A5103112411- Genomics and Phylogenetic Studies
- Parasitic Infections and Diagnostics
- Gut microbiota and health
- Plant Disease Resistance and Genetics
- Gene expression and cancer classification
- Microbial Community Ecology and Physiology
- Plant and Fungal Interactions Research
- Bacteriophages and microbial interactions
- Chromosomal and Genetic Variations
- Metabolomics and Mass Spectrometry Studies
- Plant Virus Research Studies
- Hydrocarbon exploration and reservoir analysis
- Escherichia coli research studies
- Diet and metabolism studies
- Anaerobic Digestion and Biogas Production
- Bioinformatics and Genomic Networks
- Enzyme Production and Characterization
- Microbial bioremediation and biosurfactants
- RNA modifications and cancer
- Bacterial biofilms and quorum sensing
- DNA and Biological Computing
- HIV/AIDS drug development and treatment
- Polyamine Metabolism and Applications
- Cancer, Lipids, and Metabolism
- CRISPR and Genetic Engineering
Université Clermont Auvergne
2013-2025
Centre National de la Recherche Scientifique
2008-2024
Laboratoire Microorganismes Génome et Environnement
2006-2023
Microbiologie Environnement Digestif Santé
2017
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2017
Genetique Reproduction and Developpement
2017
Teagasc - The Irish Agriculture and Food Development Authority
2013
Netherlands Environmental Assessment Agency
2013
Agriculture and Agri-Food Canada
2013
Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes
2011
A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including gastrointestinal tracts (GIT) humans and other animals may contribute significantly to methane emission global warming. Methanomassiliicoccales are phylogenetically distant from all orders methanogens belong a large evolutionary branch composed by lineages non-methanogenic archaea such as Thermoplasmatales, Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2,...
ABSTRACT We report the draft genome sequence of “ Candidatus Methanomethylophilus alvus” Mx1201, a methanogen present in human gut. It was enriched from feces under anaerobic conditions with methanol as substrate. Its circular genome, around 1.7 Mb, contains genes needed for methylotrophic methanogenesis and tri-, di-, monomethylamine.
Background Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and replicate within intestinal epithelial cells macrophages. Principal Findings We report here the complete genome sequence E. LF82, reference strain associated with ileal disease. The LF82 4,881,487 bp total size contains a circular chromosome 4,773,108 plasmid 108,379 bp. analysis predicted coding sequences (CDSs) flexible indicated that...
The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there no reference for long-term monitoring unsaturated zone. To assess potential effect air supply on hydrocarbon fate structure, two treatments (0 0.056 mol h⁻¹ molar flow rate oxygen) were performed in fixed bed reactors containing soil. Microbial activity was monitored continuously over 2 years throughout process. structure before after treatment 12 24 months...
Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through activity rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding relative contribution microbiota members and enzymes vivo. The present study used RNA-sequencing reveal both expression genes encoding carbohydrate-active (CAZymes) by lactating dairy cow microorganisms forming fiber-degrading community. Functional analysis identified 12,237 CAZymes,...
Abstract Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) subject to increased monitoring due their distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing investigate impact...
"Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1 is a methanogenic archaeon found in the human gut and representative of novel order methanogens related to Thermoplasmatales. Its complete genome sequence presented here.
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces digestive tract. Although metabolism B[a]P by host cells well known, its impacts on human gut microbiota, plays key role in health disease, remain unexplored. We performed an vitro assay using 16S barcoding, metatranscriptomics volatile metabolomics study...
Microsporidian genomes are the leading models to understand streamlining in response a pathogenic lifestyle; they gene-poor and often possess small genomes. In this study, we show feature of microsporidian that contrasts pattern genome reduction. Specifically, investigations targeted at Anncaliia algerae, human pathogen with size 23 Mb, revealed presence hitherto undetected diversity transposable elements (TEs). A total 240 TE families per were identified, exceeding found many free-living...
Microsporidia are obligate intracellular parasites able to infect a wide range of hosts from invertebrates vertebrates. The success their invasion process is based on an original organelle, the polar tube, which suddenly extruded spore inoculate sporoplasm into host cytoplasm. tube mainly composed proteins named (PTPs). A comparative analysis allowed us identify genes coding for 5 PTPs (PTP1 PTP5) in genome microsporidian Anncaliia algerae. While PTP1 and PTP2 found whole PTP3 present large...
<title>Abstract</title> Among the most severe honeybee diseases, American and European foulbroods caused by <italic>Paenibacillus larvae</italic> <italic>Melissococcus plutonius</italic>, respectively pose a significant threat to larval health colony survival. Due lack of safe effective treatments, interest is growing in use beneficial bacterial supplements as promising alternative antibiotics. This study evaluated probiotic postbiotic potential selected strains against foulbrood pathogens....
Abstract Summary: KASpOD is a web service dedicated to the design of signature sequences using k-mer–based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays. Availability: http://g2im.u-clermont1.fr/kaspod. Contact: eric.peyretaillade@udamail.fr Supplementary information: data available at Bioinformatics online.
New generations of sequencing platforms coupled to numerous bioinformatics tools have led rapid technological progress in metagenomics and metatranscriptomics investigate complex microorganism communities. Nevertheless, a combination different bioinformatic remains necessary draw conclusions out microbiota studies. Modular user-friendly would greatly improve such studies.We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated data analyses. ASaiM provides extensive...
Antigen 43 (Ag43) expression induces aggregation and biofilm formation that has consequences for bacterial colonisation infection. Ag43 is secreted through the Type 5 subtype “a” secretion system (T5aSS) a prototypical member of family self-associating autotransporters (SAATs). As T5aSS protein, modular architecture comprised (i) signal peptide, (ii) passenger domain can be subdivided into three subdomains (SL, EJ, BL), (iii) an autochaperone (AC) domain, (iv) outer membrane translocator....
Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp) and highly compact (~1 gene/kb) genome of the human parasite Encephalitozoon cuniculi has been fully sequenced. aim this study was characterize noncoding motifs that could be involved regulation gene expression E. show whether these conserved among phylum Microsporidia. To identify such signals, 5' 3'RACE-PCR experiments were performed on...
Intracellular pathogens including bacteria, viruses and protozoa hijack host cell functions to access nutrients bypass cellular defenses immune responses. These strategies have been acquired through selective pressure allowed reach an appropriate niche for their survival growth. To get new insights on how parasites functions, we developed a SILAC (Stable Isotope Labeling by Amino Acids in Cell culture) quantitative proteomics workflow. Our study focused deciphering the cross-talk...
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate genes from uncultured microorganisms. However, none the used environmental genomics allow for rapid isolation numerous eukaryotic communities. We developed an original adaptation solution hybrid selection (SHS) efficient recovery complementary DNAs (cDNAs) synthesized...
With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions these microorganisms, complete genome sequencing is routinely used. Nevertheless, proper prediction their gene catalogue challenging due to taxon-specific evolutionary features. As innovative annotation strategies are needed obtain representative snapshot overall lifestyle parasites, MicroAnnot tool,...
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of AIDS pandemic. As RNA world was largely unexplored in this parasitic lineage, we developed a dedicated silico methodology carry out exhaustive identification ncRNAs across Encephalitozoon and Nosema genera. Thus, previously missing U1 small nuclear (snRNA) nucleolar RNAs (snoRNAs) targeting only LSU rRNA were highlighted further validated using 5' 3'RACE-PCR...