Ontology highlight
ABSTRACT:
PROVIDER: PRJNA888791 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21848700_1.fastq.gz | Fastqsanger.gz | |||
| SRR21848700_2.fastq.gz | Fastqsanger.gz | |||
| SRR21848701_1.fastq.gz | Fastqsanger.gz | |||
| SRR21848701_2.fastq.gz | Fastqsanger.gz | |||
| SRR21848702_1.fastq.gz | Fastqsanger.gz |
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Project description:Cervicovaginal microbiome dysbiosis is associated with increased prevalence and incidence of sexually transmitted infections including HIV. We compared the cervicovaginal proteome as characterised by mass-spectrometry of four groups of African female sex workers (total N=50) grouped by microbiome composition as characterised by 16S rDNA microarray. Group 1 had a Lactobacillus crispatus-dominated microbiome, group 2 a L. iners-dominated microbiome, and groups 3 and 4 had a microbiome containing multiple genera of anaerobic bacteria, with group 3 representing transition to or from dysbiosis and group 4 full dysbiosis. 82 human proteins were differentially abundant among the groups, either showing an increasing or decreasing trend from microbiome groups 1 to 4. Proteins that increased included proteasome subunits and other proteins involved in catabolic metabolism, actin organising proteins and proteins involved in the immune response. Proteins that decreased included antiproteases, keratins, and cornified envelope proteins. We also compared the abundance of pre-defined proteins of interest among microbiome groups: markers of cell type, inflammation, and cell death, and mucins. The dysbiotic groups had increased abundance of proteins unique to lymphocytes and macrophages, pro-inflammatory cytokines, cell death markers, and MUC5B. We conclude that the cervicovaginal human proteome is associated with the cervicovaginal microbiome in a dose-response manner. The changes are likely caused by a pro-inflammatory influx of immune cells and an increase of cell death in dysbiosis. Dysbiosis-associated immune activation, breaches in epithelial integrity, altered mucin balance, and altered protease-antiprotease balance may all contribute to the increased risk of HIV transmission when cervicovaginal dysbiosis is present.
2015-09-25 | PXD001435 | Pride
Project description:Opioid analgesics are frequently prescribed in the United States and worldwide. However, serious side effects such as addiction, immunosuppression and gastrointestinal symptoms limit long term use. In the current study using a chronic morphine-murine model a longitudinal approach was undertaken to investigate the role of morphine modulation of gut microbiome as a mechanism contributing to the negative consequences associated with opioids use. The results revealed a significant shift in the gut microbiome and metabolome within 24 hours following morphine treatment when compared to placebo. Morphine induced gut microbial dysbiosis exhibited distinct characteristic signatures profiles including significant increase in communities associated with pathogenic function, decrease in communities associated with stress tolerance. Collectively, these results reveal opioids-induced distinct alteration of gut microbiome, may contribute to opioids-induced pathogenesis. Therapeutics directed at these targets may prolong the efficacy long term opioid use with fewer side effects.
2018-04-16 | E-MTAB-5550 | biostudies-arrayexpress
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
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Project description:To identify chromatin alterations by host-microbe interactions in cervicovaginal epithelial cells we performed ATAC-sequencing. We identified regions of chromatin that were altered in cervicovaginal epithelial cells after exposure to L. crispatus supernatant.
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Project description:The impact of mono-chronic S. stercoralis infection on the gut microbiome and microbial activities in infected participants was explored. The 16S rRNA gene sequencing of a longitudinal study with 2 sets of human fecal was investigated. Set A, 42 samples were matched, and divided equally into positive (Pos) and negative (Neg) for S. stercoralis diagnoses. Set B, 20 samples of the same participant in before (Ss+PreT) and after (Ss+PostT) treatment was subjected for 16S rRNA sequences and LC-MS/MS to explore the effect of anti-helminthic treatment on microbiome proteomes.
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