Metagenomic
Ontology highlight
ABSTRACT:
TISSUE(S): ['swab']
SUBMITTER: Xiaoran Li
PROVIDER: OEX00014450 | NODE | 2021-08-31
REPOSITORIES: NODE
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Project description:16srRNA metagenomics of Endometrial Samples
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Project description:<p>Archived self-collected vaginal swabs were utilized from a pilot study of vaginal douching cessation (NIH/NIAID R03-AI061131). Thirty-nine non-pregnant, reproductive-age women who reported the use of vaginal douche products in the two months prior to screening were enrolled. Thirty-three of these successfully completed the 16-week longitudinal study. Participants self-collected vaginal swabs and smears twice weekly. We report sequences based on the analysis of 16S rRNA gene sequences amplified from whole genomic DNA isolated from the swabs. Bacterial vaginosis (BV) is defined by Gram's stain of vaginal fluid (Nugent's score ≥7).</p> <p>The large body of information generated will facilitate understanding of vaginal microbial community dynamics, the etiology of BV, and drive the development of better diagnostic tools for BV. Furthermore, it is hoped that the information will enable a more personalized treatment of BV and ultimately, prevent adverse sequelae associated with BV.</p>
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Project description:Interventions: Analysis of bacteremia after ESD of the colon.
Primary outcome(s): Identification of bacteremia after ESD testing blood culture and 16SrRNA gene sequencing.
Study Design: Single arm Non-randomized
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Project description:Pelvic organ prolapse (POP), affecting up to 50% of elderly women, disrupts vaginal microbial homeostasis, yet the impact of first-line pessary therapy on microbiome dynamics remains poorly characterized. This prospective cohort study employed metagenomic sequencing and clinical metrics to longitudinally analyze vaginal microbiota in 41 postmenopausal POP-III/IV patients undergoing pessary therapy, compared to surgical intervention and healthy controls. Pre-treatment POP patients exhibited dysbiosis marked by elevated aerobic pathogen (e.g., Gardnerella vaginalis, Streptococcus agalactiae) and bacterial vaginosis (BV)-associated taxa, which may correlating with anatomical oxygen exposure. pessary therapy drove time-dependent microbial stabilization: within 3 months, Lactobacillus crispatus and Lactobacillus jensenii reclaimed dominance (∼90% abundance), suppressing BV-associated genera (Corynebacterium spp., Streptococcus spp.), while surgery failed to improve dysbiosis. Patients developing pessary-associated ulcers showed distinct enrichment of G. vaginalis, S. anginosus, and Atopobium vaginae, enabling a predictive model (AUC: 0.848) for complication risk. Metabolomic profiling revealed pessary-induced activation of pentose phosphate and glycerophospholipid pathways, aligning with microbial recovery. These findings establish pessary therapy as a dual restorative intervention—anatomically and microbially—while identifying actionable biomarkers for complication prevention. Our work advocates integrating microbiome-guided strategies into POP management to optimize therapeutic outcomes.
2025-07-16 | MTBLS12722 | MetaboLights
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
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