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Additional file 1: Fig. S1. Distribution of 1,198 isolates and enrichment analysis: A) The plot represents the proportion of E. coli isolates isolated from hosts in four countries. The number above each plot indicates the total number of isolates per host. B) Phylogroups enriched with different hosts (Pearson residual > 0 represents positive correlation indicating the enrichment of certain host-species in distinct clusters at p-value < 2.2e−16). Fig. S2. Core genome phylogeny of E. coli isolates from our collection (n=1,198) and reference strains (n=146) from the ECOR collection, RefSeq and cryptic clades annotated with their phylogroups (phylogroups were determined by ClermonTyper v. 1.3). Fig S3. Core-genome phylogeny and Accessory-genome clustering of 1,198 E. coli isolates showing different BAPS clusters. Each BAPS on accessory genome clustering consist of the same strains as on the core-genome phylogeny. Fig. S4. Minimum-spanning tree of MLST profiles of 1,198 E. coli isolates. Left: the number of isolates constituting an ST; Right: the proportion of hosts in each ST. Fig. S5. Genetic surroundings of the human-associated nan gene cluster in the genomes of all isolates in which it was identified.

Lactic acid bacteria strains were isolated from seafood products and clustered according to their inhibiting capacities against 14 food borne spoiling and pathogenic strains in order to develop applications in biopreservation. Most of the strains were identified as Leuconostoc gelidum and Lactococcus piscium. Detailed identification of one strain of the Lactococcus piscium strains suggests that it is a new specie. According to sensory analysis results, 2 strains belonging to the Leuconostoc gelidum specie were the most efficient for the enhancement of the shelf life of vacuum packed peeled and cooked shrimps. Similar results were obtained in cold smoked salmon with one strains of Lactococcus sp. A challenge test against three pathogenic strains (Listeria monocytogenes, Staphylococcus aureus and Vibrio cholerae) was performed in cold smoked salmon. The Lactococcus sp. EU2241 strain (non bacteriocinogenic) enabled a more efficient inhibition of the pathogens than the Ln. gelidum EU2247 strain (bacteriocinogenic). The maximum recorded inhibition was 2 logs compared to the uninoculated samples. Growth characteristics of strain Lactococcus sp. EU2241 were determined at different temperatures showed an optimal growth at 26°C and no growth at 29°C or above. Proteomic analysis showed a cold shock protein overproduction during growth at 5°C. The gene coding for this protein was identified and sequenced. Overproduction of a cold shock protein during growth at suboptimal temperature has never been described in a lactic acid bacterium before., Des souches de bactéries lactiques ont été isolées à partir de produits de la mer et regroupées en fonction de leur pouvoir inhibiteur contre 14 bactéries appartenant à la flore d'altération ou pathogène de ces produits, dans le but de développer des applications en biopréservation. Elles ont été identifiées majoritairement comme Leuconostoc gelidum, et Lactococcus piscium. L’identification approfondie d’une souche de Lc. piscium montre qu’il s’agit d’une nouvelle espèce de Lactococcus. Des analyses sensorielles ont permis de montrer que 2 souches appartenant à l'espèce Leuconostoc gelidum permettait de prolonger la durée de vie de crevettes cuites emballées sous vide et qu’une souche de Lactococcus sp. avait le même effet sur du saumon fumé. Un test d'inhibition de bactéries pathogènes (Listeria monocytogenes, Staphylococcus aureus et Vibrio cholerae) a été effectué sur du saumon fumé. La souche de Lactococcus sp. EU2241 (non productrice de bactériocine) s'est révélée plus efficace que la souche de Ln. gelidum EU2247 (productrice de bactériocine) pour inhiber ces pathogènes, avec une inhibition atteignant 2 log par rapport au témoin non biopréservé. Les caractéristiques de croissance de la souche Lactococcus sp. EU2241 à différentes températures ont montré un optimum de croissance à 26°C et aucune croissance à 29°C ou au dessus. L'analyse du protéome a révélé la surproduction d'une protéine de choc froid lors de la croissance à 5°C, et le gène correspondant a pu être identifié et séquencé. Il s'agit de la première mise en évidence de la surproduction d'une protéine de choc froid lors de la croissance à température suboptimale pour une bactérie lactique.

In this study, we have screened a colLection of Carnobacterium strains that could be used for biopreservation in order to find a natural tyramine negative strain. This screening was performed using the detection of a part of the tyrosine decarboxylase gene by PCR test. On 35 strains of Carnobacterium tested, all showed the presence of the tdc gene suggesting that they all produce tyramine. This was assessed by the quantification of tyramine production for 10 strains. In a second part, a mutation procedure using ethyl methyl sulfonate was used to select a tyramine negative mutant of Carnobacterium divergens V41 that 1S a good candidate for biopreservation applications. A mutant strain called C. divergens V41A8 was selected and characterized. The mutant was identical to the wild strain concerning carbohydrates fermentation profile, antibiogram spectrum, bacteriocin production, and bacteriocin spectrum towards Listeria monocytogenes. The growth of strain C. divergens V41A8 was tested by comparison ta the wild strain on a sterile cold smoked salmon model. The mutant grew more slowly than the wild strain on the product, but it reached nearly the same level after 28 days of storage. Moreover, the production of tyramine detected on cold smoked salmon inoculated with C. divergens V41 (122 ug/g after 28 days of storage) was not detected at all when the product was inoculated with the mutant strain C. divergens V41A8. This strain could be an interesting alternative for the application of biopreservative Carnobacterium on food products naturally contaminated with tyramine such as smoked fishes.

Different nutritional components are able, by modulating mitochondrial function and gut microbiota composition, to influence body composition, metabolic homeostasis and inflammatory state. In this study, we aimed to evaluate the effects produced by the supplementation of different milks on energy balance, inflammatory state, oxidative stress and antioxidant/detoxifying enzyme activities and to investigate the role of the mitochondrial efficiency and the gut microbiota in the regulation of metabolic functions in an animal model. We compared the intake of human milk, gold standard for infant nutrition, with equicaloric supplementation of donkey milk, the best substitute for newborns due to its nutritional properties, and cow milk, the primary marketed product. The results showed a hypolipidemic effect produced by donkey and human milk intake in parallel with enhanced mitochondrial activity/proton leakage. Reduced mitochondrial energy efficiency and proinflammatory signals (tumor necrosis factor α, interleukin-1 and lipopolysaccharide levels) were associated with a significant increase of antioxidants (total thiols) and detoxifying enzyme activities (glutathione-S-transferase, NADH quinone oxidoreductase) in donkey- and human milk-treated animals. The beneficial effects were attributable, at least in part, to the activation of the nuclear factor erythroid-2-related factor-2 pathway. Moreover, the metabolic benefits induced by human and donkey milk may be related to the modulation of gut microbiota. In fact, milk treatments uniquely affected the proportions of bacterial phyla and genera, and we hypothesized that the increased concentration of fecal butyrate in human and donkey milk-treated rats was related to the improved lipid and glucose metabolism and detoxifying activities.