Ontology highlight
ABSTRACT:
PROVIDER: PRJNA801405 | ENA |
REPOSITORIES: ENA
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Project description:<p>Marine sponges can host abundant and diverse microbiomes, which can largely influence the metabolism and other phenotypic traits of the host. However, information on the potential relationships between sponge microbiomes and metabolic signatures, other than secondary metabolites explored for biotechnological purposes, needs further investigation. Applying an integrated approach, we investigated the microbiomes associated with 4 ubiquitous Mediterranean sponge species (i.e., Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula), correlated with their metabolomic patterns (in terms of lipidomics) and microbial predicted functions. Microscopy observations of sponge tissues revealed differences in microbial abundances, which, however, were only partially linked to their diversity assessed through metabarcoding. The microbiomes of the 4 sponges showed a species-specific composition and a different core size, which was independent from the microbial diversity of the surrounding seawater. Predicted functions of the associated microbiomes allowed identifying 2 functional host clusters: one more related to heterotrophic pathways and the other more linked to phototrophic activities. Differences in the microbiomes were also associated with different metabolic profiles, mostly due to specific compounds characterizing the host and its microbiome. Overall, this study provides new insights on the functionality of sponges and their prokaryotic symbioses’, and in particular, it discloses a descriptive sketch of the diverse compartments forming the sponge holobiont.</p>
2024-02-21 | MTBLS5125 | MetaboLights
Project description:The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.
2020-04-25 | GSE149314 | GEO
Project description:Colorectal cancer (CRC), second leading cause of cancer worldwide, is associated with a poor prognosis, especially in patients with advanced disease. Therefore, there is still a need to develop new prognostic tools to replace or supplement those routinely used, with the aim to optimize treatment strategies.
Studies on gut microbiota composition provide new strategies to identify powerful biomarkers. Indeed, beyond its beneficial functions for the host, increasing evidences suggest that gut microbiota is a key factor involved in CRC carcinogenesis. Many clinical studies have described an imbalance in the gut microbiota (dysbiosis) in CRC patients, with the emergence of pathogenic bacterial species, Recent studies reported that pks-positive E. coli, a pathogenic bacterial producing toxin encoded by the pks genomic island, is more frequently detected in CRC patients, suggesting a possible role in tumor development. Therefore, this suggests the potential use of microbial signatures associated with CRC for prognostic assessment. Furthermore, influence of body composition profile (BMI, sarcopenia, metabolic syndrome) also appears to be a new relevant prognostic tool regarding surgical and oncological outcomes following CRC surgery.
The aim of this translational research project is to study the impact of these new prognostic tools on surgical and oncologic results in a prospective cohort of patients who underwent CRC surgery at the Digestive Surgery Department of the University Hospital of Clermont-Ferrand (France). This could allow to optimize treatment strategies and provide new ways to identify news promising biomarkers associations in order to better define high risk patients. Investigators aim to identify specific microbial signatures associated with some metabolic profiles in order to improve surgical morbidity and/or response to cancer therapies.
| 2297414 | ecrin-mdr-crc
Project description:<p>Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.</p>
| phs001655 | dbGaP
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.
2023-02-10 | GSE194276 | GEO
Project description:Environmental influences such as infections and dietary changes strongly affect a host’s microbiota. In the steady state, however, host genetics may influence the microbiota composition, as suggested by the greater similarity between the microbiomes of identical twin pairs compared to non-identical twins. Understanding the role of polymorphic mechanisms in regulating the commensal communities is complicated by the variability of human genomes and microbiomes, and by microbial sensitivity to the environment. Animal studies allow genetic modifications, but are also sensitive to influences known as ‘cage’ or ‘legacy’ effects. Here, we analyzed ex-germ-free mice of various genetic backgrounds, including immunodeficient and Major Histocompatibility Complex (MHC)-congenic strains repopulated with identical input microbiota. We found that the host’s genetic polymorphic mechanisms did indeed affect the gut microbiome and that both innate (e.g. anti-microbial peptides, complement, pentraxins and enzymes affecting microbial survival), as well as adaptive (both MHC-dependent and MHC-independent) pathways influenced the microbiota. These polymorphic mechanisms regulated only a limited number of microbial lineages (independently of their abundance). In addition, our comparative analyses suggested that some microbes might benefit from the specific immune responses that they elicit.
2019-08-29 | GSE136572 | GEO
Project description:Extracts of selected microbial community associated with the mesopelagic Periphylla periphylla jellyfish
2023-01-16 | MSV000091067 | MassIVE