Publications by authors named "Valentin Loux"

83 Publications

GO Enrichment Analysis for Differential Proteomics Using ProteoRE.

Methods Mol Biol 2021 ;2361:179-196

Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France.

With the increased simplicity of producing proteomics data, the bottleneck has now shifted to the functional analysis of large lists of proteins to translate this primary level of information into meaningful biological knowledge. Tools implementing such approach are a powerful way to gain biological insights related to their samples, provided that biologists/clinicians have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed ProteoRE (Proteomics Research Environment), a unified online research service that provides end-users with a set of tools to interpret their proteomics data in a collaborative and reproducible manner. ProteoRE is built upon the Galaxy framework, a workflow system allowing for data and analysis persistence, and providing user interfaces to facilitate the interaction with tools dedicated to the functional and the visual analysis of proteomics datasets. A set of tools relying on computational methods selected for their complementarity in terms of functional analysis was developed and made accessible via the ProteoRE web portal. In this chapter, a step-by-step protocol linking these tools is designed to perform a functional annotation and GO-based enrichment analyses applied to a set of differentially expressed proteins as a use case. Analytical practices, guidelines as well as tips related to this strategy are also provided. Tools, datasets, and results are freely available at http://www.proteore.org , allowing researchers to reuse them.
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http://dx.doi.org/10.1007/978-1-0716-1641-3_11DOI Listing
January 2022

Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions.

J Environ Manage 2021 Aug 28;291:112631. Epub 2021 Apr 28.

Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil. Electronic address:

Energy recovery from lignocellulosic waste has been studied as an alternative to the problem of inappropriate waste disposal. The present study aimed at characterizing the microbial community and the functional activity of reactors applied to H production through lignocellulosic waste fermentation in optimized conditions. The latter were identified by means of Rotational Central Composite Design (RCCD), applied to optimize allochthonous inoculum concentration (2.32-5.68 gTVS/L of granular anaerobic sludge), pH (4.32-7.68) and Citrus Peel Waste (CPW) concentration (1.55-28.45 g/L). After validation, the conditions identified for optimal H production were 4 gSTV/L of allochthonous inoculum, 29.8 g/L of CPW (substrate) and initial pH of 8.98. In these conditions, 48.47 mmol/L of H was obtained, which is 3.64 times higher than the concentration in unoptimized conditions (13.31 mmol H/L using 15 g/L of CPW, 2 gTVS/L of allochthonous inoculum, pH 7.0). Acetogenesis was the predominant pathway, and maximal concentrations of 3,731 mg/L of butyric acid and 3,516 mg/L of acetic acid were observed. Regarding the metataxonomic profile, Clostridium genus was dramatically favored in the optimized condition (79.78%) when compared to the allochthonous inoculum (0.43%). It was possible to identify several genes related to H (i.e dehydrogenases) and volatile fatty acids (VFA) production and with cellulose degradation, especially some CAZymes from the classes Auxiliary Activities, Glycoside Hydrolases and Glycosyl Transferase. By means of differential gene expression it was observed that cellulose degradation and acetic acid production pathways were overabundant in samples from the optimized reactors, highlighting endo-β-1,4-glucanase/cellulose, endo-β-1,4-xylanase, β-glucosidase, β-mannosidase, cellulose β-1,4-cellobiosidase, cellobiohydrolase, and others, as main the functions.
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http://dx.doi.org/10.1016/j.jenvman.2021.112631DOI Listing
August 2021

Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

Environ Microbiol Rep 2021 Jun 24;13(3):364-374. Epub 2021 Mar 24.

UMR 7618 iEES-Paris Sorbonne Université 4 place Jussieu - 75252 Paris Cedex 05, France.

Specific interactions have been highlighted between cyanobacteria and chemotrophic bacteria within the cyanosphere, suggesting that nutrients recycling could be optimized by cyanobacteria/bacteria exchanges. In order to determine the respective metabolic roles of the cyanobacterial and bacterial consortia (microbiome), a day-night metatranscriptomic analysis was performed on Dolichospermum sp. (N -fixer) and Microcystis sp. (non N -fixer) natural blooms occurring successively within a French peri-urban lake. The taxonomical and functional analysis of the metatranscriptoms have highlighted specific association of bacteria within the cyanosphere, driven by the cyanobacteria identity, without strongly modifying the functional composition of the microbiomes, suggesting functional redundancy within the cyanosphere. Moreover, the functional composition of these active communities was driven by the living mode. During the two successive bloom events, it appeared that NH (newly fixed and/or allochthonous) was preferentially transformed into amino acids for the both the microbiome and the cyanobacteria, while phosphate metabolism was enhanced, suggesting that due to a high cellular growth, P limitation might take place within the cyanosphere consortium.
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http://dx.doi.org/10.1111/1758-2229.12944DOI Listing
June 2021

Complete Genome Sequence of Staphylococcus epidermidis PH1-28, Isolated from the Forehead of a Hyperseborrheic Donor.

Microbiol Resour Announc 2021 Mar 4;10(9). Epub 2021 Mar 4.

L'Oréal R&I, Aulnay-sous-Bois, France

We report the complete genome sequence of commensal strain PH1-28, isolated from the forehead of a healthy donor. The assembled 2.6-Mbp genome consisted of one chromosome and five plasmids. These data will provide valuable information and important insights into the physiology and metabolism of this skin flora microorganism.
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http://dx.doi.org/10.1128/MRA.00165-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936632PMC
March 2021

Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of to the Environment.

Genes (Basel) 2020 08 26;11(9). Epub 2020 Aug 26.

Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France.

is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in adaptation to the environment.
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http://dx.doi.org/10.3390/genes11090999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563491PMC
August 2020

Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere.

Data Brief 2020 Jun 20;30:105453. Epub 2020 Mar 20.

INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France.

Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon. The analysis includes: the gas content in packaging, pH, chromametric measurements, plate counts (total mesophilic aerobic flora and lactic acid bacteria), sensorial properties of the products, meta-metabolomic quantification of volatile organic compounds and bacterial community metagenetic analysis. Bacterial diversity was monitored using two types of amplicon sequencing (16S rRNA and GyrB encoding genes) at different time points for the different conditions (576 samples for gyrB and 436 samples for 16S rDNA). Sequencing data were generated by using Illumina MiSeq. The sequencing data have been deposited in the bioproject PRJNA522361. Samples accession numbers vary from SAMN10964863 to SAMN10965438 for gyrB amplicon and from SAMN10970131 to SAMN10970566 for 16S.
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http://dx.doi.org/10.1016/j.dib.2020.105453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152715PMC
June 2020

The complete genome sequence of Mycobacterium bovis Mb3601, a SB0120 spoligotype strain representative of a new clonal group.

Infect Genet Evol 2020 08 30;82:104309. Epub 2020 Mar 30.

Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Animal Health Laboratory, National reference Laboratory for Tuberculosis, 94701 Maisons-Alfort cedex, France. Electronic address:

Mycobacterium bovis strain Mb3601 was isolated from the lymph node of an infected bovine in a bovine tuberculosis highly enzoonotic area of Burgundy, France. It was selected to obtain a complete genome for a new clonal complex, mainly constituted by SB0120-spoligotype strains that we propose to name "European 3". It was recently described as "clonal group I" based on whole-genome SNP analysis of 87 French strains. Here we describe the 4,365,068 bp complete genome obtained by the combination of PacBio and Illumina technologies. This genome of 65.64% G + C content includes 4024 predicted protein-coding genes, 52 tRNA, 3 rRNA and 11 copies of IS6110.
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http://dx.doi.org/10.1016/j.meegid.2020.104309DOI Listing
August 2020

The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition.

ISME J 2020 03 11;14(3):771-787. Epub 2019 Dec 11.

Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.

Despite an overall temporal stability in time of the human gut microbiota at the phylum level, strong variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses, which can evolve to become ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammal's microbiota has been largely unexplored. Here we studied temperate phage-bacteria coevolution in gnotoxenic mice colonised with Roseburia intestinalis, a dominant symbiont of the human gut microbiota, and Escherichia coli, a sub-dominant member of the same microbiota. We show that R. intestinalis L1-82 harbours two active prophages, Jekyll and Shimadzu. We observed the systematic evolution in mice of ultravirulent Shimadzu phage mutants, which led to a collapse of R. intestinalis population. In a second step, phage infection drove the fast counter-evolution of host phage resistance mainly through phage-derived spacer acquisition in a clustered regularly interspaced short palindromic repeats array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize. Our results demonstrate that prophages are a potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.
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http://dx.doi.org/10.1038/s41396-019-0566-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031369PMC
March 2020

Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses.

Food Res Int 2019 11 23;125:108643. Epub 2019 Aug 23.

UMR 787 Génie et Microbiologie des Procédés Alimentaires, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France. Electronic address:

Sodium reduction in the human diet is currently one of the main concerns for public health agencies and, consequently, has become a challenge for the food industries. In this study, the impact of reduced sodium chloride content (20%) or its partial substitution with potassium chloride in soft ("Camembert"-type) and semi-hard ("Reblochon"-type) cheeses was evaluated. Analyses included physicochemical and biochemical composition, microbial counts, 16S rRNA gene metabarcoding and metatranscriptomic analysis, volatile aroma compounds and sensory analysis. Regarding soft cheeses, the salt content of cheeses affected proteolysis at 21 days of ripening. RNA sequencing revealed that the relative activity of G. candidum increased, whereas that of P. camemberti decreased in reduced salt cheeses in comparison to the controls. Higher global intensity of odor and taste was observed in cheeses with reduced salt content, consistent with higher levels of alcohol and ester components. Regarding semi-hard cheeses, modifications of salt content did not significantly affect either their biochemical parameters and sensory characteristics or their technological microbial composition at day 21 of ripening. Finally, no impact of salt content was observed on the growth of the spoiler Yarrowia lipolytica in soft cheeses. In contrast, reducing salt content increased spoiler growth in semi-hard cheeses, as highlighted by a greater development of Pseudomonas that led to an increase in cheese proteolysis and lipolysis. In conclusion, the effect of reducing salt content is highly dependent on the cheese type. This factor should thus be taken into account by the dairy industry when the reduction of salt content is being considered. Moreover, the quality of raw products, in particular, the level of spoiler microorganisms, must be controlled before use during dairy processes.
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http://dx.doi.org/10.1016/j.foodres.2019.108643DOI Listing
November 2019

Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer.

Proteomics 2019 11 10;19(21-22):e1800489. Epub 2019 Oct 10.

University of Grenoble Alpes, INSERM, CEA, IRIG-BGE, U1038, Grenoble, 38000, France.

Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. A knowledge-based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available "omics" information. With the aim of accelerating the discovery process for novel biomarkers, a set of tools is developed and made available via a Galaxy-based instance to assist end-users biologists. These implemented tools proceed by a step-by-step strategy to mine transcriptomics and proteomics databases for information relating to tissue specificity, allow the selection of proteins that are part of the secretome, and combine this information with proteomics datasets to rank the most promising candidate biomarkers for early cancer diagnosis. Using pancreatic cancer as a case study, this strategy produces a list of 24 candidate biomarkers suitable for experimental assessment by MS-based proteomics. Among these proteins, three (SYCN, REG1B, and PRSS2) were previously reported as circulating candidate biomarkers of pancreatic cancer. Here, further refinement of this list allows to prioritize 14 candidate biomarkers along with their associated proteotypic peptides for further investigation, using targeted MS-based proteomics. The bioinformatics tools and the workflow implementing this strategy for the selection of candidate biomarkers are freely accessible at http://www.proteore.org.
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http://dx.doi.org/10.1002/pmic.201800489DOI Listing
November 2019

Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework.

Methods Mol Biol 2019 ;1959:275-289

Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France.

Knowledge-based approaches using large-scale biological ("omics") data are a powerful way to identify mechanistic biomarkers, provided that scientists have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed a set of tools under the Galaxy framework to allow biologists to define their own strategy for reproducible biomarker selection. These tools rely on retrieving experimental data from public databases, and applying successive filters derived from information relating to disease pathophysiology. A step-by-step protocol linking these tools was implemented to select tissue-leakage biomarker candidates of myocardial infarction. A list of 24 candidates suitable for experimental assessment by MS-based proteomics is proposed. These tools have been made publicly available at http://www.proteore.org , allowing researchers to reuse them in their quest for biomarker discovery.
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http://dx.doi.org/10.1007/978-1-4939-9164-8_18DOI Listing
July 2019

Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.

Microbiol Resour Announc 2018 Aug 30;7(8). Epub 2018 Aug 30.

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.

Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt and cheese. We report here the complete genome sequence of the industrial strain S. thermophilus N4L, which is used in dairy technology for its fast-acidifying phenotype.
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http://dx.doi.org/10.1128/MRA.01029-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256512PMC
August 2018

Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products.

BMC Res Notes 2018 Nov 8;11(1):802. Epub 2018 Nov 8.

MICALIS, INRA AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France.

Objectives: Sequencing of 16S rDNA V3-V4 region is widely applied for food community profiling. However, two different universal forward primers (named here MUYZER-primer1 and KLINDWORTH-primer2) targeting an identical conservative sequence upstream of the V3 region of 16S rRNA gene, and only distinguished by a single mismatch are both used. This study was carried out to compare whether the accuracy of food microbiota analysis would depend on the choice of one of these two primers.

Results: Alignment of both primers with common food-borne bacteria 16S sequences revealed that the mismatch between both primers might specifically affect the amplification of Leuconostoc, Oenococcus and Fructobacillus species but not Weissella species. Food products containing either Leuconostoc and/or Weissella were selected for a detection test. As expected from our in silico analysis, our study showed that this mismatch induced a strong biased amplification specifically associated to the OTUs belonging to the genus Leuconostoc but not to the genus Weissella. In presence of Muyzer-primer1, none of the sequences expected for Leuconostoc genus was detected whereas those sequences were correctly amplified with Klindworth-primer2. Since Leuconostoc is an important genus in food, agro-environments and in digestive tract of animals, we recommend that Muyzer-primer1 should thus be abandoned for the bacterial characterization of their associated microbiota.
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http://dx.doi.org/10.1186/s13104-018-3908-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225703PMC
November 2018

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.

PLoS One 2018 25;13(9):e0204629. Epub 2018 Sep 25.

MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.

Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204629PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155546PMC
March 2019

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater.

Sci Total Environ 2019 Feb 27;649:482-494. Epub 2018 Aug 27.

Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil.

Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LW showed similar values of LAS biological degradation (~47%) and removal (53-55%). Rarefaction analysis revealed that 1-2 million reads were sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative gene was ten times higher in UASB_SL and UASB_LW when compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.
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http://dx.doi.org/10.1016/j.scitotenv.2018.08.328DOI Listing
February 2019

Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes.

Genome Announc 2018 Apr 19;6(16). Epub 2018 Apr 19.

MICALIS institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France

We present here the complete and draft genome sequences of nine strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.
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http://dx.doi.org/10.1128/genomeA.00082-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908949PMC
April 2018

Genomic Diversity and Evolution of the Fish Pathogen .

Front Microbiol 2018 7;9:138. Epub 2018 Feb 7.

Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France.

, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout () worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of , a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.
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http://dx.doi.org/10.3389/fmicb.2018.00138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808330PMC
February 2018

The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.

J Biomed Semantics 2017 Nov 23;8(1):53. Epub 2017 Nov 23.

INRA, UR1404, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France.

Background: High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods such as bio-ontologies to extract and share valuable information. In parallel, the development of recent whole-cell models using a systemic cell description opened alternatives for data integration. Integrating a systemic cell description within a bio-ontology would help to progress in whole-cell data integration and modeling synergistically.

Results: We present BiPON, an ontology integrating a multi-scale systemic representation of bacterial cellular processes. BiPON consists in of two sub-ontologies, bioBiPON and modelBiPON. bioBiPON organizes the systemic description of biological information while modelBiPON describes the mathematical models (including parameters) associated with biological processes. bioBiPON and modelBiPON are related using bridge rules on classes during automatic reasoning. Biological processes are thus automatically related to mathematical models. 37% of BiPON classes stem from different well-established bio-ontologies, while the others have been manually defined and curated. Currently, BiPON integrates the main processes involved in bacterial gene expression processes.

Conclusions: BiPON is a proof of concept of the way to combine formally systems biology and bio-ontology. The knowledge formalization is highly flexible and generic. Most of the known cellular processes, new participants or new mathematical models could be inserted in BiPON. Altogether, BiPON opens up promising perspectives for knowledge integration and sharing and can be used by biologists, systems and computational biologists, and the emerging community of whole-cell modeling.
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http://dx.doi.org/10.1186/s13326-017-0165-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701433PMC
November 2017

Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica.

Int J Food Microbiol 2018 Jan 24;264:53-62. Epub 2017 Oct 24.

UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France.

Yeasts play a crucial role in cheese ripening. They contribute to the curd deacidification, the establishment of acid-sensitive bacterial communities, and flavour compounds production via proteolysis and catabolism of amino acids (AA). Negative yeast-yeast interaction was observed between the yeast Yarrowia lipolytica 1E07 (YL1E07) and the yeast Debaryomyces hansenii 1L25 (DH1L25) in a model cheese but need elucidation. YL1E07 and DH1L25 were cultivated in mono and co-cultures in a liquid synthetic medium (SM) mimicking the cheese environment and the growth inhibition of DH1L25 in the presence of YL1E07 was reproduced. We carried out microbiological, biochemical (lactose, lactate, AA consumption and ammonia production) and transcriptomic analyses by microarray technology to highlight the interaction mechanisms. We showed that the DH1L25 growth inhibition in the presence of YL1E07 was neither due to the ammonia production nor to the nutritional competition for the medium carbon sources between the two yeasts. The transcriptomic study was the key toward the comprehension of yeast-yeast interaction, and revealed that the inhibition of DH1L25 in co-culture is due to a decrease of the mitochondrial respiratory chain functioning.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.026DOI Listing
January 2018

Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group.

Syst Appl Microbiol 2017 Oct 24;40(7):401-410. Epub 2017 Aug 24.

Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France. Electronic address:

Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
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http://dx.doi.org/10.1016/j.syapm.2017.07.002DOI Listing
October 2017

Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements.

Genome Biol Evol 2017 05;9(5)

Université de Strasbourg, CHRU de Strasbourg, VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Institut de bactériologie, Hôpitaux Universitaires de Strasbourg, France.

Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements. S. lugdunensis also bears various putative virulence genes but only one complete genome with extensive analysis has been published with one prophage sequence (φSL2) and a unique plasmid was previously described. In this study, we performed de novo sequencing, whole genome assembly and annotation of seven strains of S. lugdunensis from VISLISI clinical trial. We searched for the presence of virulence genes and mobile genetics elements using bioinformatics tools. We identified four new prophages, named φSL2 to φSL4, belonging to the Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three plasmids are homologous to known plasmids that include, amongst others, one S. aureus plasmid. The two other plasmids were not described previously. This study provides a new context for the study of S. lugdunensis virulence suggesting the occurrence of several genetic recombination' with other staphylococci.
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http://dx.doi.org/10.1093/gbe/evx077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425232PMC
May 2017

Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study.

Sci Rep 2017 04 13;7:46409. Epub 2017 Apr 13.

STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France.

Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 10 propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We selected 23 strains with varied anti-inflammatory potentials in order to identify the protein(s) involved. After comparative genomic analysis, 12 of these strains were further analysed by surface proteomics, eight of them being further submitted to transcriptomics. The omics data were then correlated to the anti-inflammatory potential evaluated by IL-10 induction. This comparative omics strategy highlighted candidate genes that were further subjected to gene-inactivation validation. This validation confirmed the contribution of surface proteins, including SlpB and SlpE, two proteins with SLH domains known to mediate non-covalent anchorage to the cell-wall. Interestingly, HsdM3, predicted as cytoplasmic and involved in DNA modification, was shown to contribute to anti-inflammatory activity. Finally, we demonstrated that a single protein cannot explain the anti-inflammatory properties of a strain. These properties therefore result from different combinations of surface and cytoplasmic proteins, depending on the strain. Our enhanced understanding of the molecular bases for immunomodulation will enable the relevant screening for bacterial resources with anti-inflammatory properties.
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http://dx.doi.org/10.1038/srep46409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390290PMC
April 2017

A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.

Front Microbiol 2017 20;8:443. Epub 2017 Mar 20.

UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.

Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.
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http://dx.doi.org/10.3389/fmicb.2017.00443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357655PMC
March 2017

Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue.

Sci Rep 2017 03 10;7:44331. Epub 2017 Mar 10.

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.

The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.
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http://dx.doi.org/10.1038/srep44331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345009PMC
March 2017

Complete Genome Sequence of Strain OSU THCO2-90, Used for Functional Genetic Analysis.

Genome Announc 2017 Feb 23;5(8). Epub 2017 Feb 23.

VIM, INRA, Université Paris-Saclay, Jouy-en-Josas, France

We report here the complete annotated genome sequence of OSU THCO2-90, isolated from Coho salmon () in Oregon. The genome consists of a circular chromosome with 2,343 predicted open reading frames. This strain has proved to be a valuable tool for functional genomics.
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http://dx.doi.org/10.1128/genomeA.01665-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5323625PMC
February 2017

Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group.

Genome Announc 2017 Feb 2;5(5). Epub 2017 Feb 2.

UMR408 Sécurité et Qualité des Produits d'Origine Végétale, INRA, Université d'Avignon, Avignon, France.

Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through different ecotypes. Here, we present the draft genome sequences of 20 bacterial strains belonging to the contrasted psychrotolerant and thermotolerant ecotypes.
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http://dx.doi.org/10.1128/genomeA.01568-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289691PMC
February 2017

Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe.

Genome Announc 2016 Dec 1;4(6). Epub 2016 Dec 1.

Université Paris-Est, École Nationale Vétérinaire d'Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France

Anaplasma phagocytophilum is a zoonotic tick-borne intracellular bacterium responsible for granulocytic anaplasmosis. As it is difficult to isolate and cultivate, only 20 A. phagocytophilum genomes have been sequenced to date. Here, we present eight A. phagocytophilum genome sequences obtained using alternative approaches based on sequence capture technology.
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http://dx.doi.org/10.1128/genomeA.00950-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137398PMC
December 2016

Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.

Genome Announc 2016 Sep 15;4(5). Epub 2016 Sep 15.

Université de Toulouse, Université Paul Sabatier, Toulouse, France CNRS, UMR 5100, Toulouse, France Université de Toulouse, INSA, UPS, INP, Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France CNRS, UMR5504, Toulouse, France

We report here the complete genome sequence of Lactococcus lactis subsp. lactis strain A12, a strain isolated from sourdough. The circular chromosome and the four plasmids reveal genes involved in carbohydrate metabolism that are potentially required for the persistence of this strain in such a complex ecosystem.
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http://dx.doi.org/10.1128/genomeA.00692-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026425PMC
September 2016

Draft Genome Sequence of Corynebacterium variabile Mu292, Isolated from Munster, a French Smear-Ripened Cheese.

Genome Announc 2016 Jul 21;4(4). Epub 2016 Jul 21.

UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France

Here, we report the draft genome sequence of Corynebacterium variabile Mu292, which was originally isolated from the surface of Munster, a French smear-ripened cheese. This genome investigation will improve our knowledge on the molecular determinants potentially involved in the adaptation of this strain during the Munster-type cheese manufacturing process.
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http://dx.doi.org/10.1128/genomeA.00669-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956445PMC
July 2016

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

Genome Announc 2016 Mar 3;4(2). Epub 2016 Mar 3.

UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.
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http://dx.doi.org/10.1128/genomeA.00052-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777752PMC
March 2016
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