Quantification, isolation and characterization of Bifidobacterium from the vaginal microbiomes of reproductive aged women

Freitas, Aline C.; Hill, Janet E.

doi:10.1016/j.anaerobe.2017.05.012

Cited by 52 publications

(48 citation statements)

References 56 publications

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“…Due to its rarity, associations between Bifidobacterium-dominated communities and vaginal health have yet to be assessed. Although they are generally capable of producing L-lactic acid [48], we found that only about a quarter of women with Bifidobacterium-dominated communities had a vaginal pH of less than 4.5, indicating it likely does not provide the same level of pH-mediated protection as a Lactobacillus-dominated community.…”

Section: Discussionmentioning

confidence: 70%

VALENCIA: A nearest centroid classification method for vaginal microbial communities based on composition

France

Gajer

et al. 2020

Preprint

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Background: Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed Community State Types (CSTs). This approach is advantageous because collapsing a hyper dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies and statistical modeling. Vaginal communities are typically assigned to CSTs based on the results of hierarchical clustering of the pairwise distances between samples. However, this approach is problematic because it complicates between-study comparisons and because the results are entirely dependent on the particular set of samples that were analyzed. We sought to standardize and advance the assignment of samples to CSTs.Results: We developed VALENCIA (VAginaL community state typE Nearest CentroId clAssifier), a nearest centroid based tool which classifies samples based on their similarity to a set of reference centroids. The references were defined using a comprehensive set of 13,160 taxonomic profiles from 1,975 women in the United States. This large dataset allowed us to comprehensively identify, define, and characterize vaginal CSTs common to reproductive age women, and expand upon the CSTs that had been defined in previous studies. We validated the broad applicability of VALENCIA for the classification of vaginal microbial communities by using it to classify three test datasets which included reproductive age African women, adolescent girls, and menopausal women. VALENCIA performed well on all three datasets despite the substantial variations in sequencing strategies and bioinformatics pipelines, indicating its broad application to vaginal microbiota. We further describe the relationships between community characteristics (vaginal pH, Nugent score) and participant demographics (race, age) and the CSTs defined by VALENCIA. Conclusion: VALENCIA provides a much-needed solution for the robust and reproducible assignment of vaginal community state types. This will allow unbiased analysis of both small and large vaginal microbiota datasets, comparisons between datasets and meta-analyses that combine multiple datasets.

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Section: Discussionmentioning

confidence: 70%

VALENCIA: A nearest centroid classification method for vaginal microbial communities based on composition

France

Gajer

et al. 2020

Preprint

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“…Among them Shuttleworthia, enriched in the healthy women, are typically encountered in nonlactobacillus‐dominated community state types, 3 typically associated with BV states, but also commonly found in postmenopausal women 5,7 . Bifidobacteria , commonly found in healthy VM communities, are attributed a protective role similar to lactobacilli , that is, the production of lactic acid and hydrogen peroxide, 25 preventing the overgrowth of pathogens and preserving the vaginal homeostasis. Depletion of Lactobacilli and Bifidobacteria in the cancer VMs suggests a suboptimal colonization which might indicate a state of dysmicrobiosis.…”

Section: Discussionmentioning

confidence: 99%

Comparison of vaginal microbiota in gynecologic cancer patients pre‐ and post‐radiation therapy and healthy women

et al. 2020

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Background: While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy (RT) on the vaginal microbiome (VM) of postmenopausal women. Methods: We studied women with GynCa, pre-(N = 65) and post-RT (N = 25) and a group of healthy controls (N = 67) by sequencing the V4 region of the 16S rRNA gene from vaginal swabs and compared the diversity and composition of VMs between the three groups accounting for potential confounding factors in multivariate analysis of variance. Results: Comparisons of cancer vs healthy groups revealed that Lactobacillus andBifidobacterium have significantly higher relative abundance in the healthy group, while the cancer group was enriched in 16 phylogroups associated with bacterial vaginosis (BV) and inflammation, including Sneathia, Prevotella, Peptoniphilus, Fusobacterium, Anaerococcus, Dialister, Moryella, and Peptostreptococcus. In our sample, RT affected the α-diversity and correlated with higher abundance of typically rare VM species, including several members of the Lacnospiraceae family, a taxon previously linked to vaginal dysbiosis. In addition to cancer and treatment modalities, age and vaginal pH were identified as significant parameters that structure the VM. Conclusions: This is among the first reports identifying VM changes among postmenopausal women with cancer. RT alone seems to affect several phylogroups (12 bacterial genera), while gynecological cancer and its treatment modalities are associated with even greater significant shifts in the vaginal microbiota including the enrichment of opportunistic bacterial pathogens, which warrants further attention. K E Y W O R D S16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota | 3715 TSEMENTZI ET al.

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“…Studies of the vaginal microbiota using deep sequencing methods have shown that bifidobacteria are the dominant bacteria in the vaginal microbiomes of some reproductive aged women [ 19 ]. Culture-based studies have subsequently confirmed that some vaginal Bifidobacterium spp.…”

Section: Introductionmentioning

confidence: 99%

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics

Freitas

Hill

2018

PLoS ONE

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Bifidobacteria colonize the human gastrointestinal tract, vagina, oral cavity and breast milk. They influence human physiology and nutrition through health-promoting effects, play an important role as primary colonizers of the newborn gut, and contribute to vaginal microbiome homeostasis by producing lactic acid. Nevertheless, the mechanisms by which bifidobacteria are transmitted from mother to infant remains in discussion. Moreover, studies have suggested that Bifidobacterium spp. have specializations for gut colonization, but comparisons of strains of the same bifidobacteria species from different body sites are lacking. Here, our objective was to compare the genomes of Bifidobacterium breve (n = 17) and Bifidobacterium longum (n = 26) to assess whether gut and vaginal isolates of either species were distinguishable based on genome content. Comparison of the general genome features showed that vaginal and gut isolates did not differ in size, GC content, number of genes and CRISPR, either for B. breve or B. longum. Average nucleotide identity and whole genome phylogeny analysis revealed that vaginal and gut isolates did not cluster separately. Vaginal and gut isolates also had a similar COG (Cluster of Orthologous Group) category distribution. Differences in the accessory genomes between vaginal and gut strains were observed, but were not sufficient to distinguish isolates based on their origin. The results of this study support the hypothesis that the vaginal and gut microbiomes are colonized by a shared community of Bifidobacterium, and further emphasize the potential importance of the maternal vaginal microbiome as a source of infant gut microbiota.

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Quantification, isolation and characterization of Bifidobacterium from the vaginal microbiomes of reproductive aged women

Cited by 52 publications

References 56 publications

VALENCIA: A nearest centroid classification method for vaginal microbial communities based on composition

VALENCIA: A nearest centroid classification method for vaginal microbial communities based on composition

Comparison of vaginal microbiota in gynecologic cancer patients pre‐ and post‐radiation therapy and healthy women

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics

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