1,720,988 research outputs found
Host and Bacterial Functions in Bacterial Vaginosis Elucidated by Metaproteomics
Full text linkThesis (Ph.D.)--University of Washington, 2023Bacterial vaginosis (BV) is a highly prevalent dysbiosis of the vaginal microbiota which causes a variety of unpleasant symptoms and places patients at higher risk of adverse sequelae. BV is a complex condition, and many of the host and bacterial functions which contribute to its development and recurrence are unknown. This dissertation describes an optimized metaproteomic analysis of cervicovaginal lavage samples from women with and without BV to identify host and bacterial proteins that may contribute to BV. Using this approach, we uncovered new potential synergistic interactions between BV-associated bacteria (BVAB) based on glutamate and identified a possible host response to increased concentrations of free heme in BV. We also demonstrated a novel syntrophic interaction between Dialister micraerophilus and Fannyhessea vaginae to increase putrescine biosynthesis, likely through cross-feeding of the arginine metabolite ornithine. Despite past reports that human amylase is primarily responsible for breaking down vaginal glycogen into fermentable carbohydrates, we identified glycogen-degrading enzymes from L. crispatus and G. vaginalis in samples from both BV- and BV+ study participants. This observation led to our discovery that a wide range of BVAB, but only L. crispatus and L. iners among the commensal Lactobacillus spp., can directly metabolize glycogen. Finally, we described the construction of an E. coli-Gardnerella shuttle vector that can be applied for genetic manipulation of this genus. This work contains novel insights into BV and opens new avenues to study the biology of vaginal bacteria, with implications for treatment and prevention of this condition
Exploring the role of innate immune genetic variation in bacterial vaginosis and vaginal bacterial colonization
Full text linkThesis (Ph.D.)--University of Washington, 2018Background. Bacterial vaginosis (BV) is a common, vaginal dysbiosis associated with adverse gynecological and reproductive health outcomes. BV-associated bacteria (BVAB) present microbe-associated molecular patterns to Toll-like receptors (TLRs), which modulate the innate immune response. However, the role of these TLRs in BV pathogenesis remains unclear. I hypothesized that individuals possessing single nucleotide polymorphism (SNP) genotypes associated with heightened innate immune responses (TLR1, TLR6, TLR4, and TLR5 “sufficiency”; TLR10, TOLLIP “deficiency”) are at decreased risk of BV and colonization with BV-associated bacteria (BVAB). Methods. Women were enrolled in independent discovery and validation cohorts and genotyped for common, functionally-characterized SNPs: TLR1 rs5743618, TLR6 rs3821985, TLR4 rs4986790, TLR4 rs4986791, TLR5 rs5744168, TLR10 rs11096955, TLR10 rs4129009, and TOLLIP rs5743854. Genotype models (“sufficient” versus “deficient”) were based on previously published data. As my primary analysis, I compared TLR/TOLLIP sufficient and deficient study participants on the following outcomes: risk of clinically-defined BV, risk of microbiologically-defined BV, colonization with lactobacilli, and colonization with BVAB. Results – Association with BV. In both the discovery and validation cohorts, TLR10 rs11096955 TG/GG (deficiency) associated with increased risk of clinically-defined BV. TOLLIP deficiency and TLR4 deficiency were both associated with increased risk of clinically-defined BV, but only in the discovery cohort. Results – Association with bacterial colonization. TLR4, TLR10, and TLR6 deficiencies were associated with lower Lactobacillus jensenii concentrations. TOLLIP deficiency was associated with higher concentrations of Megasphaera types 1 and 2, Gardnerella vaginalis, and Atopobium vaginae. TLR4 deficiency was correlated with higher concentrations of G. vaginalis, A. vaginae, and total bacterial load. TLR5 deficiency was associated with lower concentration of flagellated species, BV-associated bacterium 1, and Mobiluncus mulieris (but not Mobiluncus curtisii). Conclusions. Individuals possessing genotypes consistent with increased TLR-mediated responses—TLR10, TOLLIP deficiency—have increased risk of clinically-defined BV. The data presented here are consistent with TLR4 deficiency being realized as a deficiency of soluble TLR4 that affects concentrations of several Gram-positive bacteria. Finally, individuals with more robust TLR5 responses (TLR5 sufficiency) appear more susceptible to colonization with specific, flagellated BVAB, although no differences in overall risk of clinically- or microbiologically-defined BV appear to exist. The data presented here are consistent with a model whereby some BVAB benefit from host innate immune response
Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis.
Full text linkBACKGROUND:A Lactobacillus-dominated cervicovaginal microbiota (VMB) protects women from adverse reproductive health outcomes, but the role of L. iners in the VMB is poorly understood. Our aim was to explore the association between the cervicovaginal L. iners and L. crispatus proteomes and VMB composition. METHODS:The vaginal proteomes of 50 Rwandan women at high HIV risk, grouped into four VMB groups (based on 16S rDNA microarray results), were investigated by mass spectrometry using cervicovaginal lavage (CVL) samples. Only samples with positive 16S results for L. iners and/or L. crispatus within each group were included in subsequent comparative protein analyses: Lactobacillus crispatus-dominated VMB cluster (with 16S-proven L. iners (ni) = 0, and with 16S-proven L. crispatus (nc) = 5), L. iners-dominated VMB cluster (ni = 11, nc = 4), moderate dysbiosis (ni = 12, nc = 2); and severe dysbiosis (ni = 8, nc = 2). The relative abundances of proteins that were considered specific for L. iners and L. crispatus were compared among VMB groups. RESULTS:Forty Lactobacillus proteins were identified of which 7 were specific for L. iners and 11 for L. crispatus. The relative abundances of L. iners DNA starvation/stationary phase protection protein (DPS), and the glycolysis enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glucose-6-phosphate isomerase (GPI), were significantly decreased in women with L. iners-containing dysbiosis compared to women with a L. iners-dominated VMB, independent of vaginal pH and L. iners abundance. Furthermore, L. iners DPS, GAPDH, GPI, and fructose-bisphosphate aldolase (ALDO) were significantly negatively associated with vaginal pH. Glycolysis enzymes of L. crispatus showed a similar negative, but nonsignificant, trend related to dysbiosis. CONCLUSIONS:Most identified Lactobacillus proteins had conserved intracellular functions, but their high abundance in CVL supernatant might imply an additional extracellular (moonlighting) role. Our findings suggest that these proteins can be important in maintaining a Lactobacillus-dominated VMB. Functional studies are needed to investigate their roles in vaginal bacterial communities and whether they can be used to prevent vaginal dysbiosis
The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women
Full text linkOBJECTIVES: To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. METHODS: Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. RESULTS: A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (p<0.030); sexual activity did not influence consistency. Women who developed BV were more likely to have clade GV4 compared to those reporting no sex/practiced non-coital activities (OR = 11.82, 95%CI:1.87,74.82,p = 0.009). Specimens were more likely to contain multiple G.vaginalis clades rather than a single clade if women engaged in penile-vaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). CONCLUSIONS: Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially pathogenic clades
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Association between vaginal microbiota and vaginal inflammatory immune markers in postmenopausal women
No full textObjective: In premenopausal individuals, vaginal microbiota diversity and lack of Lactobacillus dominance are associated with greater mucosal inflammation, which is linked to a higher risk of cervical dysplasia and infections. It is not known if the association between the vaginal microbiota and inflammation is present after menopause, when the vaginal microbiota is generally higher-diversity and fewer people have Lactobacillus dominance. Methods: This is a post hoc analysis of a subset of postmenopausal individuals enrolled in a randomized trial for treatment of moderate-severe vulvovaginal discomfort that compared vaginal moisturizer, estradiol, or placebo. Vaginal fluid samples from 0, 4, and 12 weeks were characterized using 16S rRNA gene sequencing (microbiota) and MesoScale Discovery (vaginal fluid immune markers: IL-1b, IL-1a, IL-2, IL-6, IL-18, IL-10, IL-9, IL-13, IL-8, IP10, MIP1a, MIP1b, MIP3a). Global associations between cytokines and microbiota (assessed by relative abundance of individual taxa and Shannon index for alpha, or community, diversity) were explored, adjusting for treatment arm, using linear mixed models, principal component analysis, and Generalized Linear Mixed Model + Microbiome Regression-based Kernel Association Test (GLMM-MiRKAT). Results: A total of 119 individuals with mean age of 61 years were included. At baseline, 29.5% of participants had a Lactobacillus -dominant vaginal microbiota. Across all timepoints, alpha diversity (Shannon index, P = 0.003) was highly associated with immune markers. Individual markers that were associated with Lactobacillus dominance were similar to those observed in premenopausal people: IL-10, IL-1b, IL-6, IL-8 (false discovery rate [FDR] < 0.01), IL-13 (FDR = 0.02), and IL-2 (FDR = 0.09). Over 12 weeks, change in alpha diversity was associated with change in cytokine concentration (Shannon, P = 0.018), with decreased proinflammatory cytokine concentrations observed with decreasing alpha diversity. Conclusions: In this cohort of postmenopausal individuals, Lactobacillus dominance and lower alpha diversity were associated with lower concentrations of inflammatory immune markers, as has been reported in premenopausal people. This suggests that after menopause lactobacilli continue to have beneficial effects on vaginal immune homeostasis, despite lower prevalence.
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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