scholarly journals The vagino-cervical microbiome as a woman’s life history

2019 ◽  
Author(s):  
Zhuye Jie ◽  
Chen Chen ◽  
Lilan Hao ◽  
Fei Li ◽  
Liu Tian ◽  
...  
Keyword(s):  
Sexual Behaviors ◽  
Reproductive Tract ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Amplicon Sequencing ◽  
Female Reproductive Tract ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Major Factors

The gut microbiome has been the center of attention for human commensal microbiome studies. The vaginal microbiome is also densely populated with bacteria, viruses and fungi, and the presence of microorganisms beyond the cervix is increasingly reported in non-infectious conditions1–3. Due to the over 90% of human sequences in female reproductive tract samples3,4, metagenomic information has been very limited. 16S rRNA gene amplicon sequencing studies have identified community types in the vaginal microbiota, and observed its dynamic changes due to menstrual cycles and sexual behaviors in small cohorts5,6. Here we perform metagenomic shotgun sequencing on cervical samples from 516 women of reproductive age (more than 10-fold of the Human Microbiome Project (HMP)4), and dissect major factors, especially pregnancy and delivery histories and contraception methods on the microbiome composition. Features of other body sites, such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota in the female reproductive tract and imply disease susceptibilities that may be relieved by behavioural changes.

scholarly journals The female urinary microbiota in relation to the reproductive tract microbiota

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Chen Chen ◽  
Lilan Hao ◽  
Weixia Wei ◽  
Fei Li ◽  
Liju Song ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Uterine Cavity ◽  
Detailed Comparison ◽  
Female Reproductive Tract ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Urogenital System ◽  
Urinary Microbiota

Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman’s correlation was used to explore the relationship between urine and multiple sites of the female reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.

scholarly journals Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

Influence of the digestive/reproductive tract microbiota on chicken egg production beyond host genetics

2020 ◽  
Author(s):  
Diyan Li ◽  
Shilin Tian ◽  
Wei Zhu ◽  
Yuan Su ◽  
Tao Wang ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Egg Production ◽  
Reproductive Tract ◽  
Animal Health ◽  
Design Strategies ◽  
Host Genetics ◽  
Microbiome Composition ◽  
Chicken Egg ◽  
And Performance ◽  
Major Factors

Abstract Background: The microbiota of the digestive and reproductive systems has a prominent role in animal health and performance, but the extent of its contribution is difficult to determine. In chickens, the effect of host genetics on the reproductive and digestive tract microbiota is unclear, and the means by which digestive/reproductive microbiomes help improve egg production in chicken are unknown.Results: To gain insight into this, we examined genomes from 128 chickens reared under identical conditions and described their digestive (crop, gizzard and small intestine) and reproductive tract (vagina, uterus and isthmus) microbiota. Although the diversity, composition and predicted function of the digestive and reproductive tract microbiota exhibited notable microbiota variation substantially between different parts, host genetics had limited effects on the reproductive and digestive tract microbial community. The digestive and reproductive tract microbiota had a significant effect on egg production (accounting for 52.31% - 98.86% of the variance), after correcting for host genetic effects; in particular, the uterus and isthmus microbiota accounted for an average of 93.59% and 98.86%, respectively, of variance in egg production. We further identified four reproductive tract microbial species which were related to immune system, Bacteroides fragilis, Bacteroides salanitronis, Bacteroides barnesiae and Clostridium leptum, that were significantly positively correlated with egg production. Chickens with a lower abundance of these species had produced significantly fewer eggs at 300 days of age (37.13 vs. 113.75) than those with a higher abundance of these microorganisms. These taxa indicate potential roles play in promoting reproductive performance. Especially uterus and isthmus tract microbiota were major factors in regulating the chicken egg production.Conclusions: Host genetics has limited effect on digestive/reproductive microbiome composition. The distinct site-associated chicken microbiome may be determined by the differences of their physical function. These findings may help design strategies for controlling and altering the digestive/reproductive tract microbiota in chickens to improve egg production.

scholarly journals Metagenomic Pyrosequencing and Microbial Identification

2009 ◽  
Vol 55 (5) ◽  
pp. 856-866 ◽  
Author(s):  
Joseph F Petrosino ◽  
Sarah Highlander ◽  
Ruth Ann Luna ◽  
Richard A Gibbs ◽  
James Versalovic
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Next Generation ◽  
New Era ◽  
Microbial Identification ◽  
Core Technology ◽  
Dna Pyrosequencing

Abstract Background: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. Content: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed. Bioinformatics-related topics include taxonomic systems, sequence databases, sequence-alignment tools, and classifiers. DNA sequencing based on 16S rRNA genes or entire genomes is summarized with respect to potential pyrosequencing applications. Summary: Both the approach of 16S rDNA amplicon sequencing and the whole-genome sequencing approach may be useful for human metagenomics, and numerous bioinformatics tools are being deployed to tackle such vast amounts of microbiological sequence diversity. Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases.

scholarly journals Comparison of paperpoint and curette sampling of subgingival microbiome composition as analyzed by 16S rRNA gene amplicon sequencing

2017 ◽  
Vol 9 (sup1) ◽  
pp. 1325260
Author(s):  
K. Beyer ◽  
B.W. Brandt ◽  
M.J. Buijs ◽  
J.G. Brun ◽  
W. Crielaard ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition

scholarly journals The female urinary microbiota in relation to the reproductive tract microbiota

2019 ◽  
Author(s):  
Chen Chen ◽  
Lilan Hao ◽  
Weixia Wei ◽  
Fei Li ◽  
Liju Song ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Chinese Women ◽  
Uterine Cavity ◽  
Detailed Comparison ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Urogenital System ◽  
Urinary Microbiota

AbstractHuman urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear.Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearman’s correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women.Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.

scholarly journals Endometrial microbiota composition is associated with reproductive outcome in infertile patients

2021 ◽  
Author(s):  
Inmaculada Moreno ◽  
Iolanda Garcia-Grau ◽  
David Perez-Villaroya ◽  
Marta Gonzalez-Monfort ◽  
Mustafa Bahçeci ◽  
...  
Keyword(s):  
Embryo Transfer ◽  
Live Birth ◽  
Reproductive Tract ◽  
Treatment Strategies ◽  
16S Rrna Gene Sequencing ◽  
Female Reproductive Tract ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Reproductive Outcome ◽  
Infertile Patients

ABSTRACTBackgroundPrevious evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage, or no pregnancy.MethodsHere we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments.ResultsA dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes.ConclusionsOur findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies.

scholarly journals Endometrial microbiota composition is associated with reproductive outcome in infertile patients

Microbiome ◽  
2022 ◽  
Vol 10 (1) ◽  
Author(s):  
Inmaculada Moreno ◽  
Iolanda Garcia-Grau ◽  
David Perez-Villaroya ◽  
Marta Gonzalez-Monfort ◽  
Mustafa Bahçeci ◽  
...  
Keyword(s):  
Embryo Transfer ◽  
Live Birth ◽  
Reproductive Tract ◽  
Treatment Strategies ◽  
16S Rrna Gene Sequencing ◽  
Female Reproductive Tract ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Reproductive Outcome ◽  
Infertile Patients

Abstract Background Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy. Methods Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments. Results A dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes. Conclusions Our findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies.

scholarly journals Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

2021 ◽  
Vol 368 (17) ◽  
Author(s):  
Zachary Mays ◽  
Amelia Hunter ◽  
Lindsay Glass Campbell ◽  
Camila Carlos-Shanley
Keyword(s):  
16S Rrna ◽  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Conservation Education ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Microbiome Composition ◽  
Intrinsic Factors ◽  
Captive Populations ◽  
The 16S Rrna Gene

Abstract The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

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