A5055648418- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Genetic diversity and population structure
- Statistical Methods and Inference
- Identification and Quantification in Food
- Diet and metabolism studies
- Bayesian Methods and Mixture Models
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Evolution and Paleontology Studies
- Viral gastroenteritis research and epidemiology
- Insect symbiosis and bacterial influences
- Statistical Methods and Bayesian Inference
- Environmental DNA in Biodiversity Studies
- Evolution and Genetic Dynamics
- Dietary Effects on Health
- Horticultural and Viticultural Research
- Complex Network Analysis Techniques
- Plant and animal studies
- Species Distribution and Climate Change
- Clostridium difficile and Clostridium perfringens research
- Ecology and Vegetation Dynamics Studies
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2016-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2018-2025
Université Paris-Saclay
2015-2024
Département Mathématiques et Informatique Appliquées
2008-2024
Mathématiques et Informatique Appliquées
2024
Biopolymères Interactions Assemblages
2024
Microbiologie de l’alimentation au service de la santé
2021
Centre Île-de-France - Jouy-en-Josas - Antony
2020
Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés
2017
University of Basel
2015-2016
Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools analyze their data on own.This Galaxy-supported pipeline, called FROGS, is designed large sets of amplicon sequences produce abundance tables Operational Taxonomic Units (OTUs) taxonomic affiliation. The clustering uses Swarm. chimera removal VSEARCH, combined with original cross-sample validation. affiliation returns an innovative multi-affiliation output highlight databases conflicts...
Gut microbiota is involved in the development of several chronic diseases, including diabetes, obesity, and cancer, through its interactions with host organs. It has been suggested that cross talk between gut skeletal muscle plays a role different pathological conditions, such as intestinal inflammation cachexia. However, it remains unclear whether directly influences function. In this work, we studied impact modulation on mice function investigated underlying mechanisms. We determined...
As more and network-structured data sets are available, the statistical analysis of valued graphs has become common place. Looking for a latent structure is one many strategies used to better understand behavior network. Several methods already exist binary case. We present model-based strategy uncover groups nodes in graphs. This framework can be wide span parametric random models allows include covariates. Variational tools allow us achieve approximate maximum likelihood estimation...
Alterations in gut microbiota composition and diversity were suggested to play a role the development of obesity, chronic subclinical inflammatory condition. We here evaluated impact oral consumption monostrain or multi-strain probiotic preparation high-fat diet-induced obese mice. observed strain-specific effect reported dissociation between capacity probiotics dampen adipose tissue inflammation limit body weight gain. A mixture was able improve adiposity, insulin resistance dyslipidemia...
Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral is limited by the lack knowledge phages infecting major gut commensal bacteria, such as Faecalibacterium prausnitzii, bacterial symbiont repeatedly found depleted inflammatory bowel disease (IBD) patients. In particular, no complete genomes F. prausnitzii are present databases. We identified 18 prophages 15 used comparative...
To study the evolution of several quantitative traits, classical phylogenetic comparative framework consists a multivariate random process running along branches tree. The Ornstein-Uhlenbeck (OU) is sometimes preferred to simple Brownian motion (BM) as it models stabilizing selection toward an optimum. optimum for each trait likely be changing over long periods time spanned by large modern phylogenies. Our goal automatically detect position these shifts on tree, while accounting correlations...
Background Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely a small subset of the sequences that can be associated known organisms. On other hand, de novo methods, compare whole sets sequences, either do not up ambitious provide precise and exhaustive results. Methods These limitations...
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution microscopic whose biogeographical patterns long been debated. Here we assessed global structure plankton geography and its relation to biological, chemical, physical context ocean (the ‘seascape’) by analyzing metagenomes communities sampled across oceans during Tara Oceans expedition, in light environmental data current...
Ticks transmit pathogens of medical and veterinary importance are an increasing threat to human animal health. Assessing disease risk developing new control strategies requires identifying members the tick-borne microbiota as well their temporal dynamics interactions.Using high-throughput sequencing, we studied Ixodes ricinus its dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After Poisson lognormal model was adjusted our data set,...
Several probiotic bacteria have been proposed for treatment or prevention of inflammatory bowel diseases (IBD), showing a protective effect in animal models experimental colitis and some them also human clinical trials. While most these are isolated from the digestive tract, we recently reported that Lactobacillus strain cheese, L. delbrueckii subsp. lactis CNRZ327 (Lb CNRZ327), possesses anti-inflammatory effects vitro vivo, demonstrating common dairy may be useful IBD. Here, studied...
Abstract Intestinal epithelium development is dramatically impaired in germfree rodents, but the consequences of absence microbiota have been overlooked other epithelia. In present study, we first description bacterial communities associated with olfactory and explored differences characteristics between conventional, specific pathogen-free, mice. While anatomy was not significantly different, observed a thinner cilia layer along decreased cellular turn-over Using electro-olfactogram,...
Propionibacterium freudenreichii, a dairy starter, can reach population of almost 109 propionibacteria per gram in Swiss-type cheese at the time consumption. Also consumed as probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 leukocytes. We selected 23 strains with varied potentials order to identify protein(s) involved. After comparative genomic analysis, 12 these were further analysed proteomics, eight them being submitted...
Abstract Next‐generation sequencing technologies give access to large sets of data, which are extremely useful in the study microbial diversity based on 16S rRNA gene. However, production such data is not only marred by technical biases and noise but also increases computation time disc space use. To improve accuracy OTU predictions overcome both computations, storage issues, recent studies tools suggested removing all single reads low abundant s, considering them as noise. Although effect...
Spring phenology of temperate trees has advanced worldwide in response to global warming. However, increasing temperatures may not necessarily lead further phenological advance, especially the warmer latitudes because insufficient chilling and/or shorter day length. Determining start forcing phase, that is, when buds are able respond spring, is therefore crucial predict how will change future. In this study, we used 4,056 leaf-out date observations during period 1969-2017 for clones European...
Current fructose consumption levels often overwhelm the intestinal capacity to absorb fructose. We investigated impact of malabsorption on endocrine function and addressed role microbiota in this process. To answer question, a mouse model moderate [ketohexokinase mutant (KHK)−/−] wild-type (WT) littermate mice were used received 20%-fructose (KHK-F WT-F) or 20%-glucose diet. Cholecystokinin (Cck) mRNA protein expression ileum cecum, as well preproglucagon (Gcg) neurotensin (Nts) increased...
Joint Species Distribution Models (JSDM) provide a general multivariate framework to study the joint abundances of all species from community. JSDM account for both structuring factors (environmental characteristics or gradients, such as habitat type nutrient availability) and potential interactions between (competition, mutualism, parasitism, etc.), which is instrumental in disentangling meaningful ecological mere statistical associations. Modeling dependency challenging because...
Fungi are present in all environments. They fulfil important ecological functions and play a crucial role the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi ITSs. These best documented public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads significant fraction of fungi. When these filtered out, traditional metabarcoding...
Food allergy is associated with alterations in the gut microbiota, epithelial barrier, and immune tolerance. These dysfunctions are observed within first months of life, indicating that early intervention crucial for disease prevention. Preventive nutritional strategies prebiotics an attractive option, as such galacto-oligosaccharides inulin can promote tolerance, barrier reinforcement, microbiota modulation. Nonetheless, ideal period remains unknown. Here, we investigated whether...
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists a random process running along branches phylogenetic tree relating We consider shifts parameters, which reveal fast adaptation to changes ecological niches. show that models with not identifiable general. Constraining be parsimonious number partially alleviates problem but several evolutionary scenarios can still...
Abstract Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution microscopic whose biogeographical patterns long been debated. Here we assessed global structure plankton geography and its relation to biological, chemical physical context ocean (the ‘seascape’) by analyzing metagenomes communities sampled across oceans during Tara Oceans expedition, in light environmental data...
A popular theory explaining the maintenance of genetic recombination (sex) is Red Queen Theory. This revolves around idea that time‐lagged negative frequency‐dependent selection by parasites favors rare host genotypes generated through recombination. Although has been studied for decades, one its key assumptions remained unsupported. The signature host‐parasite specificity underlying Queen, where infection depends on a match between and parasite genotypes, relies epistasis linked resistance...