A citizen-science-enabled catalogue of the vaginal microbiome and associated factors

Nature Microbiology, Год журнала: 2023, Номер 8(11), С. 2183 - 2195

Опубликована: Окт. 26, 2023

Understanding the composition and function of vaginal microbiome is crucial for reproductive overall health. Here we established Isala citizen-science project to analyse microbiomes 3,345 women in Belgium (18-98 years) through self-sampling, 16S amplicon sequencing extensive questionnaires. The was strongly tied age, childbirth menstrual cycle phase. Lactobacillus species dominated 78% samples. Specific bacterial taxa also showed co-occur modules based on network correlation analysis. Notably, module containing crispatus, jensenii Limosilactobacillus positively linked oestrogen levels contraceptive use negatively breastfeeding. Other modules, named after abundant (Gardnerella, Prevotella Bacteroides), correlated with multiple partners, menopause, hygiene use. With this resource-rich map associated health, life-course, lifestyle dietary factors, provide unique data insights follow-up clinical mechanistic research.

Язык: Английский

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The best practice for microbiome analysis using R

Protein & Cell, Год журнала: 2023, Номер 14(10), С. 713 - 725

Опубликована: Май 2, 2023

With the gradual maturity of sequencing technology, many microbiome studies have published, driving emergence and advance related analysis tools. R language is widely used platform for data powerful functions. However, tens thousands packages numerous similar tools brought major challenges researchers to explore data. How choose suitable, efficient, convenient, easy-to-learn from has become a problem researchers. We organized 324 common classified them according application categories (diversity, difference, biomarker, correlation network, functional prediction, others), which could help quickly find relevant analysis. Furthermore, we systematically sorted integrated (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, amplicon) analysis, summarized advantages limitations, will appropriate Finally, thoroughly reviewed most content in formed suitable pipeline This paper accompanied by hundreds examples with 10,000 lines codes GitHub, can beginners learn, also analysts compare test different sorts providing an important theoretical basis practical reference development better future. All code available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

Язык: Английский

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Multi-omic approaches for host-microbiome data integration

Gut Microbes, Год журнала: 2024, Номер 16(1)

Опубликована: Янв. 2, 2024

The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear these interactions can be measured across many different omics layers, including genome, transcriptome, epigenome, metabolome, proteome, among others. Multi-omic studies of provide insight into mechanisms underlying host-microbe interactions. As more layers are considered, increasingly sophisticated statistical methods required to integrate them. In this review, we an overview approaches currently used characterize multi-omic between data. While a large number have generated deeper understanding host-microbiome interactions, there still need for standardization approaches. Furthermore, would also benefit from collection curation large, publicly available multi-omics datasets.

Язык: Английский

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Experimental temperatures shape host microbiome diversity and composition

Global Change Biology, Год журнала: 2022, Номер 29(1), С. 41 - 56

Опубликована: Окт. 17, 2022

Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance help them survive stressful climatic conditions. The extent microbiome communities in response warming or cooling important predicting host under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial aquatic species, we found decrease the amplicon sequence variant-level phylogenetic diversity alteration composition both experimental cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that habitat factors than biological traits. In particular, organisms-especially marine habitats-experienced greater depletion cold conditions, compared hosts. Exposure involving sudden long static shift associated with loss, but this reduction attenuated prior-experimental lab acclimation when ramped regime (i.e., warming) used. Microbial differential abundance co-occurrence network analyses revealed several potential indicator bacterial classes hosts heated environments on different biome levels. Overall, our findings improve understanding impact changes animal plant structures across range habitats. next step is link these measures fitness, as well community functions, determine whether can buffer some species against thermally variable world.

Язык: Английский

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Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome

Cell Reports Medicine, Год журнала: 2022, Номер 3(10), С. 100753 - 100753

Опубликована: Сен. 30, 2022

Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the environment. However, changes in underlying rUTI susceptibility unknown. Here, we perform shotgun metagenomics and advanced culture on urine from controlled cohort postmenopausal to identify compositional function linked susceptibility. We candidate taxonomic biomarkers an enrichment lactobacilli taking estrogen hormone therapy. find robust correlations between Bifidobacterium Lactobacillus estrogens without (UTI) history. Functional analyses reveal distinct metabolic antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, that ARGs enriched microbiomes history independent current UTI status. Our data suggest shape women.

Язык: Английский

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Viral biogeography of the mammalian gut and parenchymal organs

Nature Microbiology, Год журнала: 2022, Номер 7(8), С. 1301 - 1311

Опубликована: Авг. 2, 2022

Язык: Английский

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Fecal microbiota and bile acids in IBD patients undergoing screening for colorectal cancer

Gut Microbes, Год журнала: 2022, Номер 14(1)

Опубликована: Май 30, 2022

Due to the potential role of gut microbiota and bile acids in pathogenesis both inflammatory bowel disease (IBD) sporadic colorectal cancer, we aimed determine whether these factors were associated with cancer IBD patients. 215 patients 51 non-IBD control subjects enrolled from 10 French centers between September 2011 July 2018. Fecal samples processed for bacterial 16S rRNA gene sequencing acid profiling. Demographic, clinical, endoscopic, histological outcomes recorded. Characteristics included: median age: 41.6 (IQR 22); duration 13.2 (13.1); 47% female; 21.9% primary sclerosing cholangitis; 109 Crohn's (CD); 106 ulcerative colitis (UC). The prevalence was 2.8% (6/215: 1 CD; 5 UC), high-grade dysplasia 3.7% (8/215) low-grade 7.9% (17/215). Lachnospira decreased while Agathobacter Escherichia-Shigella increased UC any neoplasia. Bile not or Unsupervised clustering identified three clusters composition clinical features, including a higher risk neoplasia two when compared third (relative (RR) 4.07 (95% CI 1.6–10.3, P < .01) 3.56 1.4–9.2, .01)). In this multicentre observational study, limited number taxa exploratory co-associated UC. Given very small cancers, robustness findings will require assessment validation future studies.

Язык: Английский

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Investigating differential abundance methods in microbiome data: A benchmark study

PLoS Computational Biology, Год журнала: 2022, Номер 18(9), С. e1010467 - e1010467

Опубликована: Сен. 8, 2022

The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility studying complex microbial systems. Recently, researchers have shown great interest in microorganisms that characterise different ecological niches. Differential abundance analysis aims to find differences each taxa between two classes subjects or samples, assigning a significance value comparison. Several bioinformatic methods been specifically developed, taking into account challenges microbiome data, such as sparsity, depth constraint samples compositionality. led important conclusions fields, from health environment. However, lack known biological truth makes it difficult validate results obtained. In this work we exploit metaSPARSim, count data simulator, simulate with differential features experimental groups. We perform complete comparison recently developed established on common benchmark effort reliability both simulated scenarios evaluation metrics. performance overview includes investigation numerous scenarios, effect methods’ main covariates sample size, percentage differentially abundant features, depth, feature variability, normalisation approach Mainly, show good control type I error and, generally, also false discovery rate at while recall seem depend dataset size.

Язык: Английский

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FXR Signaling-Mediated Bile Acid Metabolism Is Critical for Alleviation of Cholesterol Gallstones by Lactobacillus Strains

Microbiology Spectrum, Год журнала: 2022, Номер 10(5)

Опубликована: Авг. 29, 2022

Cholesterol gallstone (CGS) disease is characterized by an imbalance in bile acid (BA) metabolism and closely associated with gut microbiota disorders. However, the role mechanism which probiotics targeting attenuate cholesterol gallstones are still unknown. In this study, Limosilactobacillus reuteri strain CGMCC 17942 Lactiplantibacillus plantarum 14407 were individually administered to lithogenic-diet (LD)-fed mice for 8 weeks. Both Lactobacillus strains significantly reduced LD-induced gallstones, hepatic steatosis, hyperlipidemia. These modulated BA profiles serum liver, may be responsible activation of farnesoid X receptor (FXR). At molecular level, L. increased ileal fibroblast growth factor 15 (FGF15) 4 (FGFR4) small heterodimer partner (SHP). Subsequently, 7α-hydroxylase (CYP7A1) oxysterol (CYP7B1) inhibited. Moreover, two enhanced transport increasing levels multidrug resistance-associated protein homologs 3 (Mrp3/4), resistance 2 (Mdr2), salt export pump (BSEP). addition, both LD-associated dysbiosis. relative abundance Muribaculaceae, while that Akkermansia. The changed was negatively correlated incidence FXR-antagonistic BAs liver FXR signaling pathways. Furthermore, protective effects abolished global intestine-specific antagonists. findings suggest might relieve CGS through IMPORTANCE prevalent worldwide. None medical options prevention treatment recommended, surgical management has a high rate recurrence. It been reported factors involved metabolic syndrome highly connected formation. While remodeling dysbiosis microbiome during improvement well studied, less known about formation after regulating microbiome. We used lithogenic diet (LD) induce experimental model C57BL/6J investigate protection against 14407. found these altered composition improved prevented fully activating They could promising therapeutic strategy treating or preventing its

Язык: Английский

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Neisseria species as pathobionts in bronchiectasis

Cell Host & Microbe, Год журнала: 2022, Номер 30(9), С. 1311 - 1327.e8

Опубликована: Сен. 1, 2022

Neisseria species are frequently identified in the bronchiectasis microbiome, but they regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bacteriomes defined by presence spp. associate with poor clinical outcomes, including exacerbations. subflava cultivated from patients promotes loss epithelial integrity inflammation primary cells. In vivo models infection metabolipidome analysis highlight immunoinflammatory functional gene clusters provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated Neisseria-dominant samples compared disease which Pseudomonas-, an established pathogen, is dominant. Metagenomic surveillance across various disorders reveals broader importance, assessment home environment implies potential environmental sources exposure. Thus, identify pathobionts bronchiectasis, allowing improved risk stratification this high-risk group.

Язык: Английский

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