Pierre Peyret

• Professor at University of Clermont Auvergne

The discovery that the lung harbors a diverse microbiome, as revealed by next-generation sequencing, has significantly altered our understanding of respiratory health and disease. Despite the association between the lung microbiota and disease, the nature of their relationship remains poorly understood, and culture isolation of these microorganisms...

Background: Sorafenib is a standard therapeutic agent for advanced hepatocellular carcinoma (HCC). But its efficacy is moderate because the survival of patients is only extended by a few months, and the response rate is low and the mechanism of low efficacy is unclear. In this study, we investigated the effect of TLR3 on sorafenib against HCC. Meth...

In recent decades, preterm birth (PTB) has become a significant research focus in the healthcare field, as it is a leading cause of neonatal mortality worldwide. Using five independent study cohorts including 1290 vaginal samples from 561 pregnant women who delivered at term (n = 1029) or prematurely (n = 261), we analysed vaginal metagenomics data...

Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to sign...

Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used appr...

How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phe...

Metagenomic classifiers are widely used for the taxonomic profiling of metagenomics data and estimation of taxa relative abundance. Small subunit rRNA genes are a gold standard for phylogenetic resolution of microbiota, although the power of this marker comes down to its use as full-length. We aimed at identifying the tools that can efficiently lea...

Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162...

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative...

Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestratio...

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remai...

The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surfac...

Biodiversity inventory remains limited in marine systems due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remai...

Résumé La population humaine est exposée à de très nombreux contaminants chimiques environnementaux et alimentaires (métaux lourds, pesticides, nanoparticules, plastiques, polluants organiques persistants, additifs alimentaires, produits néoformés). Ces expositions pourraient perturber le microbiote intestinal, acteur clé de la santé humaine, et ai...

Objective: Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pi...

Les champignons constituent un réservoir d’enzymes considérable pouvant avoir différentes applications industrielles. Parmi les enzymes secrétées, les peroxydases à hèmes de type DyP (Dye-decolorizing Peroxidases) assurant la réaction d’oxydation d’une large variété de substrats organiques, essentiellement aromatiques, constituent des biocatalyseur...

Growing evidence indicates that the human gut microbiota interacts with xenobiotics, including persistent organic pollutants and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern since chemicals may disrupt gut microbiota functions, with a potential impairment of host homeostasis. Herein...

Background New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Mo...

Chloromethane (CH3Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH3Cl budget are approximate. The strength of the CH3Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly fer...

Background: Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discove...

Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity,...

While the xylem hydraulic properties, such as vulnerability to cavitation (VC), are of paramount importance in drought resistance, their genetic determinants remain unexplored. There is evidence that pectins and their methylation pattern are involved, but the detail of their involvement and the corresponding genes need to be clarified. We analysed...

Background New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Mod...

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 the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on...

Background High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft ge...

Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosem...

The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing env...

Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the...

Microorganisms hold key positions in ecosystem functioning, and thus in biogeochemical cycles. Among these cycles, some, such as chlorine (Cl), are still poorly understood. Recent works have revealed that natural chlorination and dechlorination of organic matter (OM) in most of the ecosystems were much more extensive and ubiquitous than previously...

Table S1. Primers and gene capture probes used in this study.

Table S2. Summary statistics from bssA gene capture coupled to Illumina sequencing.

The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this micro...

To reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in bi...

Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are su...

Stratégies de reconstruction de génomes microbiens à partir de métagénomes

Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance an...

The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of s...

Pseudomonas sp. HUK17 has been isolated from hexachlorocyclohexane (HCH) long-term contaminated soil. The genome of strain HUK17 was sequenced to elucidate its adaptation toward HCH and to evaluate the presence of pesticide degradation pathways. Here, we report the annotated draft genome sequence (~2.6 Mbp) of this strain.

Bacillus subtilis strain HUK15 has been isolated from hexachlorocyclohexane (HCH)-long-term-contaminated soil. The genome of strain HUK15 was sequenced to investigate its adaptation toward HCH and its potential capability to degrade the pesticide. Here, we report the annotated draft genome sequence (~4.3 Mbp) of this strain.

Staphylococcus aureus strain HUK16 has been isolated from hexachlorocyclohexane (HCH)-long-term contaminated soil. The genome of strain HUK16 was sequenced to understand the genetic basis of its adaptation to HCH and to find the potential metabolic pathways allowing it to degrade the pesticide. Here, we report the annotated draft genome sequence (~...

Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achiev...

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% sim...

Qualité des données NGS : de la séquence aux bases de données

The proper prediction of the gene catalogue of an organism is essential to obtain a representative snapshot of its overall lifestyle, especially when it is not amenable to culturing. Microsporidia are obligate intracellular, sometimes hard to culture, eukaryotic parasites known to infect members of every animal phylum. To date, sequencing and annot...

Metatranscriptomic data allow active microbial communities description by gene products analysis. In comparison to metagenomic studies, few metatranscriptomic data have been obtained on environmental ecosystems (soil, water, mine drainage…) as on human-associated microbiota despite health concerns. This discrepancy is due to difficulties in RNA rec...

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, l...

Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th...

The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategi...

The main methods for the study of microorganisms in the environment (water, soil, sediment, biofilms), the different techniques of sampling for measuring biomass, the activities, and the diversity of the microorganisms are presented. To respond to these various issues, techniques as varied as those of flow cytometry, molecular biology, biochemistry...

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 functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a ra...

Complete backtranslation is the step of generating all possible nucleic acid sequences from a protein sequence. This is a time-consuming task that can provide unreasonable quantities of data. Complete backtranslation was recently used to initiate probe design for functional DNA microarrays from conserved peptidic regions, in order to assess the ful...

Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem s...

Background A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of m...

Oligonucleotide microarrays have been widely used for gene detection and quantification of gene expression. Recently, they have been adapted for profiling microbial communities in a flexible and easy-to-use manner. In fact, it is possible to analyse both the microbial diversity and the metabolic capacity of complex communities in one experiment. Ho...