A5023185569- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Endoplasmic Reticulum Stress and Disease
- Protein Structure and Dynamics
- Diet and metabolism studies
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Inflammatory Bowel Disease
- IgG4-Related and Inflammatory Diseases
- Enzyme Structure and Function
- Pharmacological Effects of Natural Compounds
- Probiotics and Fermented Foods
- Bioinformatics and Genomic Networks
- Inflammatory Myopathies and Dermatomyositis
- Systemic Sclerosis and Related Diseases
- Computational Drug Discovery Methods
- Listeria monocytogenes in Food Safety
- Celiac Disease Research and Management
- Autoimmune Bullous Skin Diseases
- Mycobacterium research and diagnosis
- Colorectal Cancer Screening and Detection
- Toxin Mechanisms and Immunotoxins
- Escherichia coli research studies
- Bacteriophages and microbial interactions
Danone (France)
2022-2023
Enterome (France)
2013-2022
Broad Institute
2021
Novartis (United States)
2021
ReShape Lifesciences (United States)
2013
European Molecular Biology Organization
2004-2005
Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered the extent reference genomes that far from covering all variability, as many species still not sequenced or have only few strains available. Binning co-abundant genes obtained de novo assembly is a powerful reference-free technique to discover and reconstitute repertoire species. While current...
Smoking has a negative impact on Crohn's disease (CD), but the mechanisms underlying this association are unclear. We compared gut microbiota composition of smoking with nonsmoking patients CD using metagenomic approach. Stool samples and clinical data were collected from current smokers nonsmokers France Netherlands, matched for country, gender, age, activity, body mass index. Fecal DNA was sequenced an Illumina HiSeq 2500. On average, 40 million paired-end reads generated per sample. Gene...
Abstract Background Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in blood as well inflammation fibrosis various organs, but they have no established etiologies. Similar to other diseases, gut microbiome might encode disease-triggering or disease-sustaining factors. Methods The microbiomes from IgG4-RD SSc patients healthy individuals with recent antibiotic treatment were studied...
Abstract The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the across lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major branches were identified, within which multiple partitions observed in adulthood, with differential abundances species along branches. Different compositions metabolic functions characterized...
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial chemical microenvironment a patient's ileal mucosa clinical phenotype genotype identify factors favoring growth virulence adherent invasive E. coli (AIEC) linked Crohn's disease. We determined that niche AIEC was characterized by inflammation, dysbiosis, coculture...
Abstract Background The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health disease. Dysregulation of ER stress response has been implicated in intestinal inflammation associated with inflammatory bowel disease (IBD), chronic condition characterized by changes to mucosa alteration gut microbiota. While microbiota microbially derived metabolites have also stress, examples this connection remain...
Abstract Motivation Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered the extent reference genomes that far from covering all variability, as many species still not sequenced or have only few strains available. Binning co-abundant genes obtained de novo assembly is a powerful reference-free technique to discover and reconstitute repertoire...
Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms, possibly mediated by the gut microbiota. We previously showed that consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria improved gastrointestinal (GI) comfort response to flatulogenic dietary challenge healthy individuals. To study effects FMP on microbiota activity from those participants, we conducted metatranscriptomic...
Analysis toolkits for whole-metagenome shotgun sequencing data achieved strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered the extent reference genomes that far from covering all variability, as many species still not sequenced or have only few strains available. Binning co-abundant genes obtained de novo assembly is a powerful reference-free technique discovering and reconstituting repertoire...