Vancomycin-resistant enterococci (VRE) often originate from the gastrointestinal tract, where their proliferation precedes dissemination into the bloodstream, and can lead to systemic infection. Uncovering the actors and mechanisms reducing the intestinal colonisation by VRE is essential to control infection. We aimed to identify commensal bacteria that interfere with VRE gut colonisation or act as an ecological barrier. We performed a 3-week longitudinal analysis of the gut microbiota composition and VRE carriage levels during microbiota recovery in mice colonised with VRE after antibiotic-induced dysbiosis. By combining biological data and mathematical modelling, we identified 15 molecular species (OTUs) that negatively correlated with VRE overgrowth. Six strains representative of these OTUs were collected, cultivated and used in mixture with a seventh strain (Mix7) in two different mouse lines challenged with VRE. Of the seven strains, three belonged to Lachnospiraceae, one to Muribaculaceae, one to Ruminococcaceae and two to Lactobacillaceae. We found that Mix7 led to a better recovery of the gut microbiota composition and reduced VRE carriage. Differences in the effect of Mix7 were observed between responder and non-responder mice. These differences were associated with variations in the composition of the initial microbiota and during recovery and represent potential biomarkers for predicting response to Mix7. In a mouse model of alternative stable state of dysbiosis, response to Mix7 was associated with higher concentrations of short-chain fatty acids (acetate, propionate, butyrate) and a range of metabolites including bile acids, reflecting the recovery of the microbiota back to initial state. Furthermore, Muribaculum intestinale strain was required to obtain the Mix7 effect on VRE reduction in vivo, but the presence of at least one of the other six strains was needed. None of the supernatant of the seven strains, alone or in combination, inhibited VRE growth in vitro. Interestingly, five strains belong to species shared among humans and mice, and the other two have human functional equivalents. An innovative approach based on mathematical modelling of the microbiota composition permitted to identify a mixture of commensal bacterial strains, which improves the ecological barrier effect against VRE. The mechanisms are dependent on the recovery and initial composition of the microbiota. Ultimately, this work will enable a move towards a personalised medicine by targeting predisposed patients presenting a risk of infection, such as neutropenic or bone-marrow transplant patients, and likely to respond to supplementation with commensal strains, providing new live biotherapeutic products and biomarkers to predict response to supplementation.

Cheeses are fermented dairy products consumed worldwide. Their global diversity results from various local variables, including technological practices, as well as the metabolic activity of diverse microorganisms. In Europe, this typicity is exemplified by Protected Designation of Origin (PDO) cheeses, for which genetic diversity remains largely unexplored. Combining culturomics (n = 373 bacterial genomes) and metagenomic (n = 146 metagenomes), we performed a national-scale survey of the microbial diversity encompassing 44 French PDO cheeses. Taxonomic (bacteria, fungi and viruses) and functional profiling reveal a high diversity in the cheese rind, mainly driven by the cheese technology. We also reconstructed 1,119 bacterial metagenome-assembled genomes (MAGs) encompassing seven phyla, including Actinomycetota, Bacillota, Pseudomonadota and Bacteroidota. Using GTDB as a reference, we identified 221 MAGs encompassing 46 genera, as well as 44 bacterial isolate genomes encompassing eight genera, which represent potentially 81 new species (based on <95% ANI). These species were particularly numerous among the genera Halomonas, Psychrobacter and Brachybacterium. Similar results were observed when compared with the cFMD database. We combined our genomic and metagenomic datasets into a catalog of 26.2 million protein clusters, with 50% of these clusters remaining unassigned to a known function and taxonomy. We illustrated the potential of this resource by searching for methionine gamma-lyase (MGL), an enzyme playing a significant role in cheese flavor. This protein was predominantly found in Pseudoalteromonas, a potentially new MGL-producing genus, Serratia, Pseudomonas, Proteus and Hafnia, and its prevalence varied with cheese technology. Our study provides a substantial genomic resource for food microbiologists and cheesemakers to further explore the biotechnological potential of PDO cheese biodiversity. ### Competing Interest Statement The authors have declared no competing interest. France Génomique, ANR-10-INBS-09–08 Centre national interprofessionnel de l'économie laitière, https://ror.org/00w571a59 Genoscope, https://ror.org/028pnqf58 Commissariat à l'Énergie Atomique et aux Énergies Alternatives, https://ror.org/00jjx8s55 Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, https://ror.org/003vg9w96

The study of microbial metabolic interactions within food microbiomes represents a key scientific approach for improving the quality and health benefits of food. In such studies, methods based on gene expression levels (metatranscriptomic) analysis are promising. However specific tools are required to overcome the challenges posed by food microbiomes, in particular the high variability of microbiomes between samples and the difficulty of automatically inferring the annotation of metabolic functions across taxa. To adress this gap, we present the Food Microbiome Metabolic Modules (F3M) tool suite, which comprises (1) a curated database containing about 1,985 functional genes representing key fermentative metabolic reactions in food microbiomes, (2) a F3M Builder for generating F3M-annotated gene catalogs and mapping of metatranscriptomic reads, and then (3) an F3M R package to parse and aggregate gene expression data by taxonomic and functional categories for downstream analysis. The F3M taxonomy is organized according to the Genome Taxonomy Database (GTDB) nomenclature, whereas the F3M functional repertoire is structured hierarchically into 183 metabolic modules, which enable multi-scale analysis of inter-organism metabolic interactions and meaningful fermentative outputs (e.g., primary alcohols, acetate). Notably, a dedicated 'redox' module captures oxido-reduction mechanisms and NADH-dependent pathways central to fermentation, while an 'uptake' module complements the metabolic pathways to trace potential metabolite exchanges across taxa. Together, the F3M suite provides a robust framework for uncovering functional dynamics within food microbiomes. The F3M tool suite is available as open-source.

Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators’ sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.

Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat’s milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.

Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius . Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile and the yeasts Diutina catenulata and, to a lesser extent, by Debaryomyces hansenii and Kodamaea ohmeri . Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii . Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, implying that the milk used was from diseased herds. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.

Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria (χ¯= 80.54%), followed by Firmicutes (χ¯= 12.14%), Actinobacteria (χ¯= 4.60%), and Bacteriodetes (χ¯= 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

The objectives of the INRA plant BRCs are to gather, conserve, characterize and provide high quality plant materials to their collaborators and users, mainly researchers and breeders. For that purpose, they are ensuring a high degree of quality in their management systems and give access to their catalogs through an information system organized in two layers, (i) local information systems that allows the BRCs to manage their collection and (ii) a central system, the INRA Plant Genetic Resource Information System (GnpIS-Siregal https://urgi.versailles.inra.fr/siregal), integrated with the GnpIS information system of the URGI platform (ISO 9001). GnpIS allows linking information on plant genetic resources with genetic, genomic or phenotypic data. In the last six years, INRA has focused its efforts on the development and implementation in GnpIS of strategies and tools aiming at facilitating the access to data and at making them interoperable and re-usable. This was achieved through several international projects (e.g. FP7 TransPLANT, ARCAD FEDER, H2020 ELIXIR Excelerate) or initiatives (Wheat Initiative, Research Data Alliance, Breeding API) contributing to the development (i) of community recommendations for data standardisation (e.g. wheatis.org), (ii) of a data standard for phenotyping experiment (www.miappe.org), (iii) of several crop specific ontologies in the frame of the CropOntology (http://www.cropontology.org/), (iv) of portals giving access to data in distributed information systems and (v) of a standard Application Programming Interface for plant genetics and breeding that will facilitate the development of such portals. In addition, an effort has recently been made in curating and diffusing the data: the assignment of Digital Object Identifier (DOI) to accessions and to data sets allows to identify them more easily. Moreover, the French national collections hosted by INRA are now integrated in both Eurisco and GBIF international biodiversity portals in order to improve their accessibility.

Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis