. In sub-Saharan Africa, there is a high prevalence of bacterial vaginosis, a condition defined by bacterial overgrowth and a shift away from a Lactobacillus-dominated profile toward increased percentages of strict anaerobic species. Bacterial vaginosis is associated with an increased risk of HIV acquisition and transmission, as well as an increased risk of acquiring other sexually transmitted infections, preterm births, and pelvic inflammatory disease. Vaginal microbiota, rich in taxa of strict anaerobic species, disrupts the mucosal epithelial barrier through secretion of metabolites and enzymes that mediate inflammation. Advancements in next-generation sequencing technologies such as whole-genome sequencing have led to deeper profiling of the vaginal microbiome and further study of its potential role in HIV pathogenesis and treatment. Until recently data on the composition of the vaginal microbiome in sub-Saharan Africa have been limited; however, a number of studies have been published that highlight the critical role of vaginal microbiota in disease and health in African women. This article reviews these recent findings and identifies gaps in knowledge about variations in female genital commensal bacteria that could provide vital information to improve the effectiveness of interventions to prevent HIV and other sexually transmitted infections. In addition, we review the effects of pregnancy, contraception, and sexual practices on vaginal microbiome and the potential of vaginal microbiota on HIV transmission and prevention. A better understanding of the role of vaginal microbiota in host susceptibility to HIV infection and its prevention among African women could inform the development of novel local and systemic interventions to minimize new HIV infections among high-risk women.
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Affiliation(s)
- Lois Bayigga
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Deborah J Anderson
- Departments of Obstetrics and Gynecology, Microbiology, and Medicine, Boston University School of Medicine, Boston, MA
| | - Musa Sekikubo
- Department of Obstetrics and Gynecology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Internal Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda; Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda.
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261
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Codagnone MG, Spichak S, O'Mahony SM, O'Leary OF, Clarke G, Stanton C, Dinan TG, Cryan JF. Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease. Biol Psychiatry 2019; 85:150-163. [PMID: 30064690 DOI: 10.1016/j.biopsych.2018.06.014] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/29/2018] [Accepted: 06/18/2018] [Indexed: 02/06/2023]
Abstract
It has been nearly 30 years since Dr. David Barker first highlighted the importance of prenatal factors in contributing to the developmental origins of adult disease. This concept was later broadened to include postnatal events. It is clear that the interaction between genetic predisposition and early life environmental exposures is key in this regard. However, recent research has also identified another important factor in the microbiota-the trillions of microorganisms that inhabit key body niches, including the vagina and gastrointestinal tract. Because the composition of these maternal microbiome sites has been linked to maternal metabolism and is also vertically transmitted to offspring, changes in the maternal microbiota are poised to significantly affect the newborn. In fact, several lines of evidence show that the gut microbiota interacts with diet, drugs, and stress both prenatally and postnatally and that these exogenous factors could also affect the dynamic changes in the microbiota composition occurring during pregnancy. Animal models have shown great utility in illuminating how these disruptions result in behavioral and brain morphological phenotypes reminiscent of psychiatric disorders (anxiety, depression, schizophrenia, and autism spectrum disorders). Increasing evidence points to critical interactions among the microbiota, host genetics, and both the prenatal and postnatal environments to temporally program susceptibility to psychiatric disorders later in life. Sex-specific phenotypes may be programmed through the influence of the microbiota on the hypothalamic-pituitary-adrenal axis and neuroimmune system.
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Affiliation(s)
- Martin G Codagnone
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Siobhain M O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Olivia F O'Leary
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; Irish Centre for Fetal and Neonatal Translational Research and Cork University Maternity Hospital, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Irish Centre for Fetal and Neonatal Translational Research and Cork University Maternity Hospital, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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Brummaier T, Syed Ahamed Kabeer B, Lindow S, Konje JC, Pukrittayaamee S, Utzinger J, Toufiq M, Antoniou A, Marr AK, Suriyakan S, Kino T, Al Khodor S, Terranegra A, Nosten F, Paris DH, McGready R, Chaussabel D. A prospective cohort for the investigation of alteration in temporal transcriptional and microbiome trajectories preceding preterm birth: a study protocol. BMJ Open 2019; 9:e023417. [PMID: 30782707 PMCID: PMC6340419 DOI: 10.1136/bmjopen-2018-023417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Preterm birth (PTB) results from heterogeneous influences and is a major contributor to neonatal mortality and morbidity that continues to have adverse effects on infants beyond the neonatal period. This protocol describes the procedures to determine molecular signatures predictive of PTB through high-frequency sampling during pregnancy, at delivery and the postpartum period. METHODS AND ANALYSIS Four hundred first trimester pregnant women from either Myanmar or Thailand of either Karen or Burman ethnicity, with a viable, singleton pregnancy will be enrolled in this non-interventional, prospective pregnancy birth cohort study and will be followed through to the postpartum period. Fortnightly finger prick capillary blood sampling will allow the monitoring of genome-wide transcript abundance in whole blood. Collection of stool samples and vaginal swabs each trimester, at delivery and postpartum will allow monitoring of intestinal and vaginal microbial composition. In a nested case-control analysis, perturbations of transcript abundance in capillary blood as well as longitudinal changes of the gut, vaginal and oral microbiome will be compared between mothers giving birth to preterm and matched cases giving birth to term neonates. Placenta tissue of preterm and term neonates will be used to determine bacterial colonisation as well as for the establishment of coding and non-coding RNA profiles. In addition, RNA profiles of circulating, non-coding RNA in cord blood serum will be compared with those of maternal peripheral blood serum at time of delivery. ETHICS AND DISSEMINATION This research protocol that aims to detect perturbations in molecular trajectories preceding adverse pregnancy outcomes was approved by the ethics committee of the Faculty of Tropical Medicine, Mahidol University in Bangkok, Thailand (Ethics Reference: TMEC 15-062), the Oxford Tropical Research Ethics Committee (Ethics Reference: OxTREC: 33-15) and the local Tak Province Community Ethics Advisory Board. The results of this cooperative project will be disseminated in multiple publications staggered over time in international peer-reviewed scientific journals. TRIAL REGISTRATION NUMBER NCT02797327; Pre-results.
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Affiliation(s)
- Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Juerg Utzinger
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | | | | | | | - Sangrawee Suriyakan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | | | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Daniel H Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
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Mahalingam S, Dharumadurai D, Archunan G. Vaginal microbiome analysis of buffalo (Bubalus bubalis) during estrous cycle using high-throughput amplicon sequence of 16S rRNA gene. Symbiosis 2019. [DOI: 10.1007/s13199-018-00595-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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264
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Inhibition Studies with 2-Bromoethanesulfonate Reveal a Novel Syntrophic Relationship in Anaerobic Oleate Degradation. Appl Environ Microbiol 2019; 85:AEM.01733-18. [PMID: 30366998 PMCID: PMC6328780 DOI: 10.1128/aem.01733-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/23/2018] [Indexed: 12/25/2022] Open
Abstract
In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria. Degradation of long-chain fatty acids (LCFAs) in methanogenic environments is a syntrophic process involving the activity of LCFA-degrading bacteria and hydrogen-utilizing methanogens. If methanogens are inhibited, other hydrogen scavengers are needed to achieve complete LCFA degradation. In this work, we developed two different oleate (C18:1 LCFA)-degrading anaerobic enrichment cultures, one methanogenic (ME) and another in which methanogenesis was inhibited (IE). Inhibition of methanogens was attained by adding a solution of 2-bromoethanesulfonate (BrES), which turned out to consist of a mixture of BrES and isethionate. Approximately 5 times faster oleate degradation was accomplished by the IE culture compared with the ME culture. A bacterium closely related to Syntrophomonas zehnderi (99% 16S rRNA gene identity) was the main oleate degrader in both enrichments, in syntrophic relationship with hydrogenotrophic methanogens from the genera Methanobacterium and Methanoculleus (in ME culture) or with a bacterium closely related to Desulfovibrio aminophilus (in IE culture). A Desulfovibrio species was isolated, and its ability to utilize hydrogen was confirmed. This bacterium converted isethionate to acetate and sulfide, with or without hydrogen as electron donor. This bacterium also utilized BrES but only after 3 months of incubation. Our study shows that syntrophic oleate degradation can be coupled to desulfonation. IMPORTANCE In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria.
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265
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Lyman CC, Holyoak GR, Meinkoth K, Wieneke X, Chillemi KA, DeSilva U. Canine endometrial and vaginal microbiomes reveal distinct and complex ecosystems. PLoS One 2019; 14:e0210157. [PMID: 30615657 PMCID: PMC6322750 DOI: 10.1371/journal.pone.0210157] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023] Open
Abstract
The objective of this study was to characterize the normal microbiome of healthy canine vagina and endometrium and to determine the effect of the stage of estrous, on the resident microbiome. Cranial vaginal swabs and uterine biopsy samples were collected from twenty-five bitches in five different stages of estrous at elective ovariohysterectomy (OVH). Over 4 million reads of the V4 region of 16S rDNA gene were obtained and used for further analyses. A total of 317 genera belonging to 24 known phyla were identified. The endometrium was higher in bacterial diversity while the vagina was higher in richness. Proteobacteria, Bacteroidetes and Firmicutes were the most abundant phyla observed across all samples. Hydrotalea, Ralstonia, and Fusobacterium accounted for nearly 60% of the OTUs identified in the vagina while organisms identified in the endometrium were more evenly distributed. Pseudomonas, Staphylococcus, and Corynebacterium were the prominent genera in the endometrium. The microbiome of the endometrium was distinctly different from that of the vagina. There was large animal-to-animal variation. Other than the vaginal microbiome of bitches in estrus (i.e. in heat), there were no distinct clustering of the organisms based on the stage of estrous. These findings establish the presence of a resident microbiome of the endometrium throughout all stages of estrous cycle.
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Affiliation(s)
- C. C. Lyman
- Department of Veterinary Clinical Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail:
| | - G. R. Holyoak
- Department of Veterinary Clinical Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - K. Meinkoth
- Department of Veterinary Clinical Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - X. Wieneke
- Department of Animal Science, Oklahoma State University, Stillwater, Oklahoma, United States Of America
| | - K. A. Chillemi
- Department of Veterinary Clinical Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - U. DeSilva
- Department of Animal Science, Oklahoma State University, Stillwater, Oklahoma, United States Of America
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266
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de Valk S, Feng C, Khadem AF, van Lier JB, de Kreuk MK. Elucidating the microbial community associated with the protein preference of sludge-degrading worms. ENVIRONMENTAL TECHNOLOGY 2019; 40:192-201. [PMID: 28967292 DOI: 10.1080/09593330.2017.1384071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
Sludge predation by aquatic worms results in an increased sludge reduction rate, which is mainly due to the specific removal of a protein fraction from the sludge. As microorganisms play an essential role in sludge hydrolysis a better understanding of the microbial community involved in the worm predation process will provide more insight into the relations between the aquatic worms, their associated microbiome and the efficient sludge reduction. In this study, the microbial community associated with predation by the Tubifex tubifex was investigated. The microbial diversity in the samples of the worm faeces (WF), predated activated sludge and protein-rich substrates were compared. The results indicated that predation on sludge resulted in a microbial change from Actinobacteria (44%) in the sludge, to Proteobacteria (64%) and Bacteriodites (36%) in the WF. Interestingly, the faecal microbial community was more related to the community in (predated) protein-rich substrates than to the community in predated or endogenously respirated activated sludge samples. This similar microbial community could be due to microbial utilisation of protein hydrolysis products. Alternatively, conditions in the worm gut could facilitate a protein hydrolysing community which assists in protein hydrolysis. The genera Burkholderiales, Chryseobacterium and Flavobacterium were found to be associated with predation by T. tubifex.
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Affiliation(s)
- Steef de Valk
- a Faculty of Civil Engineering and Geosciences, Department of Water Management, Section Sanitary Engineering , Delft University of Technology , Delft , The Netherlands
| | - Cuijie Feng
- a Faculty of Civil Engineering and Geosciences, Department of Water Management, Section Sanitary Engineering , Delft University of Technology , Delft , The Netherlands
| | - Ahmad F Khadem
- a Faculty of Civil Engineering and Geosciences, Department of Water Management, Section Sanitary Engineering , Delft University of Technology , Delft , The Netherlands
| | - Jules B van Lier
- a Faculty of Civil Engineering and Geosciences, Department of Water Management, Section Sanitary Engineering , Delft University of Technology , Delft , The Netherlands
| | - Merle K de Kreuk
- a Faculty of Civil Engineering and Geosciences, Department of Water Management, Section Sanitary Engineering , Delft University of Technology , Delft , The Netherlands
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267
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Shaping Microbiota During the First 1000 Days of Life. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1125:3-24. [PMID: 30680645 DOI: 10.1007/5584_2018_312] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The data obtained in prior studies suggest that early microbial exposition begins prior to conception and gestation. Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning early microbiota exposure within the male and the female reproductive tracts at the point of conception and during gestation, focusing on the potential impact on infant development during the first 1000 days of life. Furthermore, we conclude that some dietary strategies including specific probiotics could become potentially valuable tools to modulate the gut microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.
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268
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Libertucci J, Young VB. The role of the microbiota in infectious diseases. Nat Microbiol 2018; 4:35-45. [PMID: 30546094 DOI: 10.1038/s41564-018-0278-4] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
Abstract
The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.
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Affiliation(s)
- Josie Libertucci
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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269
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The prevalence rate of periodontal pathogens and its association with oral squamous cell carcinoma. Appl Microbiol Biotechnol 2018; 103:1393-1404. [PMID: 30470868 DOI: 10.1007/s00253-018-9475-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022]
Abstract
Mounting evidence suggests a causal relationship between specific bacterial infections or microbial compositions and the development of certain malignant neoplasms. In this study, we performed research through 16S rRNA amplicon sequencing, qPCR and fluorescence in situ hybridization to certify the relationship between periodontal pathogens and oral squamous cell carcinoma (OSCC). Subgingival plaque, cancer and paracancerous tissues from 6 patients with OSCC were selected for mapping bacterial profiles by 16S rRNA amplicon sequencing. The research showed that periodontal pathogens were enriched in cancer and paracancerous tissues, while the bacterial profiles were similar between the cancer tissues and subgingival plaque. Furthermore, the relative abundance of Porphyromonas gingivalis, Fusobacterium nucleatum and Streptococcus sanguinis was detected in 61 cancer tissues, paracancerous tissues and subgingival plaque samples and in 30 normal tissues by qPCR. The results revealed that P. gingivalis and F. nucleatum existed at higher levels in cancer tissue than in normal tissues and were correlated with subgingival plaques. P. gingivalis was detected using a special oligonucleotide probe in 60.7% of OSCC tissues, 32.8% of paracancerous tissues and 13.3% of normal tissues. Relevance analysis showed that P. gingivalis infection was positively associated with late clinical staging, low differentiation and lymph node metastasis in patients with OSCC, which was accompanied by deeper periodontal pockets, severe clinical attachment loss and loss of teeth. This study revealed that there might be a close relationship between oral microorganisms, particularly periodontal pathogens, and OSCC, which might enrich the pathogenesis of oral squamous carcinoma.
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270
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Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG. Differences in the fecal microbiota of neonates born at home or in the hospital. Sci Rep 2018; 8:15660. [PMID: 30353125 PMCID: PMC6199260 DOI: 10.1038/s41598-018-33995-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/06/2018] [Indexed: 12/13/2022] Open
Abstract
Research on the neonatal microbiome has been performed mostly on hospital-born infants, who often undergo multiple birth-related interventions. Both the hospital environment and interventions around the time of birth may affect the neonate microbiome. In this study, we determine the structure of the microbiota in feces from babies born in the hospital or at home, and from vaginal samples of their mothers. We included 35 vaginally-born, breast-fed neonates, 14 of whom delivered at home (4 in water), and 21 who delivered in the hospital. Feces from babies and mothers and maternal vaginal swab samples were collected at enrollment, the day of birth, followed by days 1, 2, 7, 14, 21, and 28. At the time of birth, the diversity of the vaginal microbiota of mothers delivering in the hospital was lower than in mothers delivering at home, and showed higher proportion of Lactobacillus. Among 20 infants not exposed to perinatal maternal antibiotics or water birth, fecal beta diversity differed significantly by birth site, with hospital-born infants having lower Bacteroides, Bifidobacterium, Streptococcus, and Lactobacillus, and higher Clostridium and Enterobacteriaceae family (LDA > 3.0), than babies born at home. At 1 month of age, feces from infants born in the hospital also induced greater pro-inflammatory gene expression (TLR4, IL-8, occludin and TGFβ) in human colon epithelial HT-29 cells. The results of this work suggest that hospitalization (perinatal interventions or the hospital environment) may affect the microbiota of the vaginal source and the initial colonization during labor and birth, with effects that could persist in the intestinal microbiota of infants 1 month after birth. More research is needed to determine specific factors that alter bacterial transmission between mother and baby and the long-term health implications of these differences for the developing infant.
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Affiliation(s)
- Joan L Combellick
- New York University Rory Meyers College of Nursing, New York, 10010, USA
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, 05006, South Korea
| | - Dongjae Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, 05006, South Korea
| | - Yi Cai
- New York University School of Medicine, New York, 10016, USA
| | - Holly Hagan
- New York University Rory Meyers College of Nursing, New York, 10010, USA
| | - Corey Lacher
- Department of Biochemistry and Microbiology and Department of Anthropology, Rutgers University, New Brunswick, 08901, USA
| | - Din L Lin
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, San Francisco, 94118, USA
| | - Kathryn McCauley
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, San Francisco, 94118, USA
| | - Susan V Lynch
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, San Francisco, 94118, USA
| | - Maria Gloria Dominguez-Bello
- New York University School of Medicine, New York, 10016, USA. .,Department of Biochemistry and Microbiology and Department of Anthropology, Rutgers University, New Brunswick, 08901, USA.
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271
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Anton L, Sierra LJ, DeVine A, Barila G, Heiser L, Brown AG, Elovitz MA. Common Cervicovaginal Microbial Supernatants Alter Cervical Epithelial Function: Mechanisms by Which Lactobacillus crispatus Contributes to Cervical Health. Front Microbiol 2018; 9:2181. [PMID: 30349508 PMCID: PMC6186799 DOI: 10.3389/fmicb.2018.02181] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cervicovaginal (CV) microbiota is associated with vaginal health and disease in non-pregnant women. Recent studies in pregnant women suggest that specific CV microbes are associated with preterm birth (PTB). While the associations between CV microbiota and adverse outcomes have been demonstrated, the mechanisms regulating the associations remain unclear. As the CV space contains an epithelial barrier, we postulate that CV microbiota can alter the epithelial barrier function. We investigated the biological, molecular, and epigenetic effects of Lactobacillus crispatus, Lactobacillus iners, and Gardnerella vaginalis on the cervical epithelial barrier function and determined whether L. crispatus mitigates the effects of lipopolysaccharide (LPS) and G. vaginalis on the cervical epithelial barrier as a possible mechanism by which CV microbiota mitigates disease risk. Ectocervical and endocervical cells treated with L. crispatus, L. iners, and G. vaginalis bacteria-free supernatants alone or combined were used to measure cell permeability, adherens junction proteins, inflammatory mediators, and miRNAs. Ectocervical and endocervical permeability increased after L. iners and G. vaginalis exposure. Soluble epithelial cadherin increased after exposure to L. iners but not G. vaginalis or L. crispatus. A Luminex cytokine/chemokine panel revealed increased proinflammatory mediators in all three bacteria-free supernatants with L. iners and G. vaginalis having more diverse inflammatory effects. L. iners and G. vaginalis altered the expression of cervical-, microbial-, and inflammatory-associated miRNAs. L. crispatus mitigated the LPS or G. vaginalis-induced disruption of the cervical epithelial barrier and reversed the G. vaginalis-mediated increase in miRNA expression. G. vaginalis colonization of the CV space of a pregnant C57/B6 mouse resulted in 100% PTB. These findings demonstrate that L. iners and G. vaginalis alter the cervical epithelial barrier by regulating adherens junction proteins, cervical immune responses, and miRNA expressions. These results provide evidence that L. crispatus confers protection to the cervical epithelial barrier by mitigating LPS- or G. vaginalis-induced miRNAs associated with cervical remodeling, inflammation, and PTB. This study provides further evidence that the CV microbiota plays a role in cervical function by altering the cervical epithelial barrier and initiating PTB. Thus, targeting the CV microbiota and/or its effects on the cervical epithelium may be a potential therapeutic strategy to prevent PTB.
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Affiliation(s)
- Lauren Anton
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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Matsumoto A, Yamagishi Y, Miyamoto K, Oka K, Takahashi M, Mikamo H. Characterization of the vaginal microbiota of Japanese women. Anaerobe 2018; 54:172-177. [PMID: 30291903 DOI: 10.1016/j.anaerobe.2018.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022]
Abstract
The composition of vaginal microbiota changes throughout life in response to health status, sexual activity, and pregnancy. Here the constitution of the vaginal microbiota among non-pregnant women, pregnant woman, and commercial sex workers (CSWs) in Japan were compared. Vaginal samples were obtained from 54 women between January 2014 and February 2015 and the microbiota of each was analyzed by 16S metagenomics as well as cluster and diversity analyses to identify differences. In addition, vaginal Lactobacillus spp. were isolated for comparison. Furthermore, data regarding the use of ritodrine hydrochloride by pregnant women was collected from medical charts. The vaginal microbiota were clustered into three groups. Group 1 was most often dominated by Lactobacillus spp., whereas groups 2 and 3 included not only Lactobacillus spp. but also Bifidobacterium, Atopobium, Prevotella, and Gardnerella spp., in addition to a few other taxa. In non-pregnant women, the proportions of microbes in groups 1, 2, and 3 were 31.8%, 36.4%, and 31.8%, respectively. In pregnant women, the abundance of group 1 microbes was notably greater than that of groups 2 and 3 (66.7% vs. 12.5% and 20.8%, respectively). In CSWs, the prevalence of group 3 microbes was far greater than that of group 1 (87.5% vs. 12.5%, respectively). The alpha diversity of non-pregnant women was significantly greater than that of pregnant women. The detection rate of live Lactobacillus spp. in CSWs was lower than in pregnant and non-pregnant women (25% vs. 50% and 68.2%, respectively). The vaginal microbiota of most pregnant women (60%) who received ritodrine hydrochloride was not dominated by Lactobacillus spp. These results suggest that there were clear differences in the colonization rate of Lactobacillus spp. among non-pregnant, pregnant, and CSW women groups. In addition, the dominance of Lactobacillus may influence the risk of preterm birth among women who received ritodrine hydrochloride during pregnancy.
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Affiliation(s)
- Asami Matsumoto
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan; Tokyo R&D Center, Miyarisan Pharmaceutical Co., Ltd, 2-22-9, Torocho, Kita-ku Saitama-shi, Saitama, 331-0804, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan; Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute-shi, Aichi, 480-1195, Japan
| | - Kentaro Miyamoto
- Tokyo R&D Center, Miyarisan Pharmaceutical Co., Ltd, 2-22-9, Torocho, Kita-ku Saitama-shi, Saitama, 331-0804, Japan
| | - Kentaro Oka
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute-shi, Aichi, 480-1195, Japan; Tokyo R&D Center, Miyarisan Pharmaceutical Co., Ltd, 2-22-9, Torocho, Kita-ku Saitama-shi, Saitama, 331-0804, Japan
| | - Motomichi Takahashi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute-shi, Aichi, 480-1195, Japan; Tokyo R&D Center, Miyarisan Pharmaceutical Co., Ltd, 2-22-9, Torocho, Kita-ku Saitama-shi, Saitama, 331-0804, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan; Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute-shi, Aichi, 480-1195, Japan.
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273
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Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A, Thomas BC, Shaw GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Res 2018; 28:1467-1480. [PMID: 30232199 PMCID: PMC6169887 DOI: 10.1101/gr.236000.118] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/28/2018] [Indexed: 12/22/2022]
Abstract
Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
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Affiliation(s)
- Daniela S Aliaga Goltsman
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christine L Sun
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Diana M Proctor
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Daniel B DiGiulio
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Anna Robaczewska
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Gary M Shaw
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David K Stevenson
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.,Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - David A Relman
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
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274
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Liu F, Lv L, Jiang H, Yan R, Dong S, Chen L, Wang W, Chen YQ. Alterations in the Urinary Microbiota Are Associated With Cesarean Delivery. Front Microbiol 2018; 9:2193. [PMID: 30258432 PMCID: PMC6143726 DOI: 10.3389/fmicb.2018.02193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022] Open
Abstract
Similar to the gut, the bladder contains urinary microbiota, and its bacterial composition and structure are determined by the individual’s health status. Cesarean section is a traumatic event for women and it is correlated with postpartum complications. To better understand the urinary microbiota alterations caused by cesarean section, 16S rDNA sequencing was used to assess urine specimens collected by transurethral catheterization from 30 healthy women undergoing cesarean section pre-delivery (PreD) and post-delivery (PostD). A significant increase in bacterial diversity and more detectable bacteria at the phylum, family, and genus levels was observed in the PostD group compared to the PreD group, indicating that cesarean delivery (a process that includes surgery and delivery) altered the bacterial community. Specifically, the phylum Firmicutes and its affiliated family Lactobacillaceae and genus Lactobacillus dramatically decreased in the PostD group, suggesting that beneficial bacteria decreased after cesarean section, and clinicians should be aware that this might increase the risk of complications. Concurrently, the phylum Proteobacteria and its affiliated bacteria Pseudomonadaceae and Pseudomonas increased in the PostD group compared to the PreD group. This indicates that pathogen growth increases after cesarean section, making it important for clinicians to combat these changes to protect women from infectious diseases. Interestingly, several metabolic pathways, such as metabolism of energy, cofactors and vitamins were strengthened in the PostD group, whereas membrane transport was lessened in this group. This suggests that women’s metabolic disorders might be cured by balancing urinary microbiota. In conclusion, the altered urinary microbiota between the PreD and PostD periods appears to provide insight into how to prevent postpartum metabolic disorders.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Longxian Lv
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyong Jiang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ren Yan
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shurong Dong
- Key Laboratory of Advanced Micro/Nano Electronic Devices and Smart Systems of Zhejiang, College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, China
| | - Liping Chen
- Intensive Unit, Affiliated Yancheng Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wei Wang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yong Q Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
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275
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Dobrut A, Gosiewski T, Pabian W, Bodaszewska-Lubas M, Ochonska D, Bulanda M, Brzychczy-Wloch M. The dynamics of vaginal and rectal Lactobacillus spp. flora in subsequent trimesters of pregnancy in healthy Polish women, assessed using the Sanger sequencing method. BMC Pregnancy Childbirth 2018; 18:350. [PMID: 30157784 PMCID: PMC6114255 DOI: 10.1186/s12884-018-1987-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/17/2018] [Indexed: 12/22/2022] Open
Abstract
Background Lactobacilli play an important role in maintaining vaginal health and protection against bacterial infections in the genital tract. The aim of this study is to show the dynamics of changes of the vaginal and rectal Lactobacillus flora during pregnancy by using the Sanger sequencing method. Method The study included 31 healthy pregnant women without clinical signs of genitourinary infections. The material was taken in the three trimesters of pregnancy by vaginal and rectal swabs and grown on the MRS agar quantitatively to estimate the number of Lactobacillus spp. [CFU/ml]. Afterwards, 3 to 8 morphologically different lactobacilli colonies were taken for identification. Bacterial species identification was performed by 16 s rDNA sequence fragment analyses using the Sanger method. Results Among the patients tested, the most common species colonizing the vagina in the first trimester were: L. crispatus 29%, L. gasseri 19.4% and L. rhamnosus 16.1%, in the second trimester: L. crispatus 51.6%, L. gasseri 25.8%, L. rhamnosus 19.4% and L. amylovorus 16.1%, and in the third trimester the most common Lactobacillus species were: L. crispatus 25.8%, L. gasseri 25.8% and L. johnsonii 19.4%. In rectal species, the number decreased in the second and third trimesters in comparison to the first trimester (p = 0.003). An analysis of rectal dynamics showed that in the first trimester, the most common species were: L. johnsonii 19.4%, and L. plantarum 9.7%, in the second trimester: L. crispatus 9.7% and L. mucosae 6.5%, and in the third trimester: L. casei 9.7% and L. rhamnosus 9.7%. Individual dynamics of the Lactobacillus species composition showed variability, characterized by continuous, intermittent, or periodic colonization. The patients examined were mostly colonized by three Lactobacillus species in vagina (32.3%), whereas for the rectum, one Lactobacillus species during the whole pregnancy duration was common (32.3%). Conclusion This study showed that in the examined group of healthy, pregnant Polish women, the vaginal Lactobacillus flora, both qualitative and quantitative, was stable during the three subsequent trimesters. In contrast, the number of rectal Lactobacillus species dramatically decreased after the first trimester.
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Affiliation(s)
- Anna Dobrut
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Tomasz Gosiewski
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Wojciech Pabian
- Clinical Department of Gynecological Endocrinology and Gynecology, Jagiellonian University Medical College, Kopernika 23, 31-501, Krakow, Poland
| | - Malgorzata Bodaszewska-Lubas
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Dorota Ochonska
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Małgorzata Bulanda
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Monika Brzychczy-Wloch
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland.
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276
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Taki K, Watanabe T, Matsuo J, Sakai K, Okubo T, Matsushita M, Abe K, Minami K, Yamaguchi H. Impact of bacterial traces belonging to the Enterobacteriaceae on the prevalence of Chlamydia trachomatis in women visiting a community hospital in Japan. J Infect Chemother 2018; 24:815-821. [PMID: 30082190 DOI: 10.1016/j.jiac.2018.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
We explored the bacteria present in the vaginal microbiota facilitating the prevalence of Chlamydia trachomatis in women visiting a community hospital in Sapporo, Japan, by amplicon sequencing. A total of 273 cervical swab samples were collected, and bacterial vaginosis was evaluated in all specimens by assessment of the Nugent score. In 16 of the samples, bacterial 16S rDNA could not be detected and they were therefore omitted from subsequent experiments (n = 257). A significant negative correlation was observed between the Nugent scores and the amount of Lactobacillus 16S rDNA. Among the 257 samples, chlamydial plasmid was detected in 20 samples and was used for amplicon sequencing. No significant association between the Nugent score and the prevalence of C. trachomatis was detected. Based on the results of chlamydial plasmid detection and the Nugent score, chlamydia-negative samples (n = 27) were randomly selected. Finally, the number of operational taxonomic units (OTUs) obtained from amplicon sequencing was compared between chlamydia-positive (n = 20) and -negative samples (n = 27), revealing that a significant difference was only detected for the OTU numbers of Enterobacteriaceae between the C. trachomatis-positive and -negative groups. However, almost all of the samples utilized for amplicon sequencing failed to grow on MacConkey agar plates and produce indole. Taken together, we concluded that traces of bacteria, not live bacteria, belonging to the Enterobacteriaceae indicated the flow of bacteria through the anogenital route along with gut indole, and the resulting impact on the prevalence of C. trachomatis in the cervicogenital tract of women in Japan.
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Affiliation(s)
- Keisuke Taki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Takanori Watanabe
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Kouhei Sakai
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Mizue Matsushita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Kiyotaka Abe
- Toho Obstetrics and Gynecology Hospital, Higashi-15, Kita-17 Jo, Higashi-ku, Sapporo, 065-0017, Japan.
| | - Kunihiro Minami
- Toho Obstetrics and Gynecology Hospital, Higashi-15, Kita-17 Jo, Higashi-ku, Sapporo, 065-0017, Japan.
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
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277
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Zhang X, Liao Q, Wang F, Li D. Association of gestational diabetes mellitus and abnormal vaginal flora with adverse pregnancy outcomes. Medicine (Baltimore) 2018; 97:e11891. [PMID: 30142788 PMCID: PMC6112872 DOI: 10.1097/md.0000000000011891] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/07/2018] [Indexed: 12/26/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is associated with adverse perinatal outcomes. This study aimed to examine the association between GDM and abnormal vaginal flora, and the association between abnormal vaginal flora and adverse pregnancy outcomes.This was a prospective study of pregnant women who visited Xuanwu Hospital of the Capital Medical University (Beijing, China) between February and October 2015. All women were screened for GDM according to the International Association of the Diabetes and Pregnancy Study Groups (IADPSG) recommendations. Vaginal secretions were sampled at 28 to 30 and 37 to 40 weeks. Microorganisms were examined.The women were 28.3 ± 2.6 years and their body mass index was 22.8 ± 1.4 kg/m. GDM was associated with higher frequencies of vulvovaginal candidiasis (22.6% vs 9.7%, P < .001), premature rupture of membranes (PROM) (22.6% vs 11.5%, P = .004), premature delivery (16.1% vs 5.5%, P = .02), chorioamnionitis/puerperal infection (19.4% vs 4.5%, P < .001), macrosomia (9.7% vs 4.0%, P = .04), neonatal hypoglycemia (5.4% vs 1.0%, P = .02), and neonatal referral (15.1% vs 6.5%, P = .008). Among healthy women, abnormal flora was associated with PROM (19.4% vs 7.5%, P = .02) and chorioamnionitis/puerperal infection (11.9% vs 0.8%, P < .001). Among women with GDM, abnormal flora was associated with PROM (32.1% vs 10.0%, P < .001), premature delivery (17.7% vs 6.3%, P = .04), and chorioamnionitis/puerperal infection (32.8% vs 2.5%, P < .001).The vaginal infection rate was higher in patients with GDM compared with healthy pregnant women. GDM and abnormal vaginal flora were both associated with adverse pregnancy outcomes. The vaginal Lactobacillus species were different between the 2 groups, which could contribute to the adverse outcomes.
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Affiliation(s)
- Xinhong Zhang
- Department of Obstetrics and Gynecology, Xuanwu Hospital, Capital Medical University
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Xuanwu Hospital, Capital Medical University
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Fengying Wang
- Department of Obstetrics and Gynecology, Xuanwu Hospital, Capital Medical University
| | - Dan Li
- Department of Obstetrics and Gynecology, Xuanwu Hospital, Capital Medical University
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278
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Freitas AC, Bocking A, Hill JE, Money DM. Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth. MICROBIOME 2018; 6:117. [PMID: 29954448 PMCID: PMC6022438 DOI: 10.1186/s40168-018-0502-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/18/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND The bacterial community present in the female lower genital tract plays an important role in maternal and neonatal health. Imbalances in this microbiota have been associated with negative reproductive outcomes, such as spontaneous preterm birth (sPTB), but the mechanisms underlying the association between a disturbed microbiota and sPTB remain poorly understood. An intrauterine infection ascending from the vagina is thought to be an important contributor to the onset of preterm labour. Our objective was to characterize the vaginal microbiota of pregnant women who had sPTB (n = 46) and compare to those of pregnant women who delivered at term (n = 170). Vaginal swabs were collected from women at 11-16 weeks of gestational age. Microbiota profiles were created by PCR amplification and pyrosequencing of the cpn60 universal target region. RESULTS Profiles clustered into seven community state types: I (Lactobacillus crispatus dominated), II (Lactobacillus gasseri dominated), III (Lactobacillus iners dominated), IVA (Gardnerella vaginalis subgroup B or mix of species), IVC (G. vaginalis subgroup A dominated), IVD (G. vaginalis subgroup C dominated) and V (Lactobacillus jensenii dominated). The microbiota of women who experienced preterm birth (< 37 weeks gestation) had higher richness and diversity and higher Mollicutes prevalence when compared to those of women who delivered at term. The two groups did not cluster according to CST, likely because CST assignment is driven in most cases by the dominance of one particular species, overwhelming the contributions of more rare taxa. In conclusion, we did not identify a specific microbial community structure that predicts sPTB, but differences in microbiota richness, diversity and Mollicutes prevalence were observed between groups. CONCLUSIONS Although a causal relationship remains to be determined, our results confirm previous reports of an association between Mollicutes and sPTB and further suggest that a more diverse microbiome may be important in the pathogenesis of some cases.
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Affiliation(s)
- Aline C. Freitas
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Alan Bocking
- Departments of Obstetrics and Gynaecology and Physiology, University of Toronto, Toronto, ON M5G 1L4 Canada
- Lunenfeld-Tanenbaum Research Institute, M5T1X5, Toronto, ON Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Deborah M. Money
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Women’s Health Research Institute, BC Women’s Hospital & Health Centre, Vancouver, BC V6H 3N1 Canada
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279
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Tabatabaei N, Eren AM, Barreiro LB, Yotova V, Dumaine A, Allard C, Fraser WD. Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control study. BJOG 2018; 126:349-358. [PMID: 29791775 DOI: 10.1111/1471-0528.15299] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To explore differences in the vaginal microbiome between preterm and term deliveries. DESIGN Nested case-control study in 3D cohort (design, develop, discover). SETTING Quebec, Canada. SAMPLE Ninety-four women with spontaneous preterm birth as cases [17 early (<34 weeks) and 77 late (34-36 weeks) preterm birth] and 356 women as controls with term delivery (≥37 weeks). METHODS To assess the vaginal microbiome by sequencing the V4 region of the 16S ribosomal RNA (rRNA) gene in swabs self-collected during early pregnancy. MAIN OUTCOME MEASURES Comparison of relative abundance of bacterial operational taxonomic units and oligotypes and identifying vaginal community state types (CSTs) in early or late spontaneous preterm and term deliveries. RESULTS Lactobacillus gasseri/ Lactobacillus johnsonii (coefficient -5.36, 95% CI -8.07 to -2.65), Lactobacillus crispatus (99%)/ Lactobacillus acidophilus (99%) (-4.58, 95% CI -6.20 to -2.96), Lactobacillus iners (99%)/ Ralstonia solanacearum (99%) (-3.98, 95% CI -6.48 to -1.47) and Bifidobacterium longum/ Bifidobacterium breve (-8.84, 95% CI -12.96 to -4.73) were associated with decreased risk of early but not late preterm birth. Six vaginal CSTs were identified: four dominated by Lactobacillus; one with presence of bacterial vaginosis-associated bacteria (Gardnerella vaginalis, Atopobium vaginae and Veillonellaceae bacterium) (CST IV); and one with nondominance of Lactobacillus (CST VI). CST IV was associated with increased risk of early (4.22, 95% CI 1.24-24.85) but not late (1.63, 95% CI 0.68-5.04) preterm birth, compared with CST VI. CONCLUSIONS Lactobacillus gasseri/L. johnsonii, L. crispatus/L. acidophilus, L. iners/R. solanacearum and B. longum/B. breve may be associated with decreased risk of early preterm birth. A bacterial vaginosis-related vaginal CST versus a CST nondominated by Lactobacillus may be associated with increased risk of early preterm birth. TWEETABLE ABSTRACT Largest study of its kind finds certain species of vaginal Lactobacillus + Bifidobacterium may relate to lower risk of preterm birth.
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Affiliation(s)
- N Tabatabaei
- Research Centre of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.,Department of Obstetrics and Gynaecology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - A M Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - L B Barreiro
- Research Centre of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.,Department of Paediatrics, Research Center of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada
| | - V Yotova
- Research Centre of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.,Department of Paediatrics, Research Center of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada
| | - A Dumaine
- Research Centre of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.,Department of Paediatrics, Research Center of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada
| | - C Allard
- Research Centre of Sherbrooke University Hospital Centre (CRCHUS), Sherbrooke, QC, Canada
| | - W D Fraser
- Research Centre of CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.,Department of Obstetrics and Gynaecology, University of Sherbrooke, Sherbrooke, QC, Canada.,Research Centre of Sherbrooke University Hospital Centre (CRCHUS), Sherbrooke, QC, Canada
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280
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McMillan A, Rulisa S, Gloor GB, Macklaim JM, Sumarah M, Reid G. Pilot assessment of probiotics for pregnant women in Rwanda. PLoS One 2018; 13:e0195081. [PMID: 29912913 PMCID: PMC6005520 DOI: 10.1371/journal.pone.0195081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 02/07/2018] [Indexed: 12/14/2022] Open
Abstract
Background While the global market for probiotics is soon to reach in excess of US$50 billion, the continent of Africa has been largely ignored, despite these products having the ability to reduce the burden of disease and death. Trial design The present randomised, blinded, placebo-controlled clinical trial was undertaken in Rwanda, a country devoid of well-documented probiotics. The primary outcome aim was to examine receptivity and compliance for orally administered probiotic capsules containing Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 in pregnant women and assess any initial side effects or changes to the vaginal microbiome. Methods Pregnant women between the ages of 18 and 55 were recruited from the Nyamata District Hospital in Rwanda and randomly assigned to receive probiotic or placebo capsules for one month. Clinicians were blinded to the treatments. Results The drop-out rate was 21%, with 13 of 18 women in the placebo group and 17 of 20 in the probiotic group completing the study. Only 13 women returned for birthing and additional sample collection. No side effects of either treatment group were reported. Microbiota and metabolomics data showed similar findings to those reported in the literature, with low bacterial diversity and Lactobacillus dominance associated with a healthy vagina, and birthing associated with high diversity. Despite the small sample size and lack of changes in the microbiota, women in the placebo arm were significantly more likely to give birth pre-term. Conclusion Overall women were receptive to the probiotic concept, but the lack of information on such products and logistical and economical challenges pose problems for wider population engagement. Trial registration ClinicalTrials.gov NCT02150655
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Affiliation(s)
- Amy McMillan
- Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Stephen Rulisa
- Department of Obstetrics and Gynecology, University of Rwanda, Kigali, Rwanda
| | - Gregory B. Gloor
- Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Department of Biochemistry, and Applied Mathematics, The University of Western Ontario, London, Canada
| | - Jean M. Macklaim
- Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Department of Biochemistry, and Applied Mathematics, The University of Western Ontario, London, Canada
| | - Mark Sumarah
- Agriculture and Agri-Food Canada, London, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, Canada
- * E-mail:
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281
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Amabebe E, Anumba DOC. The Vaginal Microenvironment: The Physiologic Role of Lactobacilli. Front Med (Lausanne) 2018; 5:181. [PMID: 29951482 PMCID: PMC6008313 DOI: 10.3389/fmed.2018.00181] [Citation(s) in RCA: 350] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/29/2018] [Indexed: 11/21/2022] Open
Abstract
In addition to being a passage for sperm, menstruum, and the baby, the human vagina and its microbiota can influence conception, pregnancy, the mode and timing of delivery, and the risk of acquiring sexually transmitted infections. The physiological status of the vaginal milieu is important for the wellbeing of the host as well as for successful reproduction. High estrogen states, as seen during puberty and pregnancy, promote the preservation of a homeostatic (eubiotic) vaginal microenvironment by stimulating the maturation and proliferation of vaginal epithelial cells and the accumulation of glycogen. A glycogen-rich vaginal milieu is a haven for the proliferation of Lactobacilli facilitated by the production of lactic acid and decreased pH. Lactobacilli and their antimicrobial and anti-inflammatory products along with components of the epithelial mucosal barrier provide an effective first line defense against invading pathogens including bacterial vaginosis, aerobic vaginitis-associated bacteria, viruses, fungi and protozoa. An optimal host-microbial interaction is required for the maintenance of eubiosis and vaginal health. This review explores the composition, function and adaptive mechanisms of the vaginal microbiome in health and those disease states in which there is a breach in the host-microbial relationship. The potential impact of vaginal dysbiosis on reproduction is also outlined.
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Affiliation(s)
- Emmanuel Amabebe
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, United Kingdom
| | - Dilly O C Anumba
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, United Kingdom
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282
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Transcriptomic analysis of the heat stress response for a commercial baker's yeast Saccharomyces cerevisiae. Genes Genomics 2018; 40:137-150. [PMID: 29892925 DOI: 10.1007/s13258-017-0616-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/01/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker's yeast (Saccharomyces cerevisiae) by using microarray technology and comparative statistical data analyses. The data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis, all required statistical methods were performed comparatively. For the normalization step, among alternatives, the RMA (Robust Microarray Analysis) results were used. To determine differentially expressed genes under heat stress treatments, the fold-change and the hypothesis testing approaches were executed under various cut-off values via different multiple testing procedures then the up/down regulated probes were functionally categorized via the PAMSAM clustering. The results of the analysis concluded that the transcriptome changes under the heat shock. Moreover, the temperature-shift stress treatments show that the number of differentially up-regulated genes among the heat shock proteins and transcription factors changed significantly. Finally, the change in temperature is one of the important environmental conditions affecting propagation and industrial application of baker's yeast. This study statistically analyzes this affect via one-channel microarray data.
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283
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Taddei CR, Cortez RV, Mattar R, Torloni MR, Daher S. Microbiome in normal and pathological pregnancies: A literature overview. Am J Reprod Immunol 2018; 80:e12993. [DOI: 10.1111/aji.12993] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Carla R. Taddei
- Department of Clinical and Toxicological Analyses; School of Pharmaceutical Sciences; Universidade de São Paulo; São Paulo Brazil
| | - Ramon V. Cortez
- Department of Clinical and Toxicological Analyses; School of Pharmaceutical Sciences; Universidade de São Paulo; São Paulo Brazil
| | - Rosiane Mattar
- Department of Obstetrics; Universidade Federal de São Paulo; São Paulo Brazil
| | | | - Silvia Daher
- Department of Obstetrics; Universidade Federal de São Paulo; São Paulo Brazil
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284
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Stephens RW, Arhire L, Covasa M. Gut Microbiota: From Microorganisms to Metabolic Organ Influencing Obesity. Obesity (Silver Spring) 2018; 26:801-809. [PMID: 29687647 DOI: 10.1002/oby.22179] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/27/2017] [Accepted: 01/03/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This review summarizes the current understanding of the relationship between gut microbiota and the host as it pertains to the regulation of energy balance and obesity. METHODS The paper begins with a brief description of the gut microbiota environment, distribution, and its unique symbiotic relationship with the host. The way that enviromental factors influence microbiota composition and subsequent impact on the host are then described. Next, the mechanisms linking gut dysbiosis with obesity are discussed, and finally current challenges and limitations in understanding the role of gut microbiota in control of obesity are presented. RESULTS Gut microbiota has been implicated in regulation of fat storage, as well as gut dysbiosis, thus contributing to the development of obesity, insulin resistance, hyperglycemia and hyperlipidemia. However, the underlying mechanisms of these processes are far from being clear and will require complex preclinical and clinical interdisciplinary studies of bacteria and host cell-to-cell interactions. CONCLUSIONS There is a need for a better understanding of how changes in gut microbiota composition can impact energy balance and thus control weight gain. This may represent a promising avenue in the race to develop nonsurgical treatments for obesity.
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Affiliation(s)
- Richard W Stephens
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, California, USA
| | - Lidia Arhire
- Department of Internal Medicine, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
- Clinical Hospital Sf. Spiridon, Iasi, Romania
| | - Mihai Covasa
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Health and Human Development, University of Suceava, Romania
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285
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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286
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Chu DM, Seferovic M, Pace RM, Aagaard KM. The microbiome in preterm birth. Best Pract Res Clin Obstet Gynaecol 2018; 52:103-113. [PMID: 29753695 DOI: 10.1016/j.bpobgyn.2018.03.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]
Abstract
The microbiome is thought to play a role in the maintenance of a healthy pregnancy and thus may either contribute to or protect from preterm birth. Study of the human microbiome has been aided by metagenomic sequencing approaches, providing greater insight into the commensal bacteria that coexist in and on our bodies. The vaginal microbiome has been the most widely studied, though there have been recent efforts to explore the gut, cervical-vaginal, placental and oral microbiomes in the further search of etiologies of preterm birth. To date, a specific microbiome community or microorganism has yet to be reliably associated with preterm birth. This is partly due to the fact that the 'normal' constituents' microbiome can vary widely between healthy individuals. Before our knowledge of the microbiome can be utilized and applied in clinical practice, a greater understanding of the 'healthy' microbiome must be achieved. In particular, we must first appreciate how our microbes influence our biology to promote a healthy pregnancy or alternately render preterm birth.
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Affiliation(s)
- Derrick M Chu
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Maxim Seferovic
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Ryan M Pace
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Kjersti M Aagaard
- Maternal Fetal Medicine Division, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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287
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Salinas AM, Osorio VG, Endara PF, Salazar ER, Vasco GP, Vivero SG, Machado A. Bacterial identification of the vaginal microbiota in Ecuadorian pregnant teenagers: an exploratory analysis. PeerJ 2018; 6:e4317. [PMID: 29492333 PMCID: PMC5826987 DOI: 10.7717/peerj.4317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/12/2018] [Indexed: 12/02/2022] Open
Abstract
Background Bacterial vaginosis (BV) is a microbial imbalance (i.e., dysbiosis) that can produce serious medical effects in women at childbearing age. Little is known, however, about the incidence of BV or vaginal microbiota dysbiosis in pregnant teenagers in low and middle-income countries such as Ecuador. The scope of this exploratory analysis was to study the relationship between epidemiologic and microbial risk factors. Among the microbiology risk factors this study investigated five Lactobacillus species, two of them know in preview studies as microbiology risk factors for BV development (Lactobacillus acidophilus and Lactobacillus iners), and the last three known for being associated with a healthy vaginal tract (Lactobacillus crispatus, Lactobacillus gasseri and Lactobacillus jensenii). In addition, fastidious anaerobes known to be microbial risk factors for BV development in pregnant teenagers were searched as well, more exactly, Gardnerella vaginalis, Atopobium vaginae and Mobiluncus mulieris. Methods Ninety-five healthy adolescent pregnant women, visiting a secondary level hospital in Quito, Ecuador, were enrolled into the study in 2015. The enrolled patients were between 10 to 13 weeks of pregnancy. Four epidemiological risk factors were collected in a survey: age, civil status, sexual partners and condom use. Also, vaginal pH was measured as a health risk factor. DNA was extracted from endocervical and exocervical epithelia from all the patients’ samples. PCR analysis was performed in order to characterize the presence of the eight bacterial species known as risk factors for BV development, targeting three anaerobes and five Lactobacillus species. Univariate and multivariate analysis were performed to identify associated factors for the presence of anaerobic species using logistic regression. Results The 95 vaginal microflora samples of these teenagers were analyzed. Two of the bacterial species known to cause BV: A. vaginae (100%) and G. vaginalis (93.7%) were found in high prevalence. Moreover, the most predominant bacterial Lactobacillus species found in the pregnant teenagers’ vaginal tract were L. crispatus (92.6%), L. iners (89.5%) and L. acidophilus (87.4%). In addition, the average vaginal pH measured in the study population was 5.2, and high pH was associated with the presence of the three-anaerobic species (p = 0.001). Finally, L. jensenii’s presence in the study decreased in 72% the occupation of the three anaerobes. Discussion This work identified a high pH as a risk factor for BV anaerobes’ presence in adolescent pregnant women. Moreover, this study identified L. crispatus, L. iners and L. acidophilus to be the most abundant species in our study population. From all fastidious anaerobes analyzed in this study, A. vaginae was present in all pregnant teenagers. To conclude, L. jensenii could be a potential healthy vaginal microbiota candidate in pregnant teenagers and should be further analyzed in future studies.
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Affiliation(s)
- Ana María Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Gabriela Osorio
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Pablo Francisco Endara
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Gabriela Piedad Vasco
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | | | - Antonio Machado
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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288
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A Lactobacillus-Deficient Vaginal Microbiota Dominates Postpartum Women in Rural Malawi. Appl Environ Microbiol 2018; 84:AEM.02150-17. [PMID: 29305501 PMCID: PMC5835753 DOI: 10.1128/aem.02150-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/29/2017] [Indexed: 01/09/2023] Open
Abstract
The bacterial community found in the vagina is an important determinant of a woman's health and disease status. A healthy vaginal microbiota is associated with low species richness and a high proportion of one of a number of different Lactobacillus spp. When disrupted, the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations that may not capture the full complexity of the community or adequately predict what constitutes a healthy microbiota in all populations. In this study, we sampled and characterized the vaginal microbiota found on vaginal swabs taken postpartum from a cohort of 1,107 women in rural Malawi. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year postpartum. This Lactobacillus-deficient anaerobic community, commonly labeled community state type (CST) 4, could be subdivided into four further communities. A Lactobacillus iners-dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal postpartum vaginal microbiota is. Previous identification of community state types and associations among bacterial species, bacterial vaginosis, and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. (This study has been registered at ClinicalTrials.gov as NCT01239693.) IMPORTANCE A bacterial community in the vaginal tract is dominated by a small number of Lactobacillus species, and when not present there is an increased incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study, we characterized the postpartum vaginal bacterial community of a large group of women from a resource-poor, undersampled population in rural Malawi. The majority of women were found to have a Lactobacillus-deficient community, and even when sampled a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus-dominant community is unknown, and this could suggest that not all Lactobacillus-deficient community structures are adverse. A better understanding of this complex community state type is needed.
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289
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Hathaway NJ, Parobek CM, Juliano JJ, Bailey JA. SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res 2018; 46:e21. [PMID: 29202193 PMCID: PMC5829576 DOI: 10.1093/nar/gkx1201] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023] Open
Abstract
PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences differing by a single nucleotide polymorphism. In bacterial populations, single-base resolution can provide improved resolution towards species and strains. Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single base. It outperforms current software, particularly at low frequencies and at low input read depths, whether resolving single-base differences or traditional OTUs. SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic information.
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Affiliation(s)
- Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jonathan J Juliano
- Curriculum in Genetics and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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290
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Brown RG, Marchesi JR, Lee YS, Smith A, Lehne B, Kindinger LM, Terzidou V, Holmes E, Nicholson JK, Bennett PR, MacIntyre DA. Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin. BMC Med 2018; 16:9. [PMID: 29361936 PMCID: PMC5782380 DOI: 10.1186/s12916-017-0999-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Preterm prelabour rupture of the fetal membranes (PPROM) precedes 30% of preterm births and is a risk factor for early onset neonatal sepsis. As PPROM is strongly associated with ascending vaginal infection, prophylactic antibiotics are widely used. The evolution of vaginal microbiota compositions associated with PPROM and the impact of antibiotics on bacterial compositions are unknown. METHODS We prospectively assessed vaginal microbiota prior to and following PPROM using MiSeq-based sequencing of 16S rRNA gene amplicons and examined the impact of erythromycin prophylaxis on bacterial load and community structures. RESULTS In contrast to pregnancies delivering at term, vaginal dysbiosis characterised by Lactobacillus spp. depletion was present prior to the rupture of fetal membranes in approximately a third of cases (0% vs. 27%, P = 0.026) and persisted following membrane rupture (31%, P = 0.005). Vaginal dysbiosis was exacerbated by erythromycin treatment (47%, P = 0.00009) particularly in women initially colonised by Lactobacillus spp. Lactobacillus depletion and increased relative abundance of Sneathia spp. were associated with subsequent funisitis and early onset neonatal sepsis. CONCLUSIONS Our data show that vaginal microbiota composition is a risk factor for subsequent PPROM and is associated with adverse short-term maternal and neonatal outcomes. This highlights vaginal microbiota as a potentially modifiable antenatal risk factor for PPROM and suggests that routine use of erythromycin for PPROM be re-examined.
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Affiliation(s)
- Richard G Brown
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Julian R Marchesi
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,School of Biosciences, Cardiff University, Cardiff, CF103AX, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Ann Smith
- School of Biosciences, Cardiff University, Cardiff, CF103AX, UK
| | - Benjamin Lehne
- Department of Epidemiology & Biostatistics, Medicine, Imperial College London, London, W2 1PG, UK
| | - Lindsay M Kindinger
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Vasso Terzidou
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.,Chelsea & Westminster Hospital, Imperial College Healthcare NHS Trust, London, SW10 9NH, UK
| | - Elaine Holmes
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,Division of Computational Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Jeremy K Nicholson
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,Division of Computational Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.
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291
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The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, Rabaa MA, Hibberd M, Baker S. Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut Microbes 2018; 9:38-54. [PMID: 28767339 PMCID: PMC5914913 DOI: 10.1080/19490976.2017.1361093] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023] Open
Abstract
Diarrheal diseases remain the second most common cause of mortality in young children in developing countries. Efforts have been made to explore the impact of diarrhea on bacterial communities in the human gut, but a thorough understanding has been impeded by inadequate resolution in bacterial identification and the examination of only few etiological agents. Here, by profiling an extended region of the 16S rRNA gene in the fecal microbiome, we aimed to elucidate the nature of gut microbiome perturbations during the early phase of infectious diarrhea caused by various etiological agents in Vietnamese children. Fecal samples from 145 diarrheal cases with a confirmed infectious etiology before antimicrobial therapy and 54 control subjects were analyzed. We found that the diarrheal fecal microbiota could be robustly categorized into 4 microbial configurations that either generally resembled or were highly divergent from a healthy state. Factors such as age, nutritional status, breastfeeding, and the etiology of the infection were significantly associated with these microbial community structures. We observed a consistent elevation of Fusobacterium mortiferum, Escherichia, and oral microorganisms in all diarrheal fecal microbiome configurations, proposing similar mechanistic interactions, even in the absence of global dysbiosis. We additionally found that Bifidobacterium pseudocatenulatum was significantly depleted during dysenteric diarrhea regardless of the etiological agent, suggesting that further investigations into the use of this species as a dysentery-orientated probiotic therapy are warranted. Our findings contribute to the understanding of the complex influence of infectious diarrhea on gut microbiome and identify new opportunities for therapeutic interventions.
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Affiliation(s)
- Hao Chung The
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Song Jie
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Duy Pham Thanh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne N. Thompson
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chau Nguyen Ngoc Minh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Collins Wenhan Chu
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Tuan-Anh Tran
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas R. Thomson
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
- Infection Genomics, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Guy E. Thwaites
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Maia A. Rabaa
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Martin Hibberd
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Stephen Baker
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom
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292
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Cobbold JFL, Atkinson S, Marchesi JR, Smith A, Wai SN, Stove J, Shojaee-Moradie F, Jackson N, Umpleby AM, Fitzpatrick J, Thomas EL, Bell JD, Holmes E, Taylor-Robinson SD, Goldin RD, Yee MS, Anstee QM, Thursz MR. Rifaximin in non-alcoholic steatohepatitis: An open-label pilot study. Hepatol Res 2018; 48:69-77. [PMID: 28425154 DOI: 10.1111/hepr.12904] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/04/2017] [Accepted: 04/08/2017] [Indexed: 12/31/2022]
Abstract
AIM Gut microbial dysbiosis is implicated in the pathogenesis of non-alcoholic steatohepatitis (NASH). We investigated downstream effects of gut microbiota modulation on markers of hepatic inflammation, steatosis, and hepatic and peripheral insulin sensitivity in patients with NASH using rifaximin therapy. METHODS Patients with biopsy-proven NASH and elevated aminotransferase values were included in this open-label pilot study, all receiving 6 weeks rifaximin 400 mg twice daily, followed by a 6-week observation period. The primary endpoint was change in alanine aminotransferase (ALT) after 6 weeks of rifaximin. Secondary endpoints were change in hepatic lipid content and insulin sensitivity measured with a hyperinsulinemic-euglycemic clamp. RESULTS Fifteen patients (13 men and 2 women) with a median (range) age of 46 (32-63) years were included. Seven had diabetes on oral hypoglycemic medications and 8 had no diabetes. After 6 weeks of therapy, no differences were seen in ALT (55 [33-191] vs. 63 [41-218] IU/L, P = 0.41), peripheral glucose uptake (28.9 [19.4-48.3] to 25.5 [17.7-47.9] μmol/kg/min, P = 0.30), hepatic insulin sensitivity (35.2 [15.3-51.7]% vs. 30.0 [10.8-50.5]%, P = 0.47), or hepatic lipid content (21.6 [2.2-46.2]% vs. 24.8 [1.7-59.3]%, P = 0.59) before and after rifaximin treatment. After 12 weeks from baseline, serum ALT increased to 83 (30-217) IU/L, P = 0.02. There was a significant increase in the homeostasis model assessment-estimated insulin resistance index (P = 0.05). The urinary metabolic profile indicated a significant reduction in urinary hippurate with treatment, which reverted to baseline after cessation of rifaximin, although there was no consistent difference in relative abundance of fecal microbiota with treatment. CONCLUSION These data do not indicate a beneficial effect of rifaximin in patients with NASH.
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Affiliation(s)
- Jeremy F L Cobbold
- Department of Medicine, Imperial College London, London, UK.,Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Julian R Marchesi
- Department of Surgery and Cancer, Imperial College London, London, UK.,School of Biosciences, Cardiff University, Cardiff, UK
| | - Ann Smith
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sann N Wai
- Department of Medicine, Imperial College London, London, UK
| | - Julie Stove
- Department of Medicine, Imperial College London, London, UK
| | - Fariba Shojaee-Moradie
- Diabetes and Metabolic Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Nicola Jackson
- Diabetes and Metabolic Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - A Margot Umpleby
- Diabetes and Metabolic Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | | | - E Louise Thomas
- Institute of Clinical Science, Imperial College London, London, UK
| | - Jimmy D Bell
- Institute of Clinical Science, Imperial College London, London, UK
| | - Elaine Holmes
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Michael S Yee
- Department of Endocrinology and Diabetic Medicine, Imperial College Healthcare NHS Trust, London, UK
| | - Quentin M Anstee
- Institute of Cellular Medicine, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Mark R Thursz
- Department of Medicine, Imperial College London, London, UK
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293
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Avershina E, Slangsvold S, Simpson MR, Storrø O, Johnsen R, Øien T, Rudi K. Diversity of vaginal microbiota increases by the time of labor onset. Sci Rep 2017; 7:17558. [PMID: 29242550 PMCID: PMC5730599 DOI: 10.1038/s41598-017-17972-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 01/09/2023] Open
Abstract
Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating in a randomized placebo-controlled study of probiotic supplementation for the prevention of atopic dermatitis in offspring. Although individuals' vaginal microbiota was stable over time, several bacterial families, which are characteristic of mixed community state type (CST) IV, were overrepresented in vaginal swabs sampled at labor. Alpha-diversity also tended to increase by between 36 weeks gestation and the onset of birth. In the majority of women, CST remained the same throughout the study. Among the women who switched their vaginal microbiota from one CST to another, approximately half shifted towards CST IV. Although CST IV is often associated with bacterial vaginosis, which in turn may lead to preterm birth, in our cohort this shift was not associated with self-reported vaginosis, preterm delivery or birthweight. Probiotic consumption did not alter vaginal microbiota.
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Affiliation(s)
- Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.
| | - Silje Slangsvold
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Melanie Rae Simpson
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Ola Storrø
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
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294
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Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA, Soares MA. Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions. Sci Rep 2017; 7:17364. [PMID: 29234019 PMCID: PMC5727204 DOI: 10.1038/s41598-017-17351-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/23/2017] [Indexed: 01/24/2023] Open
Abstract
The cervical microbiota composition and diversity of HIV-positive women in the postpartum period is unknown. Using a high-throughput bacterial 16S rRNA gene sequencing, we identified four community state types (CSTs). CST III (Lactobacillusdominant) and CST IV (IV-A, IV-B.1, IV-B.2; high-diversity) were found in 41% and 59% of samples, respectively. We did not find association of any CST to postpartum period (six or twelve months), HPV infection or cytology (normal or lesion). However, five bacterial genera were associated with cervical lesions (Gardnerella, Aerococcus, Schlegelella, Moryella and Bifidobacterium), with significant odds ratio (OR) of 40 (2.28–706) for the presence of Moryella and 3.5 (1.36–8.9) for Schlegelella. Longitudinal analysis of samples at postpartum that regressed (lesion to normal), progressed (normal to lesion) and maintained the cytology (lesion or normal) evidenced Gardnerella with a significantly higher abundance in regressing lesions. In the current study, we report the first data on the cervical microbiota of HIV-positive women in the postpartum period. Consistent with previous studies of HIV-negative cohorts, HIV-positive women present a stable cervical microbiota of high-diversity in the postpartum period. Our results highlight that specific microbiota species may serve as sensors for changes in the cervical microenvironment associated with cervical lesions.
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Affiliation(s)
- Gislaine Curty
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Raquel L Costa
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Angela I Meyrelles
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil.
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295
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The human female urogenital microbiome: complexity in normality. Emerg Top Life Sci 2017; 1:363-372. [PMID: 33525775 DOI: 10.1042/etls20170042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/13/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
Microbial communities of the urogenital tract have long been recognised to play an important role in disease states. A revolution in methodological approaches is permitting the assessment of complex urogenital tract microbiota-host interactions and the metabolic and protein milieu of the mucosal interface. There is now great potential for significant advances in biomarker discovery and disease risk stratification, and for the elucidation of mechanisms underpinning the microbial community dynamics involved in urogenital tract pathology. Microbiota-host interactions in the female genital tract have a particular significance, because unlike in the male, there is direct communication between the external genitalia, the uterus and the peritoneal cavity. This review examines the microbial community composition at differing sites of the female urogenital tract and its relationship with health and disease. Key factors involved in the modulation of vaginal microbiome stability and structure, such as endocrine, immune and inflammatory pathways, are considered in the context of a woman's life cycle and disease pathogenesis.
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296
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Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. PLoS One 2017; 12:e0187612. [PMID: 29095928 PMCID: PMC5667760 DOI: 10.1371/journal.pone.0187612] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/23/2017] [Indexed: 02/01/2023] Open
Abstract
Objective To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. Methods A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Results Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. Conclusions High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.
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297
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Abstract
Worldwide, 10% of babies are born preterm, defined as birth before 37 weeks' gestation. We have had little success in developing strategies to prevent preterm births, the majority of which are due to infection or are idiopathic. An emerging hypothesis is that the maternal microbiome-the bacteria that inhabit the mother's body and play vital functions in normal health-contributes to the etiology of preterm birth. Here, we highlight the latest data revealing correlations between preterm birth and maternal intestinal, vaginal, cervical, and placental microbiomes. Additionally, we describe the most commonly used comparative microbiome analysis methods and highlight important issues to consider when conducting such studies.
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Affiliation(s)
- Lindsay A Parnell
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO
| | - Catherine M Briggs
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO
| | - Indira U Mysorekar
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110.
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298
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Li HL, Lu L, Wang XS, Qin LY, Wang P, Qiu SP, Wu H, Huang F, Zhang BB, Shi HL, Wu XJ. Alteration of Gut Microbiota and Inflammatory Cytokine/Chemokine Profiles in 5-Fluorouracil Induced Intestinal Mucositis. Front Cell Infect Microbiol 2017; 7:455. [PMID: 29124041 PMCID: PMC5662589 DOI: 10.3389/fcimb.2017.00455] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022] Open
Abstract
Disturbed homeostasis of gut microbiota has been suggested to be closely associated with 5-fluorouracil (5-Fu) induced mucositis. However, current knowledge of the overall profiles of 5-Fu-disturbed gut microbiota is limited, and so far there is no direct convincing evidence proving the causality between 5-Fu-disturbed microbiota and colonic mucositis. In mice, in agreement with previous reports, 5-Fu resulted in severe colonic mucositis indicated by weight loss, diarrhea, bloody stool, shortened colon, and infiltration of inflammatory cells. It significantly changed the profiles of inflammatory cytokines/chemokines in serum and colon. Adhesion molecules such as vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and VE-Cadherin were increased. While tight junction protein occludin was reduced, however, zonula occludens-1 (ZO-1) and junctional adhesion molecule-A (JAM-A) were increased in colonic tissues of 5-Fu treated mice. Meanwhile, inflammation related signaling pathways including NF-κB and mitogen activated protein kinase (MAPKs) in the colon were activated. Further study disclosed that 5-Fu diminished bacterial community richness and diversity, leading to the relative lower abundance of Firmicutes and decreased Firmicutes/Bacteroidetes (F/B) ratio in feces and cecum contents. 5-Fu also reduced the proportion of Proteobacteria, Tenericutes, Cyanobacteria, and Candidate division TM7, but increased that of Verrucomicrobia and Actinobacteria in feces and/or cecum contents. The fecal transplant from healthy mice prevented body weight loss and colon shortening of 5-Fu treated mice. In addition, the fecal transplant from 5-Fu treated mice reduced body weight and colon length of vancomycin-pretreated mice. Taken together, our study demonstrated that gut microbiota was actively involved in the pathological process of 5-Fu induced intestinal mucositis, suggesting potential attenuation of 5-Fu induced intestinal mucositis by manipulating gut microbiota homeostasis.
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Affiliation(s)
- Hong-Li Li
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lan Lu
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Shuang Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li-Yue Qin
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ping Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shui-Ping Qiu
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hui Wu
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fei Huang
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bei-Bei Zhang
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hai-Lian Shi
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Jun Wu
- Shanghai Key Laboratory of Compound Chinese Medicines, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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299
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Watkins C, Stanton C, Ryan CA, Ross RP. Microbial Therapeutics Designed for Infant Health. Front Nutr 2017; 4:48. [PMID: 29124056 PMCID: PMC5662644 DOI: 10.3389/fnut.2017.00048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022] Open
Abstract
Acknowledgment of the gut microbiome as a vital asset to health has led to multiple studies attempting to elucidate its mechanisms of action. During the first year of life, many factors can cause fluctuation in the developing gut microbiome. Host genetics, maternal health status, mode of delivery, gestational age, feeding regime, and perinatal antibiotic usage, are known factors which can influence the development of the infant gut microbiome. Thus, the microbiome of vaginally born, exclusively breastfed infants at term, with no previous exposure to antibiotics, either directly or indirectly from the mother, is to be considered the "gold standard." Moreover, the use of prebiotics as an aid for the development of a healthy gut microbiome is equally as important in maintaining gut homeostasis. Breastmilk, a natural prebiotic source, provides optimal active ingredients for the growth of beneficial microbial species. However, early life disorders such as necrotising enterocolitis, childhood obesity, and even autism have been associated with an altered/disturbed gut microbiome. Subsequently, microbial therapies have been introduced, in addition to suitable prebiotic ingredients, which when administered, may aid in the prevention of a microbial disturbance in the gastrointestinal tract. The aim of this mini-review is to highlight the beneficial effects of different probiotic and prebiotic treatments in early life, with particular emphasis on the different conditions which negatively impact microbial colonisation at birth.
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Affiliation(s)
- Claire Watkins
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - C. Anthony Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
- School of Science, Engineering and Food Science, University College Cork, Cork, Ireland
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300
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Koskella B, Hall LJ, Metcalf CJE. The microbiome beyond the horizon of ecological and evolutionary theory. Nat Ecol Evol 2017; 1:1606-1615. [DOI: 10.1038/s41559-017-0340-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/07/2017] [Indexed: 01/16/2023]
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