Ontology highlight
ABSTRACT:
PROVIDER: PRJNA548447 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA extraction method targeted loci environmental
| PRJNA315949 | ENA
Project description:Methods for the extraction of bacterial DNA
| PRJEB25932 | ENA
Project description:<p><strong>Background</strong></p><p>Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over three months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. </p><p><strong>Results</strong></p><p>While the bacterial community recovered mostly over three months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared three months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrate in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.</p><p><strong>Conclusions</strong></p><p>We demonstrate that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition.</p><p><br></p><p><strong>Linked data:</strong></p><p>Metagenomics has been submitted to NCBI SRA repository as projects PRJNA573821, PRJNA573905 and PRJNA579284.</p>
2020-09-28 | MTBLS1846 | MetaboLights
Project description:Microbiome nucleic acid extraction kit model is a Named Entity Recognition (NER) model that identifies and annotates the name of the kits used in extracting microbiome nucleic acids in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with kits metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
2022-02-21 | MODEL2202170007 | BioModels
Project description:The impact of the DNA extraction methods on the gut bacterial and fungal microbiota community recovery
| PRJEB29363 | ENA
Project description:In this study we have analysed the regulation of miRNA in bone marrow derived macrophages in response to the fungal pathogen heat killed Candida albicans and bacterial cell wall component, LPS. The aim of the study was to identify and validate miRNAs involved in the innate immune system in response to fungal and bacterial stimuli and investigate potential mechanisms for their transcription.
2010-12-31 | GSE21970 | GEO
Project description:Fungal proteomics is a developing field that requires renewed interest and attention from the scientific community in many aspects. One of the most compelling objectives of fungal biology is to find out how fungal pathogens colonize a host, in order to find new ways of impeding this colonization, and proteomics is an important and useful tool to this end. However, fungi are also taxonomically interesting and are important biochemical model organisms for the study of many cellular processes, such as cytoskeletal regulation. Additionally, fungi are sources of secondary metabolites, many of which serve as medications for humans. Nevertheless, much work remains in developing systems-biology approaches to understanding fungal gene expression and secondary metabolism. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, an application of a modified Folch extraction to protein extraction was used to perform de novo peptide sequencing of the proteome from the plant and human pathogen Lasiodiplodia theobromae, which greatly streamlined and simplified the analysis process. Using a metaproteomics bioinformatics approach, many novel proteins for L. theobromae were identified and targeted for further biochemical characterization and annotation efforts.
2017-04-05 | PXD005283 | Pride
Project description:Liquid-liquid extraction of bacterial cultures. Non-targeted metabolomics
2023-01-24 | MSV000091128 | MassIVE