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BackgroundTicks transmit pathogens of medical and veterinary importance, and represent an increasing threat for human and animal health. Important steps in assessing disease risk and developing possible new future control strategies involve identifying tick-borne microbes, their temporal dynamics and interactions.MethodsUsing high throughput sequencing, we studied the microbiota dynamics ofIxodes ricinusfrom 371 nymphs collected monthly over three consecutive years in a peri-urban forest. After adjusting a Poisson Log Normal model to our data set, the implementation of a principal component analysis as well as sparse network reconstruction and differential analysis allowed us to assess inter-annual, seasonal and monthly variability ofI. ricinusmicrobial communities as well as their interactions.ResultsAround 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and potentially circulating in ticks: CandidatusMidichloria, Rickettsia, Spiroplasma, ArsenophonusandWolbachia. The structure of theI. ricinusmicrobiota was temporally variable with interannual recurrence and seemed to be mainly driven by OTUs belonging to environmental genera. The total network analysis revealed a majority of positive (partial) correlations. We identified strong relationships between OTUs belonging toWolbachiaandArsenophonus, betraying the presence of the parasitoid waspIxodiphagus hookeriin ticks, and the well known arthropod symbiontSpiroplasma, previously documented to be involved in the defense against parasitoid wasp inDrosophila melanogaster. Other associations were observed between the tick symbiont CandidatusMidichloriaand pathogens belonging toRickettsia, probablyRickettsia helvetica. More specific network analysis finally suggested that the presence of pathogens belonging to generaBorrelia, AnaplasmaandRickettsiamight disrupt microbial interactions inI. ricinus.ConclusionsHere, we identified theI. ricinusmicrobiota and documented for the first time the existence and recurrence of marked temporal shifts in the tick microbial community dynamics. We statistically showed strong relationships between the presence of some pathogens and the structure of theI. ricinusnon-pathogenic microbes. We interestingly detected close links between some tick symbionts and the potential presence of either pathogenicRickettsiaor a parasitoid in ticks. All these new findings might be very promising for the future development of new control strategies of ticks and tick-borne diseases.

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance, but the extent of their functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built the first equine gut microbial gene catalog comprising more than 25 million non-redundant genes representing 4,696 genera spanning 95 phyla. The unprecedented resolution unrevealed functional pathways relevant for both the structure of the microbiome and the host health and recovered 369 novel metagenome-assembled bacterial genomes, providing useful reference for future studies. Integration of microbial and host omic datasets suggested that microbiomes harboring rare species were functionally dissimilar from those enriched in Lachnospiraceae taxa. Moreover, they offered expanded metabolic pathways to fine-tune the cardiovascular capacity through mitochondria-mediated mechanisms. The results identify an associative link between horse endurance capability and its microbiome gene function, laying the basis for nutritional interventions that could benefit endurance athletes.

International audience; Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35°C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25°C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.

International audience

International audience; 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 H2 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 H2 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 H2 was obtained, which is 3.64 times higher than the concentration in unoptimized conditions (13.31 mmol H2/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 H2 (i.e dehydrogenases) and volatile fatty acids (VFA) production and withcellulose 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 endoβ-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.

International audience; 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 bioinWith 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 themformatics 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.

International audience; Specific interactions have been highlighted betweencyanobacteria and chemotrophic bacteria within thecyanosphere, suggesting that nutrients recycling couldbe optimized by cyanobacteria/bacteria exchanges. Inorder to determine the respective metabolic roles ofthe cyanobacterial and bacterial consortia (micro-biome), a day–night metatranscriptomic analysis wasperformed onDolichospermumsp. (N2-fixer) andMicro-cystissp. (non N2-fixer) natural blooms occurringsuccessively within a Frenchperi-urban lake. The taxo-nomical and functional analysis of the metatran-scriptoms have highlighted specific association ofbacteria within the cyanosphere, driven by the cyano-bacteria identity, without strongly modifying the func-tional composition of the microbiomes, suggestingfunctional redundancy within the cyanosphere. More-over, the functional composition of these active com-munities was driven by the living mode. During the twosuccessive bloom events, it appeared that NH4+(newlyfixed and/or allochthonous) was preferentially trans-formed into amino acids for the both the microbiomeand the cyanobacteria, while phosphate metabolismwas enhanced, suggesting that due to a high cellulargrowth, P limitation might take place within the cyano-sphere consortium.

Fungi are present in all environments. They fulfil important ecological functions and play a crucial role in the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi are ITSs. These markers are the best documented in public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads in a significant fraction of the fungi. When these reads are filtered out, traditional metabarcoding pipelines lose part of the information and consequently produce biased pictures of the composition and structure of the environment under study. We developed a solution that enables processing of the entire set of reads including both overlapping and non-overlapping, thus providing a more accurate picture of fungal communities. Our comparative tests using simulated and real data demonstrated the effectiveness of our solution, which can be used by both experts and non-specialists on a command line or through the Galaxy-based web interface.

Summary Genoscapist is a tool to design web interfaces generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus. Availability and implementation Websites and source code freely accessible at https://genoscapist.migale.inrae.fr

The cotton bollworm Helicoverpa armigera H&uuml, bner (Lepidoptera: Noctuidae) is an important pest of many crops that has developed resistance to almost all groups of insecticides used for its management. Insecticide resistance was often related to Transposable Element (TE) insertions near specific genes. In the present study, we deeply retrieve and annotate TEs in the H. armigera genome using the Pipeline to Retrieve and Annotate Transposable Elements, PiRATE. The results have shown that the TE library consists of 8521 sequences representing 236,132 TE copies, including 3133 Full-Length Copies (FLC), covering 12.86% of the H. armigera genome. These TEs were classified as 46.71% Class I and 53.29% Class II elements. Among Class I elements, Short and Long Interspersed Nuclear Elements (SINEs and LINEs) are the main families, representing 21.13% and 19.49% of the total TEs, respectively. Long Terminal Repeat (LTR) and Dictyostelium transposable element (DIRS) are less represented, with 5.55% and 0.53%, respectively. Class II elements are mainly Miniature Inverted Transposable Elements (MITEs) (49.11%), then Terminal Inverted Repeats (TIRs) (4.09%). Superfamilies of Class II elements, i.e., Transib, P elements, CACTA, Mutator, PIF-harbinger, Helitron, Maverick, Crypton and Merlin, were less represented, accounting for only 1.96% of total TEs. In addition, we highlighted TE insertions in insecticide resistance genes and we successfully identified nine TE insertions belonging to RTE, R2, CACTA, Mariner and hAT superfamilies. These insertions are hosted in genes encoding cytochrome P450 (CyP450), glutathione S-transferase (GST), and ATP-binding cassette (ABC) transporter belonging to the G and C1 family members. These insertions could therefore be involved in insecticide resistance observed in this pest.

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International audience; Brazil, the first Citrus fruit producer worldwide, produces annually 88 million tons of this fruit; a large part of it is processed, generating waste, composed mainly by peels and bagasse, which accounts for half of the processed mass. More than half of this waste is not yet valorized, although it could be used in biorefineries to produce various invaluable compounds, including biogas. In this project, we focused on the production of hydrogen from Citrus Peel Waste by anaerobic microbial communities. We used a shotgun metagenomics approach to identify key strains and biological functions for this process, by comparing the inoculum (not yet adapted) with the microbial communities sampled after hydrogen production in optimized conditions. We developed a bioinformatics pipeline for shotgun metagenomics data analysis. After a preprocessing step, reads were co-assembled using metaSPADES. Coding regions were predicted with Prodigal. The taxonomic assignments of the predicted genes were obtained with kaiju against NCBI nr database. For the functional annotation, the predicted genes were affiliated with ghostKoala against KEGG database and with dbCAN against the CAZY database. For each dataset individually, reads were mapped on the co-asssembled contigs. It was thus possible to build a table, which included, for each predicted gene, the counts by sample as well as the functional and taxonomic annotations. This pipeline was developed with snakemake to favour reproducible and scalable data analysis. It was run on the cluster of the INRAE MIGALE bioinformatics platform. It is accessible to the community on GitLab (https://gitlab.irstea.fr/cedric.midoux/workflow_metagenomics).We were able to identify key strains and biological functions selected during this process, especially those related to lignocellulose deconstruction and to hydrogen production. A strong and reproducible microbial selection was observed, leading to the dominance of C. beijerinckii and C. butyricum, known to be hydrogen producers. The glycoside hydrolase 48 family, thought to be critical for cellulose hydrolysis, was in low proportion and it was associated to C. puniceum, a cellulosome-producing bacterium. C. puniceum could thus in the present case be key for some steps of the lignocellulose deconstruction, despite its low proportion.

International audience; Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome data sets available for Bacillus subtilis and Staphylococcus aureus. Websites and source code freely accessible at https://

Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.