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Abstract
To investigate the influence of menses on the vaginal microbiota and determine whether tampons that differ in material composition influence these bacterial communities in different ways.
A single-centre trial with randomised, complete block design.
Procter & Gamble facility.
Seven self-declared healthy, female volunteers of reproductive age.
Volunteers used a pad and two types of tampons during the study, one product exclusively each month for three sequential menstrual cycles. During menses and once each mid-cycle, vaginal bacterial community composition was characterised by cultivation-independent methods based on pyrosequencing of V1–V2 variable regions of 16S ribosomal RNA genes.
Changes in the species composition, abundance and diversity in vaginal bacterial communities over time and between treatments.
The vaginal microbiotas of all seven women were dominated by Lactobacillus spp. at mid-cycle, and the compositions of those communities were largely consistent between cycles. Community dynamic patterns during menses varied considerably and were more or less individualised. In three of the seven women the community diversity during pad use was significantly different from at least one tampon cycle.
Changes in the composition of the vaginal microbiota during menses were common, but the magnitude of change varied between women. Despite these changes, most communities were capable of resuming a composition similar to previous mid-cycle sampling times following menstruation. Overall we conclude that the two tampons tested do not significantly impact the vaginal microbiota in different ways; however, larger studies should be performed to confirm these findings.
... Among women undergoing hysteroscopy or laparoscopy (Pelzer et al., 2018), endometrial facultative anaerobes were more abundant in women with dysmenorrhea (n = 24) compared to women with menorrhagia (n = 17). However, the cross-sectional design did not sample the vaginal microbiome nor account for potential microbiome change within a menstrual cycle (Gajer et al., 2012;Hickey et al., 2013). Other limitations were a highly select clinical population, invasive sampling, and no measurement of dysmenorrhea symptom heterogeneity. ...
... The sample size was based on funding availability and funding timeline and was comparable to some previous studies involving longitudinal vaginal microbiome sample collections (Gajer et al., 2012;Hickey et al., 2013). Inclusion criteria were (a) females aged 14-24; (b) onset of menarche > 2 years prior to the study; (c) regular menstrual cycles (24-38 days) for 3 months preceding enrollment; and (d) in good general health. ...
... Compared to provider-collected specimens, previous research suggests that self-collected specimens have the same microbial diversity and high validity (Forney et al., 2010). Vaginal swabs were collected on-menses (Days 1-3 of the menstrual cycle) and off-menses (midcycle day +/−5 days), as research suggests the vaginal microbiome profile can change during menstruation (Gajer et al., 2012;Hickey et al., 2013). This meant that for each participant the two sample collections were separated by 13 to 20 days depending on the length of their menstrual cycle. ...
Background:
Dysmenorrhea is highly prevalent; it places women at risk for other chronic pain conditions. There is a high degree of individual variability in menstrual pain severity, the number of painful sites, and co-occurring gastrointestinal symptoms. Distinct dysmenorrhea symptom-based phenotypes were previously identified, but the biological underpinnings of these phenotypes are less known. One underexplored contributor is the vaginal microbiome. The vaginal microbiota differs significantly among reproductive-age women and may modulate as well as amplify reproductive tract inflammation, which may contribute to dysmenorrhea symptoms.
Objectives:
The objective of this study was to examine associations between dysmenorrhea symptom-based phenotypes and vaginal microbiome compositions on- and off-menses.
Methods:
We conducted a prospective, longitudinal, pilot study of 20 women (aged 15-24) grouped into three dysmenorrhea symptom-based phenotypes: "mild localized pain," "severe localized pain," and "severe multiple pain and gastrointestinal symptoms." Over one menstrual cycle, participants provided vaginal swabs when they were on-menses and off-menses. We assayed the vaginal microbiome using 16S rRNA gene sequencing. Permutational multivariate analysis of variance tests were used to compare microbiome compositions across phenotypes, with heat maps generated to visualize the relative abundance of bacterial taxa.
Results:
The vaginal microbiome compositions (n = 40) were different across the three phenotypes. After separating the on-menses (n = 20) and off-menses (n = 20) specimens, the statistically significant difference was seen on-menses, but not off-menses. Compared to the "mild localized pain" phenotype, participants in the "multiple severe symptoms" phenotype had a lower lactobacilli level and a higher abundance of Prevotella, Atopobium, and Gardnerella when on-menses. We also observed trends of differences across phenotypes in vaginal microbiome change from off- to on-menses.
Discussion:
The study provides proof-of-concept data to support larger studies on associations between dysmenorrhea symptom-based phenotypes and vaginal microbiome that might lead to new intervention targets and/or biomarkers for dysmenorrhea. This line of research has the potential to inform precision dysmenorrhea treatment that can improve women's quality of life.
... Using clustering methods to categorize the taxonomic profiles, we are able to associate microbiota composition with variables of interest. These community state types (Ravel et al., 2011) or cervicotypes (Anahtar et al., 2015) (see Figure 1B), have been associated with race/ethnicity, menstrual cycle (Gajer et al., 2012;Hickey et al., 2013), and inflammatory profiles (Anahtar et al., 2015;Gosmann et al., 2017). ...
... Given the role of estrogen which is thought to mediate the stabilizing effect of pregnancy on VMB composition (Romero et al., 2014) and cyclical instability induced by the menstrual cycle (Gajer et al., 2012;Hickey et al., 2013), it is likely that hormonal contraception usage would be an important influence. However, systematic review and meta-analyses reveal inconsistent results thus far, largely due to the variety of hormonal contraceptive methods available (Achilles and Hillier, 2013;Vodstrcil et al., 2013;Anahtar et al., 2018). ...
... A study that compared the menstrual fluid microbiome from tampons cultured S. aureus from the menstrual blood of 40% of healthy women but found no clear difference in the other microbiota between those who had S. aureus colonization and those who did not. In a small longitudinal study comparing mid-cycle and during menses vaginal microbiota of women with baseline Lactobacillusdominant VMB who used study-provided menstrual hygiene products, Hickey et al. found that menses itself caused alterations of the microbiota from baseline (Hickey et al., 2013), but that there were not specific patterns associated with particular products. Differences in menstrual hygiene product use between geographic and demographic sub-populations (Romo and Berenson, 2012) may be a confounding factor in studies that show differences between in the VMB composition between racial or ethnic groups. ...
There is increasing evidence that the composition of a woman's vaginal microbiota significantly influences her sexual and reproductive health, including her risk of miscarriage, preterm birth, HIV and other sexually transmitted infections. Efforts to modulate the vaginal microbiota using antibiotic or probiotic therapy have shown limited lasting or reliable success. To explore the natural dynamics and causal pathways responsible for heterogeneity of vaginal microbiota composition we review the existing literature on its determinants, from the perspective of microorganism- and host-related factors. We then discuss how molecular approaches can be harnessed to advance our understanding of individual and population-level vaginal microbiota composition patterns. Work has been done to investigate determinants of microbial composition patterns in other body niches, but very little in the female genital tract so far. There is an urgent need to better understand vaginal microbiota composition patterns, across the lifespan, outside of the context of sexual health clinics, and in Sub-Saharan African women in whom vaginal microbiota composition may be a risk factor for HIV acquisition. More work is needed to clarify causal relationships between clinical symptoms, host genetic, host behavior, and molecular vaginal microbiota profiles. These insights will lay the groundwork for novel and targeted interventional approaches to improve women's sexual and reproductive health.
... Vaginal It has been established that microbial composition can change dramatically during the menses cycle and later return to a 'stable' state before the next menstrual period [35,36]. Previous studies have identified a subset of individuals in this data set as exhibiting a microbial composition dominated by L. crispatus with a notable increase of L. iners around the start of each menstrual period [4,35] (Additional file 2: Figure S1a). ...
... Vaginal It has been established that microbial composition can change dramatically during the menses cycle and later return to a 'stable' state before the next menstrual period [35,36]. Previous studies have identified a subset of individuals in this data set as exhibiting a microbial composition dominated by L. crispatus with a notable increase of L. iners around the start of each menstrual period [4,35] (Additional file 2: Figure S1a). These interactions were also captured by the learned DBN model in the form of a directed triangle involving L. crispatus and L. iners (Fig. 3b). ...
... Relationship between alignment parameters and gestational age at birth. Figure shows the relationship between alignment parameters a and b and gestational age at birth (measured in weeks) for the aligned infant gut microbiome data set. Each blue dot represent an aligned infant sample i where x-axis shows −b a from transformation function τ i (t) = (t−b)a and y-axis shows the gestational age at birth of infant i. Pearson correlation coefficient = 0.35 ...
Background
Several studies have focused on the microbiota living in environmental niches including human body sites. In many of these studies, researchers collect longitudinal data with the goal of understanding not only just the composition of the microbiome but also the interactions between the different taxa. However, analysis of such data is challenging and very few methods have been developed to reconstruct dynamic models from time series microbiome data.
Results
Here, we present a computational pipeline that enables the integration of data across individuals for the reconstruction of such models. Our pipeline starts by aligning the data collected for all individuals. The aligned profiles are then used to learn a dynamic Bayesian network which represents causal relationships between taxa and clinical variables. Testing our methods on three longitudinal microbiome data sets we show that our pipeline improve upon prior methods developed for this task. We also discuss the biological insights provided by the models which include several known and novel interactions. The extended CGBayesNets package is freely available under the MIT Open Source license agreement. The source code and documentation can be downloaded from https://github.com/jlugomar/longitudinal_microbiome_analysis_public.
Conclusions
We propose a computational pipeline for analyzing longitudinal microbiome data. Our results provide evidence that microbiome alignments coupled with dynamic Bayesian networks improve predictive performance over previous methods and enhance our ability to infer biological relationships within the microbiome and between taxa and clinical factors.
Electronic supplementary material
The online version of this article (10.1186/s40168-019-0660-3) contains supplementary material, which is available to authorized users.
... A few studies have reported the detection, increase and transition to L. inersdominated microbiota during menses Hickey et al., 2013;Santiago et al., 2012;Srinivasan et al., 2012Srinivasan et al., , 2010. L. iners has also been implicated in both the development of BV during pregnancy and preterm birth (Skarin & Sylwan, 1986). ...
... A few molecular-based studies reported that menses exerts a strong influence upon the stability of the vaginal ecosystem (Chaban et al., 2014;Gajer et al., 2012;Hickey et al., 2013;Jespers et al., 2012;Lambert et al., 2013;Santiago et al., 2011Santiago et al., , 2012Srinivasan et al., 2010). Srinivasan et al. (2010) used taxon-specific qPCR to examine the longitudinal fluctuations of vaginal bacterial communities in 22 reproductiveaged women, 8 of whom were diagnosed with BV. ...
... In a small study, Hickey et al. (2013) used pyrosequencing of the V1-V2 region of the 16S rRNA genes to determine the effect of tampons and menses upon the vaginal microbiotas of seven women and observed that while community dynamics varied during menses, these changes were largely individualized. Moreover, neither tampon nor pad use affected the vaginal microbiome (Hickey et al., 2013). ...
The human vagina harbours one of the most ecologically interesting and important microbial ecosystems of our holobiome. The healthy human vagina is typically dominated by Lactobacillus species. Therein, vaginal lactobacilli provide the first line of protection against potential pathogens and, consequently, in the protection and maintenance of female gynecologic and reproductive health. Although much of our understanding of this system was elucidated from early studies and the application of traditional microbiological techniques, newer and more sophisticated technologies have added considerably to the depth of that understanding. Among these, molecular-based techniques have both augmented and reinforced these findings, providing a refined understanding of microbial:microbial and microbial:host interactions within the vaginal microbial ecosystem, while also providing new and important insights. Studies based upon 16S rRNA gene sequencing have enabled the vaginal microbiome of reproductive-aged women to be categorized into five major microbial community states and revealed that not all Lactobacillus spp. are equal in their maintenance of reproductive health. Further, recent genomic, proteomic, metagenomic, metabolomic, and immunological studies have provided novel insight into potential mechanisms by which various Lactobacillus species may uniquely interact with the host and contribute towards vaginal health and the mechanisms through which the system may be perturbed. Herein, we provide a comprehensive review of our contemporary understanding of the vaginal microbiota's role in maintaining female gynecologic and reproductive health, summarizing seminary findings, and highlighting where molecular techniques have improved our overall understanding of the vaginal microbiota.
... 13,14,23 Temporary, mostly short-lived, deviations from a Lactobacillus-dominated ground state and accompanying metabolome shifts are common in reproductive-aged women, typically observed in association with menses and sexual activity. Studies consistently suggest that menses is the major disturbing factor to VMB during the menstrual cycle, with large reductions in lactobacilli, 13,24,25 shifts from L. crispatus to L. iners, 24,26 or the appearance of BV-associated bacteria. 26,27 However, longitudinal studies also suggest a "dynamic stability" wherein most women retain their CST or alternate between certain CSTs, mostly in correspondence to menses. ...
... Studies consistently suggest that menses is the major disturbing factor to VMB during the menstrual cycle, with large reductions in lactobacilli, 13,24,25 shifts from L. crispatus to L. iners, 24,26 or the appearance of BV-associated bacteria. 26,27 However, longitudinal studies also suggest a "dynamic stability" wherein most women retain their CST or alternate between certain CSTs, mostly in correspondence to menses. 13,24,27,28 Overall, the distinct Lactobacillus-dominated community states are thought to be the most optimal 3,4 with, as further discussed, numerous associations with reproductive health. ...
Objective:
This series of articles, titled The Vaginal Microbiome, written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the current findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.
Materials and methods:
A database search of PubMed was performed, using the search terms "vaginal microbiome" (VMB) with "research," "normal," "neonate," "puberty," "adolescent," "menopause," and "ethnicities," as well as "human microbiome project." Full article texts were reviewed. Reference lists were screened for additional articles.
Results:
In the last 2 decades, many studies applying molecular techniques were performed, intending to characterize the vaginal microbiota. These studies advanced our understanding of how vaginal health is defined. The first article in this series focuses on the advancement of VMB research, technical definitions, the definition of "normal" VMB, and the dynamics of VMB throughout women's lives.
Conclusions:
Understanding how microorganisms inhabiting the vagina interact with each other and with the host is important for a more complete understanding of vaginal health. The clinical application of microbial community sequencing is in its beginning, and its interpretation regarding practical clinical aspects is yet to be determined.
... In both studies the VM was sampled and sequenced with similar protocols to the ones used in the current study. The first study longitudinally evaluated the effect of menses on the composition of the vaginal microbiome, by sampling eight healthy reproductive age women 15 times during a period of 3 months (Hickey et al., 2013). The second study evaluated the temporal microbiome dynamics of 32 women and obtained 32 samples from each individual during a period of four months (Gajer et al., 2012). ...
... Further, it is plausible that the presence of vaginal symptoms is not always correlated with a specific community structure, but rather with some equilibrium states that are maintained in an otherwise healthy vagina and varies among individuals, as our data suggests. Hickey et al., 2013); and 32 women sampled over four months (Gajer et al., 2012). ...
Postmenopausal women often suffer from vaginal symptoms associated with atrophic vaginitis. Additionally, gynecologic cancer survivors may live for decades with additional, clinically significant, persistent vaginal toxicities caused by cancer therapies, including pain, dyspareunia, and sexual dysfunction. The vaginal microbiome (VM) has been previously linked with vaginal symptoms related to menopause (i.e. dryness). Our previous work showed that gynecologic cancer patients exhibit distinct VM profiles from healthy women, with low abundance of lactobacilli and prevalence of multiple opportunistic pathogenic bacteria. Here we explore the association between the dynamics and structure of the vaginal microbiome with the manifestation and persistence of vaginal symptoms, during one year after completion of cancer therapies, while controlling for clinical and sociodemographic factors. We compared cross-sectionally the vaginal microbiome in 134 women, 64 gynecologic patients treated with radiotherapy and 68 healthy controls, and we longitudinally followed a subset of 52 women quarterly (4 times in a year: pre-radiation therapy, 2, 6 and 12 months post-therapy). Differences among the VM profiles of cancer and healthy women were more pronounced with the progression of time. Cancer patients had higher diversity VMs and a variety of vaginal community types (CTs) that are not dominated by Lactobacilli, with extensive VM variation between individuals. Additionally, cancer patients exhibit highly unstable VMs (based on Bray-Curtis distances) compared to healthy controls. Vaginal symptoms prevalent in cancer patients included vaginal pain (40%), hemorrhage (35%), vaginismus (28%) and inflammation (20%), while symptoms such as dryness (45%), lack of lubrication (33%) and dyspareunia (32%) were equally or more prominent in healthy women at baseline. However, 24% of cancer patients experienced persistent symptoms at all time points, as opposed to 12% of healthy women. Symptom persistence was strongly inversely correlated with VM stability; for example, patients with persistent dryness or abnormally high pH have the most unstable microbiomes. Associations were identified between vaginal symptoms and individual bacterial taxa, including: Prevotella with vaginal dryness, Delftia with pain following vaginal intercourse, and Gemillaceaea with low levels of lubrication during intercourse. Taken together our results indicate that gynecologic cancer therapy is associated with reduced vaginal microbiome stability and vaginal symptom persistence.
... Culture-based studies have led to variable conclusions, with some studies reporting no changes in the microbiota throughout the menstrual cycle (Wilks and Tabaqchali, 1987), and others describing a greater proportion of non-Lactobacillus species during menses (Eschenbach et al., 2000). Recent culture-independent studies have demonstrated that although shifts in the vaginal microbiota are relatively common, those changes are unlikely to be associated with menstrual phases Hickey et al., 2013). After menopause, the decrease in estrogen is accompanied by a decline in glycogen in the vaginal epithelium, which results in changes in the epithelial structure and a decline in lactobacilli (Cruickshank and Sharman, 1934). ...
... Direct amplicon sequencing is currently the most common approach to study the composition of the vaginal microbiota, either based on the PCR amplification of 16S rRNA gene (Hummelen et al., 2010;Ravel et al., 2013;MacIntyre et al., 2015;Hickey et al., 2013;Aagaard et al., 2012;Shipitsyna et al., 2013;Huang et al., 2015;Gajer et al., 2012;Ravel et al., 2011) or the cpn60 gene (Schellenberg et al., 2011(Schellenberg et al., , 2009Chaban et al., 2014;Albert et al., 2015). As a result of application of DNA sequence based methods to characterize the composition of the vaginal microbiome, there is a growing appreciation of "atypical" (i.e. ...
The vaginal microbiome plays an important role in women's reproductive health. Imbalances in this microbiota are associated with bacterial vaginosis, increased susceptibility to sexually transmitted infections, and negative reproductive outcomes. The causes of such variations, however, are poorly understood. A healthy vaginal microbiota is defined as Lactobacillus-dominated and an overgrowth of other species is often associated with unhealthy conditions. An appreciation of "atypical" microbiomes in healthy women, such as Bifidobacterium-dominated, has been gradually increasing. Although bifidobacteria play an important role in gut health, vaginal bifidobacteria have not yet been fully characterized. In this study, a baseline description of the "healthy" vaginal microbiome in pregnancy has been established based on cpn60 gene amplicon sequencing. The vaginal microbiota of pregnant women relative to non-pregnant women had lower richness and diversity, higher Lactobacillus abundance and lower Mollicutes/Ureaplasma prevalence. This gives a better understanding of the vaginal microbiome in healthy pregnancies and provides a control group for a subsequent comparison to women who experienced preterm birth. An association between Mollicutes and preterm was confirmed, and further suggested that a more rich and diverse microbiome is associated with prematurity. To better understand the relationship between reproductive outcomes and microbiota, an improved definition of the healthy microbiome is also needed, which should include evaluation of "atypical" microbiomes, such as Bifidobacterium-dominated. Phenotypic characterization of vaginal bifidobacteria indicated that they have health promoting characteristics similar to beneficial vaginal lactobacilli. Considering the importance of bifidobacteria as one of the primary colonizers of the neonatal gut, the genomes of vaginal and gut isolates of Bifidobacterium breve and Bifidobacterium longum were compared. Results indicated that vaginal and gut microbiomes are colonized by a shared community of Bifidobacterium, which may be transferred from mother to infant. Taken together, the results presented in this thesis provide a better understanding of the vaginal microbiome of pregnant women with low and high risk for preterm birth. It also improves the understanding of a healthy microbiome by phenotypically characterizing vaginal bifidobacteria, and contributes to elucidate aspects of bifidobacteria ecology by comparing the genomes of vaginal and gut bifidobacteria.
... In a cross-sectional baseline analysis of all 430 women in the Vaginal Biomarkers Study using qPCRs, 16% had S. agalactiae 29 and 28% E. coli in their VMB 16 . The limited number of other molecular VMB studies that reported on S. agalactiae and E. coli carriage showed varying results, with generally lower detection in studies that employed 16 S sequencing compared to qPCR 18,30,31 . Vaginal carriage of these pathobionts should be further investigated, preferably by qPCR in longitudinal studies, given their associations with vaginitis, reproductive health, and neonatal meningitis and sepsis 32 . ...
... Amenorrhoeic women had a reduced concentration of lactobacilli, (notably L. crispatus), compared to women with a menstrual cycle even after controlling for PSA presence and recent vaginal cleansing, and this may be due to the induction of a hypo-oestrogenic state during injectable progestin use. Current evidence suggests that the VMB destabilising effect of hypo-oestrogenism in these women is larger than any potential protective effect associated with the absence of regular menstrual bleeding 30 . Amenorrhoeic women also had increased concentrations of several proinflammatory immune mediators. ...
In cross-sectional studies increased vaginal bacterial diversity has been associated with vaginal inflammation which can be detrimental for health. We describe longitudinal changes at 5 visits over 8 weeks in vaginal microbiota and immune mediators in African women. Women (N = 40) with a normal Nugent score at all visits had a stable lactobacilli dominated microbiota with prevailing Lactobacillus iners. Presence of prostate-specific antigen (proxy for recent sex) and being amenorrhoeic (due to progestin-injectable use), but not recent vaginal cleansing, were significantly associated with microbiota diversity and inflammation (controlled for menstrual cycle and other confounders). Women (N = 40) with incident bacterial vaginosis (Nugent 7–10) had significantly lower concentrations of lactobacilli and higher concentrations of Gardnerella vaginalis, Atopobium vaginae, and Prevotella bivia, at the incident visit and when concentrations of proinflammatory cytokines (IL-1β, IL-12p70) were increased and IP-10 and elafin were decreased. A higher ‘composite-qPCR vaginal-health-score’ was directly associated with decreased concentrations of proinflammatory cytokines (IL-1α, IL-8, IL-12(p70)) and increased IP-10. This longitudinal study confirms the inflammatory nature of vaginal dysbiosis and its association with recent vaginal sex and progestin-injectable use. A potential role for proinflammatory mediators and IP-10 in combination with the vaginal-health-score as predictive biomarkers for vaginal dysbiosis merits further investigation.
... Van de Wijgert et al. [47] found that, in most studies, menses were the strongest disturbing factor, sometimes with large reductions in lactobacilli, shifts from L. crispatus to L. iners [50,54,55] or the appearance of BV-associated bacteria, streptococci or other Gram-positive cocci. ...
... Possibly, these conflicting data can be partially reconciled by the observation that large numbers of L. iners can replace L. crispatus during the menses [50,54,55]. ...
Monopolization of the vaginal econiche by a limited number of Lactobacillus species, resulting in low pH of 3.5-4.5, has been shown to protect women against vaginal dysbiosis, sexually transmitted infections and adverse pregnancy outcomes. Still, controversy exists as to which characteristics of lactobacilli are most important with regard to colonization resistance and to providing protection. This review addresses the antimicrobial and anti-inflammatory roles of lactic acid (and low pH) and hydrogen peroxide (and oxidative stress) as means of lactobacilli to dominate the vaginal econiche.
... In clinical cases, the shift in the vaginal microbiota from dominant Lactobacillus to a polymicrobial microbiota is usually diagnosed as bacterial vaginosis (BV) (Onderdonk et al., 2016). The microbial composition of the vagina is believed to be dynamic in a transitional period, such as pregnancy or menstruation (Hickey et al., 2013;Gupta et al., 2020). Previous studies have suggested that acute heat stress could cause intestinal metabolism disorders and microbiota changes in mice (Wen et al., 2021), pigs (Xiong et al., 2020), and poultry (Zhu et al., 2019). ...
Heat stress can have an impact on parental gamete maturation and reproduction functions. According to current research, the microbial composition of the vaginal cavity is species specific. Pregnancy, menstruation, and genital diseases have been linked to the dynamics of vaginal ecology. In this study, we characterized the vaginal microbiota and metabolites after heat stress. At the phylum level, the rabbit’s vaginal microbial composition of rabbit showed high similarity with that of humans. In the Heat group, the relative abundance of the dominant microbiota Actinobacteria, Bacteroidetes, and Proteobacteria increased, while the relative abundance of Firmicutes decreased. Furthermore, heat stress significantly increased the relative abundance of W5053, Helcococcus, Thiopseudomonas, ldiomaarina, atopostipes, and facklamia, whereas the relative abundance of 12 genera significantly decreased, including Streptococcus, UCG-005, Alistipes, [Eubacterium]_xylanophilum_group, Comamonas, RB41, Fastidiosipila, Intestinimonas, Arthrobacter, Lactobacillus, Leucobacter, and Family_xlll_AD3011_group. Besides, the relative concentrations of 158 metabolites differed significantly between the Heat and Control groups. Among them, the endocrine hormone estradiol (E2) increased in the Heat group and was positively associated with a number of metabolites such as linolelaidic acid (C18:2N6T), N-acetylsphingosine, N-oleoyl glycine, trans-petroselinic acid, syringic acid, 2-(1-adamantyl)-1-morpholinoethan-1-one, 5-OxoETE, and 16-heptadecyne-1,2,4-triol. Further, the majority of the differential metabolites were enriched in steroid biosynthesis and endocrine and other factor-regulated calcium reabsorption pathways, reflecting that heat stress may affect calcium metabolism, hormone-induced signaling, and endocrine balance of vaginal ecology. These findings provide a comprehensive depiction of rabbit vaginal ecology and reveal the effects of heat stress on the vagina via the analysis of vaginal microbiome and metabolome, which may provide a new thought for low female fertility under heat stress.
... This may explain why there was so much variation temporally, as in each generation a different subset of the microbial community may have been activated. It is also possible that the composition of the bacterial community is variable over time within each generation and as a consequence also among generations (Hannula et al. 2019;Hickey et al. 2013;Lauber et al. 2013). Moreover, in this study we only focused on the microbial community from the rhizosphere samples of J. vulgaris, and we did not examine the endophytic microbial community which can be strongly affected by application of SA to plant leaves (Noman et al. 2021). ...
Background and aims
Jacobaea vulgaris plants grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on plant growth. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the soil.
Methods
We studied the composition of the microbial community over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris . We initiated the experiment with an inoculum of live soil collected from the field, and at the start of each subsequent plant cycle, we inoculated a small part of the soil from the previous plant cycle into sterile bulk soil.
Results
Application of SA did not significantly increase or decrease the Shannon diversity at genus level within each generation, but several specific genera were enriched or depleted after foliar SA application. The composition of bacterial communities in the rhizosphere significantly differed between plant cycles (generations), but application of SA did not alter this pattern. In the first generation no genera were significantly affected by the SA treatment, but in the second, third and fourth generations, specific genera were significantly affected. 89 species out of the total 270 (32.4%) were present as the “core” microbiome in all treatments over four plant cycles.
Conclusions
Overall, our study shows that the composition of bacterial genera in the rhizosphere significantly differed between plant cycles, but that it was not strongly affected by foliar application of SA on J. vulgaris leaves. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere bacterial community.
... Lactobacillus was undoubtedly the most dominant genus with a relative abundance of 71.55% in the 111 women in this study. Oddly, we did not find at species level the presence of L. vaginalis, L. crispatus, L.gasseri and L. jensenii as reported in previous studies from Western countries and non Asians [22][23][24]. Indeed, the dominant members of Lactobacillus species have been limited and elusive based on the context of studies conducted in different locations and different populations. In most cases, the vaginal microbiota through a menstrual cycle demonstrated that L.crispatus, L.iners, and L.jensenii were the dominant members [11]. ...
Background
This study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.
Results
This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Vaginal swabs were collected and stored at − 70 °C until assayed. The V3-V4 region of 16S rRNA gene was amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was varied with urogenital tract infections, childbearing history and menstrual cycle. The vaginal microbial richness (Alpha diversity measured by PD_whole tree) was decreased in normal women (without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of infected and non-pregnant. The top 10 genus relative abundance, especially Lactobacillus , which was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis. Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus . We also found that a higher L.helveticus / L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although these comparisons lack statistical significance.
Conclusions
The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The composition of the main lactobacillus species may shift upon phases of a menstrual cycle and the status of reproductive tract infections.
... showed dominance at the end of the cycle. The change in microbial composition in the vagina was normal and potentially switched to original after menstruation (Hickey et al., 2013). ...
According to the WHO (World Health Organization), cancer leads to the death of 1 in 6 people making it the second leading cause of death in the world. It has taken the lives of an estimated 9.6 million people in 2018 only in various developing as well as developed counties. There are several causes of cancer such as physical carcinogens e.g., ultraviolet and ionizing radiation, chemical carcinogens e.g., aflatoxins, tobacco, etc., and biological carcinogens e.g., bacteria, parasites, etc (www.who.int/news-room/factsheets/detail/cancer). Genetic mutation during DNA replication greatly improves the growth of cancer. Several epidemiologic and occupational health studies state that environmental factors play a role in the spike of cancer. The noteworthy relationship exists between microbiome composition and cancer inclusive of cancer therapy. Approximately 15%–20% of the recorded cancer cases are due to the various infectious microbes (Bhatt et al., 2017). The human body comprises a plethora of microbes inhabiting the anatomical sites. These microbes include bacteria and viruses that have been studied using culture-dependent and cultureindependent methods. Microbes inhabit various body sites such as mouth, skin, stomach, gastrointestinal tract, as well as vagina. Effortsweredonetostudythefecalmicrobiota directlyusingthefecalmicrobialDNA(Kumaretal.,2016)tostudythepronounced difference in the microbial communities within healthy and unhealthy people. Evidence also indicates that the manipulation of microbiota assists in cancer treatment.
... Some women have vaginal microbial communities that appear to be more stable when oestrogen levels are at their highest, whereas other experience fluctuations timed with the menses. 27 The high level of oestrogen causes a thickening of the vaginal epithelium and prompts the accumulation of glycogen and increased lactobacillus species. Molecular-independent techniques have shown that vaginal microbial community varied among women, and each woman's VMB composition fluctuates throughout her reproductive lifespan ( Figure 2). ...
Our knowledge of the composition of the vaginal environment in healthy women stands greatly improved. An imbalance in microbial communities is associated with a number of different diseases, disorders and other adverse health outcomes. Cultivation-independent studies have been published indicating that each woman has unique vaginal microbiota. The vaginal microbiome in pregnant women is more stable and associated with high level of Lactobacillus, particularly, Lactobacillus crispatus and low bacterial diversity. The current review was planned to provide a more complete picture of the abundance of various bacteria species in the vagina and how they impact women's reproductive health and pregnancy outcomes. This should provide a better understanding of what is considered a "healthy" or "unhealthy" vaginal microbiome and how the dysibiosis of the vagina affects the women. Additionally, it was planned to identify factors that influence the structure and / or composition of the microbial community.
... This may explain why we saw so much variation temporally as in each generation a different subset of the microbial community may have been activated. It is also possible that the composition of the bacterial community is variable over time within each generation and as a consequence also among generations (Gilbert et al. 2009;Hannula et al. 2019;Hickey et al. 2013;Lauber et al. 2013). ...
Background and aims
Many plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil.
Methods
We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris.
Results
Our study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant.
Conclusions
Overall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.
... Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all 111 samples in this study. However, we did not nd the presence of Lactobacillus vaginalis, L. crispatus, L.gasseri and L. jensenii at species level as reported in previous studies [15][16][17]. Indeed, the dominant members of Lactobacillus species has been limited and elusive based on the context of each study. ...
Background: The association of the normal physiological cycle to the structural pattern of microbiota in reproductive tract of women at reproductive age has not been extensively explored. This study was undertaken to determine whether the vaginal microbes of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.
Results: This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Samples of vaginal swabs were collected and stored at -70℃ until assayed. The V3-V4 regions of 16S rRNA genes were amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was different between women with different urogenital tract infections, childbearing history and menstrual cycle. We showed that the vaginal microbial richness(Alpha diversity measured by PD_whole tree) was decreased in normal women(without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of uninfected and non-pregnant. The top 10 genus relative abundance, especially that Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis.
Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus. It is proposed that a higher L.helveticus/L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although this comparison lacks statistical significance.
Conclusions: The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age, characterized with 16S rRNA gene sequence and QIIME based analysis, were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The compositional ratio of the main lactobacillus species may shift depending on the normal physiological cycle and reproductive tract infections.
... Use of pantyliners during menstruation was also associated with L. jensenii, with the conditional probability of L. jensenii being present in the vaginal microbiome increasing from 37.4% to 60.7% with use of panty liners during menstruation. While the directionality of this relationship is not immediately intuitive, previous work has shown that use of emollient pads changes the vaginal epithelium and that some women's vaginal microflora does shift with pad versus tampon use [66,67], although the evidence on this is mixed [68]. NMDS/ANOSIM testing indicated that tampon use was associated with the vaginal microbiome, lending further support to the hypothesis that menstrual habits could impact the microbiome (S5 and S6 Files). ...
The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella , Gardnerella , Dialister , Sneathia and Ruminococcaceae ), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii , Corynebacteria , and Proteobacteria . No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future studies of the vaginal microbiome and vaginal pathologies should include detailed surveys of participants’ sanitary, sexual and birth control habits, as these can act as confounders in the relationship between the microbiome and disease. Although the BN approach is powerful in revealing complex associations within multidimensional datasets, the need in some cases to discretize the data for use in BN analysis can result in loss of information. Future research is required to alleviate such limitations in constructing BN networks. Large sample sizes are also required in order to allow for the incorporation of a large number of variables (nodes) into the BN, particularly when studying associations between metadata and the microbiome. We believe that this approach is of great value, complementing other methods, to further our understanding of complex associations characteristic of microbiome research.
... Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all 111 samples in this study. However, we did not nd the presence of Lactobacillus vaginalis, L. crispatus, L.gasseri and L. jensenii at species level as reported in previous studies [15][16][17]. Indeed, the dominant members of Lactobacillus species has been limited and elusive based on the context of each study. ...
Background: The association of the normal physiological cycle to the structural pattern of microbiota in reproductive tract of women at reproductive age has not been extensively explored. This study was undertaken to determine whether the vaginal microbes of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.
Results: This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Samples of vaginal swabs were collected and stored at -70℃ until assayed. The V3-V4 regions of 16S rRNA genes were amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was different between women with different urogenital tract infections, childbearing history and menstrual cycle. We showed that the vaginal microbial richness(Alpha diversity measured by PD_whole tree) was decreased in normal women(without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of uninfected and non-pregnant. The top 10 genus relative abundance, especially that Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis.
Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus. It is proposed that a higher L.helveticus/L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although this comparison lacks statistical significance.
Conclusions: The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age, characterized with 16S rRNA gene sequence and QIIME based analysis, were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The compositional ratio of the main lactobacillus species may shift depending on the normal physiological cycle and reproductive tract infections.
... Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all 111 samples in this study. However, we did not nd the presence of Lactobacillus vaginalis, L. crispatus, L.gasseri and L. jensenii at species level as reported in previous studies [15][16][17]. Indeed, the dominant members of Lactobacillus species has been limited and elusive based on the context of each study. ...
Background: The association of the normal physiological cycle to the structural pattern of microbiota in reproductive tract of women at reproductive age has not been extensively explored. This study was undertaken to determine whether the vaginal microbes of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.
Results: This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Samples of vaginal swabs were collected and stored at -70℃ until assayed. The V3-V4 regions of 16S rRNA genes were amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was different between women with different urogenital tract infections, childbearing history and menstrual cycle. We showed that the vaginal microbial richness(Alpha diversity measured by PD_whole tree) was decreased in normal women(without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of uninfected and non-pregnant. The top 10 genus relative abundance, especially that Lactobacillus was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis.
Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus. It is proposed that a higher L.helveticus/L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although this comparison lacks statistical significance.
Conclusions: The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age, characterized with 16S rRNA gene sequence and QIIME based analysis, were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The compositional ratio of the main lactobacillus species may shift depending on the normal physiological cycle and reproductive tract infections.
... Human microbiota profiles have been correlated to genetics [250], host immune status [251], body site [252][253][254], and lifestyle choices [241,253,255]. Temporal fluctuations in microflora populations have been observed across hours to months, though the causes and mechanisms of such temporal effects are not yet well understood [241,253,256]. Although the possible significance of each variable has yet to be fully investigated, all of these factors likely correlate to microbiome diversity and fluctuations and all may impact the response of a given microbiome profile to a dietary intervention such as the inclusion of cranberry products. ...
Cranberry is a well-known functional food, but the compounds directly responsible for many of its reported health benefits remain unidentified. Complex carbohydrates, specifically xyloglucan and pectic oligosaccharides, are the newest recognized class of biologically active compounds identified in cranberry materials. Cranberry oligosaccharides have shown similar biological properties as other dietary oligosaccharides, including effects on bacterial adhesion, biofilm formation, and microbial growth. Immunomodulatory and anti-inflammatory activity has also been observed. Oligosaccharides may therefore be significant contributors to many of the health benefits associated with cranberry products. Soluble oligosaccharides are present at relatively high concentrations (~20% w/w or greater) in many cranberry materials, and yet their possible contributions to biological activity have remained unrecognized. This is partly due to the inherent difficulty of detecting these compounds without intentionally seeking them. Inconsistencies in product descriptions and terminology have led to additional confusion regarding cranberry product composition and the possible presence of oligosaccharides. This review will present our current understanding of cranberry oligosaccharides and will discuss their occurrence, structures, ADME, biological properties, and possible prebiotic effects for both gut and urinary tract microbiota. Our hope is that future investigators will consider these compounds as possible significant contributors to the observed biological effects of cranberry.
... During times of elevated estrogen, such as immediately prior to ovulation, Lactobacillus tends to stabilize, while during menstruation Lactobacillus tends to decrease (40). While menses appears to alter the composition of the vaginal microbiome, the change appears to depend on the initial CST and other factors, such as the use of pads or tampons (41). The above studies suggest the dynamic nature of the vaginal microbiome, questioning whether one can reliability predict microbiome between menstrual cycles. ...
Understanding what happens at the time of embryo implantation has been the subject of significant research. Investigators from many differing fields including maternal fetal medicine, microbiology, genetics, reproductive endocrinology and immunology have all been studying the moment the embryo interacts with the maternal endometrium. A perfect relationship between the uterus and the embryo, mediated by a tightly controlled interaction between the embryo and the endometrium, is required for successful implantation. Any factors affecting this communication, such as altered microbiome may lead to poor reproductive outcomes. Current theories suggest that altered microbiota may trigger an inflammatory response in the endometrium that affects the success of embryo implantation, as inflammatory mediators are tightly regulated during the adhesion of the blastocyst to the epithelial endometrial wall. In this review, we will highlight the various microbiome found during the periconceptual period, the microbiomes interaction with immunological responses surrounding the time of implantation, its effect on implantation, placentation and ultimately maternal and neonatal outcomes.
... These shifts were often transient and the VM usually reverted back to its original state within 1 week after menses. That menses alters the VM is well established [37][38][39][40][41][42][43] and it is thought that the drop in estrogen levels and the presence of menstrual blood may favor BV-associated bacteria such as G. vaginalis, but also L. iners. We did not observe an association between VM and having had sexual intercourse on the day of sampling. ...
Background:
Over-the-counter intra-vaginal lactic-acid containing douches are marketed as vaginal hygiene products that support optimal vaginal pH balance. We report the effect of a commercially available douche (Etos®) on the vaginal microbiota (VM) in a prospective study.
Results:
Twenty-five healthy women were recruited through advertisements in 2015-2017 (ethical approval: METC-2014_413) and followed over three menstrual cycles. The participants had a median age of 24 years [IQR: 22-29], were mostly Dutch-Caucasian (88%), and 60% used combined oral contraceptives. All participants douched three times a week during the second cycle, starting on the first day of that cycle. Participants completed a questionnaire at baseline, kept a daily diary to report douching, menses, and sexual activity, self-collected vaginal swabs every other day during the first and third cycle and daily during the second cycle, and measured vaginal pH mid-cycle. A median of 44 vaginal swabs [inter-quartile range (IQR): 41-50] were assessed per participant by 16S rRNA gene (V3-V4 region) sequencing and a Candida albicans PCR was done at four time-points. At baseline, 21 participants (84%) had Lactobacillus-dominated VM (Lactobacillus crispatus (n = 14), L. iners (n = 6), or diverse Lactobacillus species (n = 1) and 4 participants (16%) had VM consisting of diverse anaerobes. In multinomial logistic regression models, a trend towards increased odds were observed for having diverse anaerobic VM in the second and third cycle, compared to the first cycle, after adjusting for menses [odds ratio (OR) = 1.4 (95% CI: 0.9-2.1) and OR = 1.7 (95% CI: 0.9-3.1), respectively] (p = 0.376). Douching did not affect vaginal pH. Menses increased the odds for having VM consisting of diverse anaerobes almost two-fold (OR = 1.7; 95% CI: 1.0-2.8), while douching during menses increased the odds 2.6 fold (OR = 2.6; 95% CI: 1.0-6.5), compared to not menstruating (p = 0.099). Participants were more likely to test positive for C. albicans after cycle 2, compared to cycle 1 [OR = 3.0 (95% CI: 1.2-7.2); p = 0.017].
Conclusion:
The Etos® douche did not significantly affect the vaginal pH or VM composition, although increased odds for having diverse anaerobic VM was observed, especially when douching during menses. Furthermore, douching may promote C. albicans infections.
... tend to decrease in relative abundance (31), with the exception of L. iners (20). In general, molecular and culture-based methods are somewhat in agreement that menses significantly alters the composition of the vaginal microbiota (27,(32)(33)(34), but change appears to depend on the initial CST present, as well as other factors (20) such as the use of menstrual pads or tampons (20,35). Figure 1 shows the interplay of microbiome status throughout the menstrual cycle, (20). ...
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.
... However, consistent with previous studies assessing vaginal microbial diversity, we found that the tampon microbiota varied largely among healthy women and were, in a certain manner, specific to each woman 24,35,[54][55][56]58 . Most women (11/16) with differential carriage of S. aureus between two menses presented changes in the microbiota composition. ...
Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons' microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.
... Use of pantyliners during menstruation was also associated with L. jensenii, with the conditional probability of L. jensenii being present in the vaginal microbiome increasing from 37.4% to 60.7% with use of panty liners during menstruation. While the directionality of this relationship is not immediately intuitive, previous work has shown that use of emollient pads changes the vaginal epithelium and that some women's vaginal microflora does shift with pad versus tampon use [66,67], although the evidence on this is mixed [68]. NMDS/ANOSIM testing indicated that tampon use was associated with the vaginal microbiome, lending further support to the hypothesis that menstrual habits could impact the microbiome (S5 and S6 Files). ...
The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future studies of the vaginal microbiome and vaginal pathologies should include detailed surveys of participants’ sanitary, sexual and birth control habits, as these can act as confounders in the relationship between the microbiome and disease. Although the BN approach is powerful in revealing complex associations within multidimensional datasets, the need in some cases to discretize the data for use in BN analysis can result in loss of information. Future research is required to alleviate such limitations in constructing BN networks. Large sample sizes are also required in order to allow for the incorporation of a large number of variables (nodes) into the BN, particularly when studying associations between metadata and the microbiome. We believe that this approach is of great value, complementing other methods, to further our understanding of complex associations characteristic of microbiome research.
... The observed fluctuation throughout the menstrual cycle may be explained by evidence that high levels of E2 may favor a lactobacilli-dominant environment [53,60,61]. ...
Menstrual hygiene management is an important sacred aspect of women's life. The sanitary napkin is one of the major factors for proper menstrual hygiene but the proper education is not disseminated how to use, how long that can be used. The menstrual problems are not still under the umbrella of modern medicalization system in Bangladesh. Menstrual problems are treated by the popular sectors (female relatives and near and dear ones) who use their previous experience. During menstruation unhygienic practices makes female reproductive health more prone to infections. 25 residential female students of Jahangirnagar University aseptically performed a semi structured questionnaire and provided prolonged used sanitary pad. The microbial growth on the used sanitary pad provided the evidence of growth of E.coli and Staphylococcus aureus. The aim of the research is to determine harmful micro bacterial growth on the prolonged used sanitary pad and finding out the practice of the menstrual hygiene and sanitary pad use of university students.
Background
Miscarriage is one of the main causes of reproductive loss, which can lead to a number of physical and psychological complications and other long-term consequences. However, the role of vaginal and uterine microbiome in such complications is poorly understood.
The aim of the study
To review the published data on the function of the female reproductive tract microbiome in the pathogenesis of early miscarriages.
Materials and methods
The articles published over the past 20 years and deposited in Pubmed, Google Academy, Scopus, Elibrary, ResearchGate, and EBSCO databases were analyzed.
Results
The review presents new data on the impact of the vaginal and uterine microbiome on the local immunity, including defense against sexually transmitted infections, and its association with other factors of miscarriages. The studies on the microbiome of non-pregnant women with recurrent miscarriages in the anamnesis, patients undergoing IVF, and pregnant women with miscarriages, as well as new directions in the microbiome research are discussed.
Conclusion
The majority of studies have demonstrated that the dominant species of the vaginal and uterine microbiome in patients with early miscarriages are non-Lactobacillus bacteria. As many of these bacteria have not previously been detected by cultural studies and their role in obstetric complications is not well defined, further research on the female reproductive tract microbiome, including the microbiome of the cervix uteri, is needed to develop new approaches for the prognosis and prevention of miscarriages.
The microbial communities are an indispensable part of the human defense system and coexist with humans as symbionts, contributing to the metabolic functions and immune defense against pathogens. An ecologically stable vaginal microbiota is dominated by Lactobacillus species, which plays an important role in the prevention of genital infections by controlling the vaginal pH, reducing glycogen to lactic acid, and stimulating bacteriocins and hydrogen peroxide. In contrast, an abnormal vaginal microbial composition is associated with an increased risk of bacterial vaginosis, trichomoniasis, sexually transmitted diseases, preterm labor and other birth defects. This microbial diversity is affected by race, ethnicity, pregnancy, hormonal changes, sexual activities, hygiene practices and other conditions. In the present review, we discuss the changes in the microbial community of the vaginal region at different stages of a female's life cycle and its influence on her reproductive health and pathological conditions.
Relevance: The health status of desired children born after the successful use of assisted reproductive technologies (ART) remains one of the most discussed in modern medicine. Existing publications on the use of ART, including extensive registry studies and systematic reviews/meta-analyses, have conflicting data regarding the health status of children conceived through in-vitro fertilization compared to those conceived naturally.
Most studies are mainly devoted to short-term observations of the state of somatic or mental childrens’/offspring health after ART, while publications concerning long-term results are much less common.
The study aimed to analyze modern publications on physical and sexual development features, psychosocial status, endocrine system status, risks of cardiometabolic diseases, and conformational abnormalities of children conceived using ART.
Methods: This review includes an analysis of the currently available data on the childrens’/offspring health born after ART. The literature was searched in online databases, including Medline, Scopus, Web of Science, Google Scholar, Springer, PubMed, ResearchGate, and CyberLeninka. The search was carried out on all types of studies published in English and Russian, using the keywords: “assisted reproductive technologies (ART),” “in vitro fertilization (IVF),” “offspring,” “children,” “childrens’/offspring health,” “state of health,” “psychosocial health.”
Results: The literature data analysis revealed several studies on the possible impact of the state of health of their parents on the health of offspring in the cases when the parents decreased fertility is an indication for ART. Excluding such factors levels the probability of an adverse effect of ART on future children’s health.
Conclusion: Considering the active development of ART in Kazakhstan, a large cohort of children born after ART, and the lack of studies on their morbidity’s health status and structure, an active study of this problem in our country is required.
Keywords: assisted reproductive technologies (ART), in vitro fertilization (IVF), offspring, children, the children’s health, state of health, psychosocial health.
It has been widely reported that members of the genus Lactobacillus dominate the vaginal microbiota, which is represented by the most prevalent species Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Lactobacillus iners. L. crispatus is furthermore considered an important microbial biomarker due to its professed beneficial implications on vaginal health. In order to identify molecular mechanisms responsible for health-promoting activities that are believed to be elicited by L. crispatus, we performed in silico investigations of the intraspecies biodiversity of vaginal microbiomes followed by in vitro experiments involving various L. crispatus strains along with other vaginal Lactobacillus species mentioned above. Specifically, we assessed their antibacterial activities against a variety of pathogenic microorganisms that are associated with vaginal infections. Moreover, coculture experiments of L. crispatus strains showing the most antibacterial activity against different pathogens revealed distinct ecological fitness and competitive properties with regard to other microbial colonizers. Interestingly, we observed that even phylogenetically closely related L. crispatus strains possess unique features in terms of their antimicrobial activities and associated competitive abilities, which suggests that they exert marked competition and evolutionary pressure within their specific environmental niche.
Background
Body fluids are one of the common biological traces at crime scenes. Understanding the sources of these biological traces could provide key clues for the investigations of violence cases. In recent years, 16 S rRNA gene partial hypervariable region (V) sequencing and full-length 16 S rRNA gene sequencing (16 S rRNA gene V1-V9) have attracted the interest of researchers and we intend to explore which method can be better applied for forensic researches.
Methods
In this study, 16 S rRNA gene V3-V4 (short-read) sequencing based on next-generation sequencing technology and full-length 16 S rRNA gene sequencing based on Single Molecule Real-Time sequencing method were used to classify microbiomes in saliva, peripheral blood, vaginal secretion and menstrual blood samples.
Results
Alpha diversity metrics in short-read sequencing were larger than that of full-length sequencing. Phylum-level bacteria at four body fluids obtained from the two platforms were similar, while their abundances were different. The results of Principal Coordinates Analysis and Molecular Analysis of Variance indicated the microbial compositions of vaginal secretion and menstrual blood samples were similar, and the microbial compositions among saliva, peripheral blood and vaginal samples were significantly different. The Linear Discriminant Analysis Effect Size showed the differential bacteria screened among the four kinds of body fluid were variant in two sequencing results.
Conclusion
Both sequencing methods could be used to detect bacterial diversities in four body fluids and provide potential tools for microbes to identify body fluids in forensic investigations, in which full-length sequencing could provide more accurate taxonomy.
Data Availability Statement
The raw data of 16S rRNA gene V3-V4 sequencing and 16 S rRNA gene full-length sequencing in this study can be found in NCBI Sequence Read Archive under BioProject PRJNA722618.
Zusammenfassung
In der Vagina der gesunden prämenopausalen Frau wurden bisher 561 verschiedene Bakterien-Arten identifiziert, darunter > 30 von 261 bekannten Laktobazillus-Arten, von denen Lactobacillus (L.) crispatus, L. gasseri, L. jensenii und L. iners signifikant unterschiedlich je nach Ethnie und Individuum diverse Communitiy State Types (CST) mit unterschiedlichen pH-Werten dominieren. Die häufigsten Bakterien sind von den Stämmen (Phyla) Firmicutes (z. B. Lactobacillus oder Streptococcus), Proteobacteria (z. B. Escherichia oder Pseudomonas), Actinobacteria (z. B. Bifidobacterium) und Bacteroidetes, (z. B. Prevotella oder Bacteroides). Die wichtigsten Gattungen sind neben Laktobazillen Gardnerella (mit 4 Arten und 13 Subspezies), Atopobium, Prevotella, Streptococcus, Corynebacterium, Gemella, Dialister, Snethia, Megasphera, Mobiluncus, Ureaplasma, Mycoplasma u. a. In etwa 70 % werden auch Candida (C.)-Arten, meist C. albicans, gefunden. Tampons beeinflussen die vaginale Mikrobiota nicht wesentlich. Das menstruelle Toxic-Schock-Syndrom kommt mit und ohne Tampons und auch bei Menstruationstassen vor.
Im Rektosigmoid sind > 90 % Firmicutes und Bacteroidetes, von denen neben Laktobazillen viele Gattungen und Arten in Vagina und Rektum gemeinsam vorkommen können. Im Darm bilden diese Bakterien je nach (u. a.) „Lifestyle“ kurzkettige Fettsäuren, die elementare Bedeutung für die Eubiose, Hemmung von proinflammatorischen Zytokinen und die Gesundheit haben.
Die praktische und empfohlene Diagnostik gynäkologischer Infektionen und der sexuell übertragbaren Dysbiose Bakterielle Vaginose (BV) ist nicht die bakteriologische Kultur, sondern das Nativpräparat aus dem Fluor mit 400-facher Phasenkontrastmikroskopie. Die „klassischen“ sexuell übertragbaren Genitalinfektionen können heute mit Nuklearamplifikations-Techniken nicht-kulturell identifiziert werden. Die BV kann auch mit solchen Techniken anhand typischer Konstellationen von bestimmten Laktobazillen und typischen Anaerobiern zueinander diagnostiziert werden. Der häufige kulturelle Nachweis von z. B. G. vaginalis, Kolibakterien, Ureaplasmen, B-Streptokokken usw. ist klinisch ohne Wert und sollte unterlassen werden.
Objective:
The objective of this study was to evaluate the relationship between vaginal mesh exposure and vaginal bacterial community composition.
Methods:
Vaginal swab samples were collected from 13 women undergoing excision of vaginal mesh with vaginal mesh exposure. Samples were collected at the midvagina, site of exposure, and underneath the vaginal epithelium at the exposure. Control samples were collected vaginally during 15 new patient examinations. For all samples, we extracted genomic DNA and polymerase chain reaction amplified and sequenced the 16S rRNA gene V4 region. We tested for differences in the microbiota among control and exposure samples with PERMANOVA tests of beta diversity measures (Morisita-Horn dissimilarity) and Wilcoxon rank sum tests of Lactobacillus distribution.
Results:
Vaginal bacterial communities in both control and case groups were divided into 2 primary community types, one characterized by Lactobacillus dominance (>50% of community) and the other by low Lactobacillus and a high diversity of vaginal anaerobes. In 10 of 13 case women, bacterial communities were highly similar between the 3 vaginal sites (adonis R2 = 0.86, P = 0.0099). In the 3 women with community divergence, all 3 were characterized by decreased Lactobacillus abundance at the exposure site. Overall, Lactobacillus abundance was lower at the site of mesh exposure and under the epithelium than in the experimental control (W = 137, P = 0.072, r = 0.41; W = 146, P = 0.025, r = 0.50). Common putative pathogenic mesh colonizing bacteria were common (in 51 of 54 samples), but generally not abundant (median relative abundance = 0.014%).
Conclusions:
In vaginal mesh exposure cases, a woman is more likely to have a diverse, non-Lactobacillus-dominant community.
The perception of menstruation is currently changing—it is no longer viewed as an imposition, but rather increasingly as a symbol of female potency. Outdated tabus are questioned by young women, not rarely provocatively, and menstrual hygiene products are displayed on brightly lit supermarket shelves. This change in menstruationʼs image should be actively encouraged by gynecologists, who should see consultations for menstrual complaints—the most frequent reason for young girls seeking a consultation—as a valuable opportunity to inform patients about the fascinating processes in the female body in the sense of primary prevention. Moreover, gynecologists should have substantiated scientific knowhow regarding the sometimes-confusing information of competitors in the hygiene industry regarding the correct use and alleged infection-promoting attributes of their products.
Objective
To determine whether prophylactic azithromycin associates with the vaginal bacterial microbiome and clinical outcomes in subfertile women undergoing in vitro fertilization (IVF).
Design
Prospective exploratory cohort study
Setting
Single academic fertility center
Patients
Subfertile women age 18-43 undergoing their first IVF cycle and fresh embryo transfer
Intervention
Primary exposure was prophylactic azithromycin 1-gram oral once at baseline
Main outcome Measures
The primary outcome was examining the effect of azithromycin on the vaginal microbiome between two groups at three timepoints throughout the IVF cycle (baseline, retrieval and embryo transfer). Secondary outcomes were associations of vaginal bacterial communities with clinical outcomes.
Results
A planned a prior exploratory cohort of 27 subjects (12 in the azithromycin treatment group; 15 in the control group) contributed 79 vaginal swabs for analysis as part of an ongoing randomized controlled non-inferiority trial. No specific taxa associated with azithromycin or pregnancy at any time point. Azithromycin did not affect alpha diversity or community stability. Although there were trends toward lower bacterial load and higher percentage Lactobacilli in the azithromycin group at transfer, these were not statistically significant. In women who did not become pregnant, the percentage Lactobacilli was lower (P=0.048; HL 0.41; 95% CI 0.08 to 0.65) and change in community composition over time trended higher. The percent Lactobacilli at baseline was not predictive of percent Lactobacilli at time of embryo transfer.
Conclusion
Prophylactic azithromycin at baseline does not associate with changes in vaginal bacterial communities. Bacterial community features at the time of embryo transfer associated with pregnancy. Bacterial community structures at baseline were not predictive of those at the time of embryo transfer.
Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
In the 1980s, menstrual toxic shock syndrome (mTSS) became a household topic, particularly among mothers and their daughters. The research performed at the time, and for the first time, exposed the American public as well as the biomedical community, in a major way, to understanding disease progression and investigation. Those studies led to the identification of the cause, Staphylococcus aureus and the pyrogenic toxin superantigen TSS toxin 1 (TSST-1), and many of the risk factors, for example, tampon use. Those studies in turn led to TSS warning labels on the outside and inside of tampon boxes and, as important, uniform standards worldwide of tampon absorbency labeling. This review addresses our understanding of the development and conclusions related to mTSS and risk factors. We leave the final message that even though mTSS is not commonly in the news today, cases continue to occur. Additionally, S. aureus strains cycle in human populations in roughly 10-year intervals, possibly dependent on immune status. TSST-1-producing S. aureus bacteria appear to be reemerging, suggesting that physician awareness of this emergence and mTSS history should be heightened.
Following the discovery of the collective human urinary microbiota, important knowledge gaps remain, including the stability and variability of this microbial niche over time. Initial urinary studies preferentially utilized samples obtained by transurethral catheterization to minimize contributions from vulvovaginal microbes. However, catheterization has the potential to alter the urinary microbiota; therefore, voided specimens are preferred for longitudinal studies. In this report, we describe microbial findings obtained by daily assessment over 3 months in a small cohort of adult women. We found that, similarly to vaginal microbiotas, lower urinary tract (LUT) microbiotas are dynamic, with changes relating to several factors, particularly menstruation and vaginal intercourse. Our study results show that LUT microbiotas are both dynamic and resilient. They also offer novel opportunities to target LUT microbiotas by preventative or therapeutic means, through risk and/or protective factor modification.
The vaginal microbiota has importance in preserving vaginal health and defending the host against disease. The advent of new molecular techniques and computer science has allowed researchers to discover microbial composition in depth and associate the structure of vaginal microbial communities. There is a consensus that vaginal flora is grouped into a restricted number of communities, although the structure of the community is constantly changing. Certain Community-Sate Types (CSTs) are more associated with poor reproductive outcomes and sexually transmitted diseases (STDs) meanwhile, CSTs dominated by Lactobacillus species-particularly Lactobacillus crispatus-are more related to vaginal health. In this work, we have reviewed how modifiable and non-modifiable factors may affect normal vaginal microbiota homeostasis-including sexual behavior, race or ethnicity, and hygiene. Special interest has been given to how the use of probiotics, diet intake, and use of hormone replacement therapies (HRTs) can potentially impact vaginal microbiota composition.
An intrepid group of eight passionate herbalists had the ultimate Sri Lankan herbal medicine immersion experience in March 2018, where they witnessed traditional herbal medicine in action in the 21st century. The majority of the excursion was set in an enchanted sanctuary of exceptional beauty in Sri Lanka’s heartland. The tour included Ayurvedic healing practices taking place in a traditional working village, including soothing massages and oil applications, medicated steam baths, herbal saunas, medicine making classes with an acclaimed Ayurveda practitioner, a visit to the oldest planted tree in the world in the ancient city of Anuradhapura, a personal tour of a working Ayurveda hospital and manufacturing facility, but mostly just surrendering to Mother Nature herself.
Background
Several studies have focused on the microbiota living in environmental niches including human body sites. In many of these studies researchers collect longitudinal data with the goal of understanding not just the composition of the microbiome but also the interactions between the different taxa. However, analysis of such data is challenging and very few methods have been developed to reconstruct dynamic models from time series microbiome data.
Results
Here we present a computational pipeline that enables the integration of data across individuals for the reconstruction of such models. Our pipeline starts by aligning the data collected for all individuals. The aligned profiles are then used to learn a dynamic Bayesian network which represents causal relationships between taxa and clinical variables. Testing our methods on three longitudinal microbiome data sets we show that our pipeline improve upon prior methods developed for this task. We also discuss the biological insights provided by the models which include several known and novel interactions.
Conclusions
We propose a computational pipeline for analyzing longitudinal microbiome data. Our results provide evidence that microbiome alignments coupled with dynamic Bayesian networks improve predictive performance over previous methods and enhance our ability to infer biological relationships within the microbiome and between taxa and clinical factors.
Eine bakterielle Vaginose kann das Risiko für gynäkologische Infektionen oder geburtshilfliche Komplikationen deutlich steigern. Die hohe Rezidivquote lässt sich durch den bakteriellen Biofilm erklären, der einer leitliniengerechten Therapie bislang nicht zugänglich ist. Bei Rezidiven könnte eine Prophylaxe mit Probiotika sinnvoll sein.
Die bakterielle Vaginose (BV) ist durch Ersatz von Laktobazillen und Zunahme von BV-assoziierten, Biofilm-bildenden Bakterien und veränderte Eigenschaften der Vaginalflüssigkeit charakterisiert. Die polybakteriellen Biofilme widerstehen den empfohlenen Antibiotika und erklären Rezidive in über 50 % der Fälle.Eine BV erhöht die Gefahr von Fehl‑, Spät- und Frühgeburten. Die antibiotische Therapie führt nur zur signifikanten Reduktion, wenn im ersten Trimenon oral Clindamycin gegeben wurde (off-label). Laktobazillen reduzieren die Rückfallquote, besonders wenn sie oral genommen wurden. Die (Vulvo‑)Vaginalcandidose (VVC) kommt unter Östrogeneinfluss bei lokaler oder allgemeiner Immunsuppression vor. Die vaginale Candidabesiedlung erhöht das Frühgeburtsrisiko. Die chronisch rezidivierende Vulvovaginalcandidose (CRVVC) kann zurzeit nur mit Fluconazol unterdrückt werden. Einige Studien zeigen, dass vaginal applizierte Laktobazillen im Anschluss an eine leitliniengerechte Therapie die Rezidivquote reduzieren können.
Die (Vulvo-)Vaginalkandidose kann unter Östrogeneinfluss bei lokaler oder allgemeiner Immunsuppression auftreten. Bei etwa 30–50 % der prämenopausalen Frauen finden sich vaginal Candidaarten. Die genitale Kolonisation bei Schwangeren erhöht die Gefahr von Frühgeburten. Neugeborene, die bei der vaginalen Geburt mit Candida in Kontakt kommen, entwickeln häufig Mundsoor und Windeldermatitis. Die Therapie der akuten Form besteht in der Applikation von marktüblichen Antimykotika. Als prophylaktische Maßnahme können sich Laktobazillen eignen und auch eine Immunisierung wird erforscht.
Therapeutic Opportunities in the Vaginal Microbiome, Page 1 of 2
Abstract
The reproductive tract of females lies at the core of humanity. The immensely complex process that leads to successful reproduction is miraculous yet invariably successful. Microorganisms have always been a cause for concern for their ability to infect this region, yet it is other, nonpathogenic microbial constituents now uncovered by sequencing technologies that offer hope for improving health. The universality of Lactobacillus species being associated with health is the basis for therapeutic opportunities, including through engineered strains. The manipulation of these and other beneficial constituents of the microbiota and their functionality, as well as their metabolites, forms the basis for new diagnostics and interventions. Within 20 years, we should see significant improvements in how cervicovaginal health is restored and maintained, thus providing relief to the countless women who suffer from microbiota-associated disorders.
The vegan package (available from: https://cran.r-project.org/package=vegan) provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.
The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package https://CRAN.R-project.org/package=BiodiversityR provides a Graphical User Interface (GUI) for a large subset of vegan functionality.
The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports. Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package. To see the preferable citation of the package, type citation("vegan").
We describe existing models of the relationship between species diversity and ecological function, and propose a conceptual
model that relates species richness, ecological resilience, and scale. We suggest that species interact with scale-dependent
sets of ecological structures and processes that determine functional opportunities. We propose that ecological resilience
is generated by diverse, but overlapping, function within a scale and by apparently redundant species that operate at different
scales, thereby reinforcing function across scales. The distribution of functional diversity within and across scales enables
regeneration and renewal to occur following ecological disruption over a wide range of scales.
This paper examines how to obtain species biplots in unconstrained or constrained ordination without resorting to the Euclidean distance [used in principal-component analysis (PCA) and redundancy analysis (RDA)] or the chi-square distance [preserved in correspondence analysis (CA) and canonical correspondence analysis (CCA)] which are not always appropriate for the analysis of community composition data. To achieve this goal, transformations are proposed for species data tables. They allow ecologists to use ordination methods such as PCA and RDA, which are Euclidean-based, for the analysis of community data, while circumventing the problems associated with the Euclidean distance, and avoiding CA and CCA which present problems of their own in some cases. This allows the use of the original (transformed) species data in RDA carried out to test for relationships with explanatory variables (i.e. environmental variables, or factors of a multifactorial analysis-of-variance model); ecologists can then draw biplots displaying the relationships of the species to the explanatory variables. Another application allows the use of species data in other methods of multivariate data analysis which optimize a least-squares loss function; an example is K-means partitioning.
The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses – the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferroni-type procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.
The means by which vaginal microbiomes help prevent urogenital diseases in women and maintain health are poorly understood. To gain insight into this, the vaginal bacterial communities of 396 asymptomatic North American women who represented four ethnic groups (white, black, Hispanic, and Asian) were sampled and the species composition characterized by pyrosequencing of barcoded 16S rRNA genes. The communities clustered into five groups: four were dominated by Lactobacillus iners, L. crispatus, L. gasseri, or L. jensenii, whereas the fifth had lower proportions of lactic acid bacteria and higher proportions of strictly anaerobic organisms, indicating that a potential key ecological function, the production of lactic acid, seems to be conserved in all communities. The proportions of each community group varied among the four ethnic groups, and these differences were statistically significant [χ(2)(10) = 36.8, P < 0.0001]. Moreover, the vaginal pH of women in different ethnic groups also differed and was higher in Hispanic (pH 5.0 ± 0.59) and black (pH 4.7 ± 1.04) women as compared with Asian (pH 4.4 ± 0.59) and white (pH 4.2 ± 0.3) women. Phylotypes with correlated relative abundances were found in all communities, and these patterns were associated with either high or low Nugent scores, which are used as a factor for the diagnosis of bacterial vaginosis. The inherent differences within and between women in different ethnic groups strongly argues for a more refined definition of the kinds of bacterial communities normally found in healthy women and the need to appreciate differences between individuals so they can be taken into account in risk assessment and disease diagnosis.
This study compared the safety of a new tampon with a four-winged apertured film cover over its nonwoven cover to improve
leakage performance with that of a commercial tampon with a nonwoven cover only. Healthy women (evaluable, n = 69) were randomized to crossover between test and reference tampons in two consecutive menstrual cycles. Qualitative and
quantitative analyses of vaginal cultures were conducted pre-, mid-, and postmenstrually for a broad panel of microorganisms,
and colposcopy was performed. Similar to previous studies, prevalence and mean colony counts of the majority of microorganisms
generally increased midmenstrually and returned or began to return postmenstrually. In contrast to most previous studies,
Lactobacillus species remained at similar levels throughout the cycles with both tampons. Neither tampon was associated with clinically
significant microbiological changes or abnormalities or with vaginal/cervical epithelial integrity changes on colposcopy.
Microbiological and colposcopic evaluations indicate that the apertured film-covered tampon is safe.
Perinatally, and between menarche and menopause, increased levels of estrogen cause large amounts of glycogen to be deposited in the vaginal epithelium. During these times, the anaerobic metabolism of the glycogen, by the epithelial cells themselves and/or by vaginal flora, causes the vagina to become acidic (pH approximately 4). This study was designed to test whether the characteristics of acid production by vaginal flora in vitro can account for vaginal acidity. Eight vaginal Lactobacillus isolates from four species-L. gasseri, L. vaginalis, L. crispatus, and L. jensenii-acidified their growth medium to an asymptotic pH (3.2 to 4.8) that matches the range seen in the Lactobacillus-dominated human vagina (pH 3.6 to 4.5 in most women) (B. Andersch, L. Forssman, K. Lincoln, and P. Torstensson, Gynecol. Obstet. Investig. 21:19-25, 1986; L. Cohen, Br. J. Vener. Dis. 45:241-246, 1969; J. Paavonen, Scand. J. Infect. Dis. Suppl. 40:31-35, 1983; C. Tevi-Bénissan, L. Bélec, M. Lévy, V. Schneider-Fauveau, A. Si Mohamed, M.-C. Hallouin, M. Matta, and G. Grésenguet, Clin. Diagn. Lab. Immunol. 4:367-374, 1997). During exponential growth, all of these Lactobacillus species acidified their growth medium at rates on the order of 10(6) protons/bacterium/s. Such rates, combined with an estimate of the total number of lactobacilli in the vagina, suggest that vaginal lactobacilli could reacidify the vagina at the rate observed postcoitally following neutralization by the male ejaculate (W. H. Masters and V. E. Johnson, Human sexual response, p. 93, 1966). During bacterial vaginosis (BV), there is a loss of vaginal acidity, and the vaginal pH rises to >4.5. This correlates with a loss of lactobacilli and an overgrowth of diverse bacteria. Three BV-associated bacteria, Gardnerella vaginalis, Prevotella bivia, and Peptostreptococcus anaerobius, acidified their growth medium to an asymptotic pH (4.7 to 6.0) consistent with the characteristic elevated vaginal pH associated with BV. Together, these observations are consistent with vaginal flora, rather than epithelial cells, playing a primary role in creating the acidity of the vagina.
The objective of this study was to examine genital tissue, vaginal fluid, and vaginal microbial flora at 3 phases of the menstrual
cycle in asymptomatic women. Vaginal examinations were performed 3 times in 74 women: at the menstrual phase (days 1–5), the
preovulatory phase (days 7–12), and the postovulatory phase (days 19–24). Flora of 50 women without bacterial vaginosis (BV)
was analyzed separately from flora of 24 women with BV. The volume of vaginal discharge increased and the amount of cervical
mucus decreased over the menstrual cycle. Among subjects without BV, the rate of recovery of any Lactobacillus changed little (range, 82% to 98%; P = .2); however, a small increase occurred in the rate of recovery of heavy (3+ to 4+ semiquantitative) growth of Lactobacillus over the menstrual cycle (P = .04). A linear decrease occurred in the rate of recovery of heavy growth of any non-Lactobacillus species, from 72% at days 1–5 to 40% at days 19–24 (P = .002). A linear decrease also occurred in the rate of recovery of Prevotella species, from 56% on days 1–5 to 28% on days 19–24 (P = .007), while a small linear increase occurred in the rate of recovery of Bacteroides fragilis (P = .05). Among subjects with BV, the only significant change was an increase in the rate of recovery of Lactobacillus, from 33% at days 1–5 to 54% at days 19–24 (P = .008). Among all subjects, the rate of recovery of heavy growth of Lactobacillus increased over the menstrual cycle and, in contrast, the concentration of non-Lactobacillus species tended to be higher at menses, which is evidence that the vaginal flora becomes less stable at this time.
Species of the Lactobacillus acidophilus complex are generally considered to constitute most of the vaginal Lactobacillus flora, but the flora varies between studies. However, this may be due to difficulties in identifying the closely related
species within the L. acidophilus complex by using traditional methods and to variations in the vaginal status of the participants. Two hundred two isolates
from the vaginal fluids of 23 Swedish women without bacterial vaginosis, as defined by the criteria of Nugent et al. (R. P.
Nugent, M. A. Krohn, and S. L. Hillier, J. Clin. Microbiol. 29:297-301, 1991), were typed by randomly amplified polymorphic
DNA (RAPD) analysis and identified to the species level by temporal temperature gradient gel electrophoresis, multiplex PCR,
and 16S ribosomal DNA sequencing. The vaginal flora of most participants was dominated by a single RAPD type, but five of
them harbored two RAPD types representing two different species or strains. The most frequently occurring species were Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii. L. iners has not previously been reported as one of the predominant Lactobacillus species in the vagina.
To confirm the safety of a new experimental Tampax tampon and applicator compared with that of a currently marketed Tampax tampon and applicator using comprehensive gynecological and microbiological assessments.
A 2-month, single-blind, randomized, crossover study was conducted in which each subject served as her own control. Safety was evaluated by comparing potential product-related irritation (using colposcopic examination and subject diary data), assessment of vaginal discharge, vaginal pH, and effects on selected microorganisms (yeast, Escherichia coli, Staphylococcus aureus and group B streptococci) obtained by vaginal swab cultures after normal menstrual use in the experimental and control groups.
In total, 110 women completed the study. There were no significant differences between the groups that used either the experimental or control tampon with regard to prevalence or mean cell density for the selected microorganisms. No differences were observed in the incidence or severity of erythema, in abrasion or ulceration of the cervix, vagina, introitus, vulva or perineum, or in mean vaginal pH and discharge assessments. There were equivalent low incidences of reported symptoms such as discomfort during insertion, wear or removal, and a similar low incidence of burning, stinging or itching during use of either the control or experimental tampon. There was a more favorable overall product rating for the experimental tampon (p = 0.003).
This approach provides a combination of gynecological, microbiological and self-reported (diary recall) methodologies in order to assess tampon safety during use more thoroughly than has previously been reported, and it supports a comparable safety profile for the experimental tampon and a currently marketed tampon.
Using solely a gene-based procedure, PCR amplification of the 16S ribosomal RNA gene coupled with very deep sequencing of the amplified products, the microbes on 20 human vaginal epithelia of healthy women have been identified and quantitated. The Lactobacillus content on these 20 healthy vaginal epithelia was highly variable, ranging from 0% to 100%. For four subjects, Lactobacillus was (virtually) the only bacterium detected. However, that Lactobacillus was far from clonal and was a mixture of species and strains. Eight subjects presented complex mixtures of Lactobacillus and other microbes. The remaining eight subjects had no Lactobacillus. Instead, Bifidobacterium, Gardnerella, Prevotella, Pseudomonas, or Streptococcus predominated.
To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting amplicons made using bacterial primers 8f and 926r with HaeIII; fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, samples from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of Lactobacillus. In contrast, the communities of two other women included numerically abundant populations that differed from Lactobacillus strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of samples from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present.
Healthy women with normal menstrual cycles were randomly assigned to use either a test tampon during cycle 1 and a reference tampon during cycle 2 or a reference tampon during cycle 1 and a test tampon during cycle 2. Tampons were identical except for their cover materials: apertured film for the test tampon and nonwoven fleece for the reference tampon. Product use was doubly blinded. Qualitative and quantitative analyses of vaginal cultures were done pre-, mid-, and postmenstrually for a broad panel of microorganisms, colposcopy was performed, and diary reports were collected; 101 of 105 enrolled subjects completed the study. Midmenstrual findings for a variety of organisms differed from pre- and postmenstrual observations whether subjects were using test or reference tampons. No statistically significant differences were noted in prevalence or colony counts at premenstrual versus mid- and postmenstrual visits for most microorganisms. Prevalences of Gardnerella and anaerobic gram-negative rods were significantly different between tampons at the premenstrual visit, when unusually low values were observed for the test and reference tampons, respectively. None of the changes or differences in microflora were considered to be clinically significant. It is noteworthy, however, that declines in the prevalence and abundance of Lactobacillus during the menstrual periods were less pronounced during the use of both test and reference tampons than those reported from previous studies. Colposcopy showed no abnormal findings with either tampon and no changes in vaginal or cervical epithelial integrity. Thus, all evidence from both microbiological and colposcopic evaluations indicates that the apertured film cover of the test tampon is as safe as the nonwoven cover of the reference tampon.
The maintenance of a low pH in the vagina through the microbial production of lactic acid is known to be an important defense against infectious disease in reproductive age women. Previous studies have shown that this is largely accomplished through the metabolism of lactic acid bacteria, primarily species of Lactobacillus. Despite the importance of this defense mechanism to women's health, differences in the species composition of vaginal bacterial communities among women have not been well defined, nor is it known if and how these differences might be linked to differences in the risk of infection. In this study, we defined and compared the species composition of vaginal bacterial communities in 144 Caucasian and black women in North America. This was carried out based on the profiles of terminal restriction fragments of 16S rRNA genes, and phylogenetic analysis of 16S rRNA gene sequences of the numerically dominant microbial populations. Among all the women sampled, there were eight major kinds of vaginal communities ('supergroups') that occurred in the general populace at a frequency of at least 0.05 (P=0.99). From the distribution of these supergroups among women, it was possible to draw several conclusions. First, there were striking, statistically significant differences (P=0.0) in the rank abundance of community types among women in these racial groups. Second, the incidence of vaginal communities in which lactobacilli were not dominant was higher in black women (33%) as compared to Caucasian women (7%). Communities not dominated by lactobacilli had Atopobium and a diverse array of phylotypes from the order Clostridiales. Third, communities dominated by roughly equal numbers of more than one species of Lactobacillus were rare in black women, but common in Caucasian women. We postulate that because of these differences in composition, not all vaginal communities are equally resilient, and that differences in the vaginal microbiota of Caucasian and black women may at least partly account for known disparities in the susceptibility of women in these racial groups to bacterial vaginosis and sexually transmitted diseases.
The effect of vaginal tampons on the microbial flora during menstruation has recently been studied by several investigators. However, little information regarding the qualitative effects attributable to particular tampon fibers is available. The purpose of the present study was to compare the effects of polyacrylate rayon tampons and cotton-viscose rayon blend tampons on the qualitative bacterial counts obtained from tampons and concomitant vaginal swabs and to determine whether either of these tampon types alters the qualitative makeup of the vaginal microflora when compared with the microflora in the same women using all-cotton tampons or external catamenial pads. Tampon and swab samples were obtained as described previously (A. B. Onderdonk, G. R. Zamarchi, M. L. Rodriguez, M. L. Hirsch, A. Muñoz, and E. H. Kass, Appl. Environ. Microbiol. 53:2774-2778). The genus and species of the six dominant bacterial species in each sample were identified, if possible. A statistical evaluation of the qualitative makeup of the microflora revealed that the same numerically dominant phenotypes were present regardless of sample type, sample time, or catamenial product. Predictable changes in total numbers among the dominant species were also noted when the data were evaluated by day of menstrual cycle. The correlation between the total numbers of each dominant species present was evaluated by day of cycle, and the findings are discussed.
The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses — the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferronitype procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.
Perinatally, and between menarche and menopause, increased levels of estrogen cause large amounts of glycogen to be deposited in the vaginal epithelium. During these times, the anaerobic metabolism of the glycogen, by the epithelial cells themselves and/or by vaginal flora, causes the vagina to become acidic (pH similar to 4). This study was designed to test whether the characteristics of acid production by vaginal flora in vitro can account for vaginal acidity. Eight vaginal Lactobacillus isolates from four species-L. gasseri, L. vaginalis, L. crispatus, and L. jensenii-acidified their growth medium to an asymptotic pH (3.2 to 4.8) that matches the range seen in the Lactobacillus-dominated human vagina (pH 3.6 to 4.5 in most women) (B. Andersch, L. Forssman, K, Lincoln, and P. Torstensson, Gynecol. Obstet. Investig. 21:19-25, 1986; L. Cohen, Br. J. Vener. Dis. 45:241-246, 1969; J. Paavonen, Scand. J. Infect. Dis. Suppl. 40:31-35, 1983; C. Tevi-Benissan, L. Belec, M. Levy V. Schneider-Fauveau, A. Si Mohamed, M.-C. Hallouin, M. Matta, and G. Gresenguet, Clin. Diagn. Lab. Immunol. 4:367-374, 1997). During exponential growth, all of these Lactobacillus species acidified their growth medium at rates on the order of 10(6) protons/bacterium/s. Such rates, combined with an estimate of the total number of lactobacilli in the vagina, suggest that vaginal lactobacilli could reacidify the vagina at the rate observed postcoitally following neutralization by the male ejaculate (W. H. Masters and V. E. Johnson, Human sexual response, p. 93, 1966). During bacterial vaginosis (BV), there is a loss of vaginal acidity, and the vaginal pH rises to >4.5. This correlates with a loss of lactobacilli and an overgrowth of diverse bacteria. Three BV-associated bacteria, Gardnerella vaginalis, Prevotella bivia, and Peptostreptococcus anaerobius, acidified their growth medium to an asymptotic pH (4.7 to 6.0) consistent with the characteristic elevated vaginal pH associated with BV. Together, these observations are consistent with vaginal Bore, rather than epithelial cells, playing a primary role in creating the acidity of the vagina.
Bell System Technical Journal, also pp. 623-656 (October)
Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk of diseases that affect women's health. Here, we describe the temporal dynamics of the composition of vaginal bacterial communities in 32 reproductive-age women over a 16-week period. The analysis revealed the dynamics of five major classes of bacterial communities and showed that some communities change markedly over short time periods, whereas others are relatively stable. Modeling community stability using new quantitative measures indicates that deviation from stability correlates with time in the menstrual cycle, bacterial community composition, and sexual activity. The women studied are healthy; thus, it appears that neither variation in community composition per se nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis.
A procedure for forming hierarchical groups of mutually exclusive subsets, each of which has members that are maximally similar with respect to specified characteristics, is suggested for use in large-scale (n > 100) studies when a precise optimal solution for a specified number of groups is not practical. Given n sets, this procedure permits their reduction to n − 1 mutually exclusive sets by considering the union of all possible n(n − 1)/2 pairs and selecting a union having a maximal value for the functional relation, or objective function, that reflects the criterion chosen by the investigator. By repeating this process until only one group remains, the complete hierarchical structure and a quantitative estimate of the loss associated with each stage in the grouping can be obtained. A general flowchart helpful in computer programming and a numerical example are included.
This paper examines how to obtain species biplots in unconstrained or constrained ordination without resorting to the Euclidean distance[used in principal-components-analysis(PCA), and redundancy analysis(RDA), or the chi-square distance[preserved in correspondence analysis(CA) and canonical correspondence analysis(CCA)] which are not always appropriate for the analysis of community composition data. To achieve this goal, transformations are proposed for species data tables. They allow ecologists to use ordination methods such as PCA and RDA, which are Euclidean-based, for the analysis of community data, while circumventing the problems associated with Euclidean distance, and avoiding CA and CCA which can present problems of their own in some cases. This allows the use of the original (transformed) species data in RDA carried out to test for relationships with explanatory variables(i.e. environmental variables, or factors of a multi-factorial analysis-of-variance model); ecologists can then draw biplots displaying the relationships of the species to the explanatory variables. Another application allows the use of species data in other methods of multi-variate data analysis which optimise a least-squares loss function; an example is K-means partitioning.
To determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy Japanese women in Tokyo, Japan, and compared them with those of White and Black women from North America. The composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences of the numerically dominant bacterial populations. The types of vaginal communities found in Japanese women were similar to those of Black and White women. As with White and Black women, most vaginal communities were dominated by lactobacilli, and only four species of Lactobacillus (Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus gasseri) were commonly found. Communities dominated by multiple species of lactobacilli were common in Japanese and White women, but rare in Black women. The incidence, in Japanese women, of vaginal communities with several non-Lactobacillus species at moderately high frequencies was intermediate between Black women and White women. The limited number of community types found among women in different ethnic groups suggests that host genetic factors, including the innate and adaptive immune systems, may be more important in determining the species composition of vaginal bacterial communities than are cultural and behavioral differences.
Quantitative bacteriology was performed on vaginal secretions from healthy adult women. The analysis included a single sample
from 17 college students and 35 samples from five volunteers collected at intervals of three to five days throughout the menstrual
cycle. Mean concentrations in all 52 specimens were 108.1 aerobic bacteria/ g and 109.1 anaerobic bacteria/g. The rank of predominant organisms, according to rates of recovery in concentrations of > 105 colony-forming units/g, was anaerobic and facultative Lactobacillus species, Peptococcus species, Bacteroides species, Staphylococcus epidermidis, Corynebacterium species, Peptostreptococcus species, and Eubacterium species. Sequential samples collected throughout the menstrual cycle showed relatively consistent mean levels of anaerobes
and a significant decrease in concentrations of aerobes in premenstrual specimens compared with those in the specimens collected
in the week following onset of menses. Analysis of sequential specimens from each of the five individuals showed considerable
variation in species recovered. These data indicate that the vaginal flora in healthy adult women is a dynamic ecosystem in
which anaerobes are usually the numerically dominant bacteria.
The effect of tampon usage on the vaginal microflora of 35 healthy women was determined following their random allocation
to either tampon or napkin use for three consecutive menstrual cycles. Sequential and semiquantitative vaginal cultures were
obtained on days 3 ± 2, 15 ± 2, and 25 ± 2 of the menstrual cycle (day 1, first day of menses) before and after randomization.
Before randomization, the rate of isolation and median counts of facultative lactobacilli were significantly higher (P<.05) and that of eubacteria was significantly lower (P = .026) among regular tampon users than among exclusive napkin users. After randomization, only median counts of coagulase-negative
staphylococci were significantly increased (P = .025) during tampon use compared with the rates for the same women during napkin use. These shifts in vaginal microflora
occurred only in samples obtained during menstruation and not in those obtained at other sampling times. The data presented
here support the notion that the use of tampons may result in alterations in the autochthonous vaginal microflora. It remains
to be determined if these ecologic shifts in the vaginal microflora may adversely affect resistance to colonization by potential
pathogens in the lower female genital tract.
Although the effect of vaginal tampons on the microbial flora during menstruation has recently been studied by several investigators, quantitative effects attributable to particular tampon fibers have received less attention. The purposes of the present study were (i) to determine and then to compare the effects of polyacrylate rayon tampons and viscose rayon tampons on the normal vaginal flora, (ii) to compare quantitative bacterial counts obtained from these tampons with those obtained from concomitant vaginal swabs, and (iii) to determine whether either of these tampon types alters the vaginal microflora when compared with the microflora in the same women using all-cotton tampons or external catamenial pads. Tampon and swab samples were obtained at predetermined times from 18 women for an average of seven menstrual cycles. Samples consisting of swabs from women wearing menstrual pads were compared with swab and tampon samples taken at predetermined times during the menstrual cycle from women using cotton, polyacrylate rayon, or viscose rayon tampons. Samples were analyzed for total aerobic, facultative, and anaerobic bacterial counts. Statistical evaluation of the results indicated that, on the whole, total bacterial counts decreased during menstruation and that the numbers of bacteria in tampons tended to be lower than those in swab samples taken at the same time. The tampon type had little effect on the vaginal microflora.
The vaginal bacteriology of 10 healthy asymptomatic women was assessed during the menstrual cycle. Samples were taken from the posterior vaginal fornix for quantitative analysis. There were no significant alterations in the total vaginal flora at different stages of the menstrual cycle. The mean number of species isolated per specimen declined from 4.6 in week 1 to 2.9 in week 4. This decline was not caused by a decrease in the occurrence or concentration of any one organism or group of organisms. The vaginal pH decreased from a mean of 6.6 in week 1 to 4.3 in week 4, this increased acidity could not be attributed to the action of lactobacilli as their total incidence or concentration did not change during the menstrual cycle.
The quantitative and qualitative changes in the bacterial flora of the vagina during menstruation have received inadequate study. Similarly, the effect of vaginal tampons on the microbial flora as well as the relationship between the microbial flora of the vagina and that of the tampon has not been adequately evaluated. The purposes of the present study were (i) to develop quantitative methods for studying the vaginal flora and the flora of tampons obtained during menstruation and (ii) to determine whether there were differences between the microflora of the tampon and that of the vaginal vault. Tampon and swab samples were obtained at various times from eight young healthy volunteers for 8 to 10 menstrual cycles. Samples consisted of swabs from women wearing menstrual pads compared with swab and tampon samples taken at various times during the menstrual cycle. Samples were analyzed for total facultative and anaerobic bacterial counts, and the six dominant bacterial species in each culture were identified. Statistical evaluation of the results indicates that total bacterial counts decreased during menstruation and that swab and tampon samples yielded similar total counts per unit weight of sample. The numbers of bacteria in tampons tended to be lower than in swabs taken at the same time. Overall, during menstruation, the concentrations of lactobacilli declined, but otherwise there was little difference among the species found during menstruation compared with those found in intermenstrual samples. Cotton tampons had little discernible effect on the microbial flora.