Kim, T. K. et al. Heterogeneity of vaginal microbial communities within individuals. J. Clin. Microbiol. 47, 1181-1189

Host-Microbe Systems Theme, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
Journal of clinical microbiology (Impact Factor: 3.99). 02/2009; 47(4):1181-9. DOI: 10.1128/JCM.00854-08
Source: PubMed


Recent culture-independent studies have revealed that a healthy vaginal ecosystem harbors a surprisingly complex assemblage
of microorganisms. However, the spatial distribution and composition of vaginal microbial populations have not been investigated
using molecular methods. Here, we evaluated site-specific microbial composition within the vaginal ecosystem and examined
the influence of sampling technique in detection of the vaginal microbiota. 16S rRNA gene clone libraries were prepared from
samples obtained from different locations (cervix, fornix, outer vaginal canal) and by different methods (swabbing, scraping,
lavaging) from the vaginal tracts of eight clinically healthy, asymptomatic women. The data reveal that the vaginal microbiota
is not homogenous throughout the vaginal tract but differs significantly within an individual with regard to anatomical site
and sampling method used. Thus, this study illuminates the complex structure of the vaginal ecosystem and calls for the consideration
of microenvironments when sampling vaginal microbiota as a clinical predictor of vaginal health.

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    • "Perioperative transfundal needle aspiration is a procedure that might be considered in selected patients undergoing elective abdominal surgery procedures, and allows for the collection of endometrial fluid. Microbiome study of the vagina (Kim et al., 2009) and the gut (Marteau et al., 2001;Zoetendal et al., 2002;Eckburg et al., 2005;Gillevet et al., 2010) has shown however that luminal bacteria do not adequately reflect the mucosal microbiome, which is also a constraint to gut microbiome studies based on faecal sampling for instance. Approaches were the uterine cavity can be sampled directly during surgery or following hysterectomy clearly provide the most unbiased approach. "
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    ABSTRACT: Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar inasmuch B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.
    Full-text · Article · Jan 2016 · PeerJ
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    • "Recent studies (Zhou et al., 2010; Ravel et al., 2011; Ravel et al., 2013) have revealed Lactobacillus spp. in low abundance in the vaginal tract of a subpopulation of apparently healthy women with high Nugent scores, who have been categorized as 'asymptomatic BV' (ABV) in contrast to 'symptomatic BV' (SBV) subjects. Indeed, two human subjects (Hm403 and Hm409) in our study could be categorized as ABV, as they had reduced relative abundance of Lactobacilli, 65.9 and 3.0% with corresponding Nugent scores of 6 and 9, respectively (Kim et al., 2009; Yeoman et al., 2013). We considered the possibility that the ABV-like and SBV-like human microbiomes might be more similar to that of NHPs. "
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    ABSTRACT: Bacterial communities colonizing the reproductive tracts of primates (including humans) impact the health, survival and fitness of the host, and thereby the evolution of the host species. Despite their importance, we currently have a poor understanding of primate microbiomes. The composition and structure of microbial communities vary considerably depending on the host and environmental factors. We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. The nine primate species included: humans (Homo sapiens), yellow baboons (Papio cynocephalus), olive baboons (Papio anubis), lemurs (Propithecus diadema), howler monkeys (Alouatta pigra), red colobus (Piliocolobus rufomitratus), vervets (Chlorocebus aethiops), mangabeys (Cercocebus atys) and chimpanzees (Pan troglodytes). Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and diversity. In contrast to the gut microbiome, the vaginal microbiome showed limited congruence with host phylogeny, and neither captivity nor diet elicited substantial effects on the vaginal microbiomes of primates. Permutational multivariate analysis of variance and Wilcoxon tests revealed correlations among vaginal microbiota and host species-specific socioecological factors, particularly related to sexuality, including: female promiscuity, baculum length, gestation time, mating group size and neonatal birth weight. The proportion of unclassified taxa observed in nonhuman primate samples increased with phylogenetic distance from humans, indicative of the existence of previously unrecognized microbial taxa. These findings contribute to our understanding of host-microbe variation and coevolution, microbial biogeography, and disease risk, and have important implications for the use of animal models in studies of human sexual and reproductive diseases.The ISME Journal advance online publication, 18 July 2014; doi:10.1038/ismej.2014.90.
    Full-text · Article · Jul 2014 · The ISME Journal
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    • "Even phylogenetically similar bacterial species may exhibit different ecological and virulence properties (Jaspers and Overmann, 2004). New direct DNA analyses show functional diversity in Lactobacillus and many other taxa (Verhelst et al., 2004; Verstraelen et al., 2004; Zhou et al., 2004; Hyman et al., 2005; Kim et al., 2009; Yeoman et al., 2010, 2013). In addition, bacterial communities composed of different species may still occupy similar ecological niches and exhibit similar metabolic functions (Langenheder et al., 2005). "
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    ABSTRACT: The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions. Our goals here are to review what is known about microbiomes of the female reproductive tract and to explore several factors that influence variation within individuals, as well as within and between primate species. Much of our knowledge of microbial variation derives from studies of humans, and from microbes located in nonreproductive regions (e.g., the gut). We review work suggesting that the vaginal microbiota affects female health, fecundity, and pregnancy outcomes, demonstrating the selective potential for these agents. We explore the factors that correlate with microbial variation within species. Initial colonization by microbes depends on the manner of birth; most microbial variation is structured by estrogen levels that change with age (i.e., at puberty and menopause) and through the menstrual cycle. Microbial communities vary by location within the vagina and can depend on the sampling methods used (e.g., swab, lavage, or pap smear). Interindividual differences also exist, and while this variation is not completely understood, evidence points more to differences in estrogen levels, rather than differences in external physical environment. When comparing across species, reproductive-age humans show distinct microbial communities, generally dominated by Lactobacillus, unlike other primates. We develop evolutionary hypotheses to explain the marked differences in microbial communities. While much remains to be done to test these hypotheses, we argue that the ample variation in primate mating and reproductive behavior offers excellent opportunities to evaluate host-microbe coevolution and adaptation.
    Full-text · Article · Dec 2013 · American Journal of Physical Anthropology
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