Search

Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety. [ABSTRACT FROM AUTHOR]

Diversity of viruses infecting non‐extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head‐tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near‐complete genomes of spindle‐shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head‐tailed virus‐like particles and the presence of spindle‐shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer screening programs with fecal sample collection may provide a platform for population-based gut microbiome disease research. We investigated sample collection and storage method impact on the accuracy and stability of the V3-V4 region of the 16S rRNA genes and bacterial quantity across seven different collection methods [i.e., no solution, two specimen collection cards, and four types of fecal immunochemical test (FIT) used in four countries] among 19 healthy volunteers. Methods: Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the most abundant genera, alpha diversity metrics, and the first principal coordinates of the beta diversity matrices to estimate the stability of microbial profiles after storage for 7 days at room temperature, 4°C or 30°C, and after screening for the presence of occult blood in the stool. In addition, accuracy was estimated for samples frozen immediately compared to samples with no solution (i.e., the putative gold standard). Results: When compared with the putative gold standard, we observed significant variation for all collection methods. However, interindividual variability was much higher than the variability introduced by the collection method. Stability ICCs were high (=0.75) for FIT tubes that underwent colorectal cancer screening procedures. The relative abundance of Actinobacteria (0.65) was an exception and was lower for different FIT tubes stored at 30°C (range, 0.41-0.90) and room temperature (range, 0.06-0.94). Conclusions: Paper-based collection cards and different types of FIT are acceptable tools for microbiome measurements. Impact: Our findings inform on the utility of commonly used fecal sample collection methods for developing microbiome-focused cohorts nested within screening programs. [ABSTRACT FROM AUTHOR]

Food allergy is associated with alterations in the gut microbiota, epithelial barrier, and immune tolerance. These dysfunctions are observed within the first months of life, indicating that early intervention is crucial for disease prevention. Preventive nutritional strategies with prebiotics are an attractive option, as prebiotics such as galacto-oligosaccharides and inulin can promote tolerance, epithelial barrier reinforcement, and gut microbiota modulation. Nonetheless, the ideal period for intervention remains unknown. Here, we investigated whether galacto-oligosaccharide/inulin supplementation during gestation could protect offspring from wheat allergy development in BALB/cJRj mice. We demonstrated that gestational prebiotic supplementation promoted the presence of beneficial strains in the fecal microbiota of dams during gestation and partially during mid-lactation. This specific microbiota was transferred to their offspring and maintained to adulthood. The presence of B and T regulatory immune cell subsets was also increased in the lymph nodes of offspring born from supplemented mothers, suggestive of a more tolerogenic immune environment. Indeed, antenatal prebiotic supplementation reduced the development of wheat allergy symptoms in offspring. Our study thus demonstrates that prebiotic supplementation during pregnancy induces, in the offspring, a tolerogenic environment and a microbial imprint that mitigates food allergy development. [ABSTRACT FROM AUTHOR]

A causal correlation between the metabolic disorders associated with sugar intake and disruption of the gastrointestinal (GI) homeostasis has been suggested, but the underlying mechanisms remain unclear. To unravel these mechanisms, we investigated the effect of physiological amounts of fructose and glucose on barrier functions and inflammatory status in various regions of the GI tract and on the cecal microbiota composition. C57BL/6 mice were fed chow diet and given 15% glucose or 15% fructose in drinking water for 9 weeks. We monitored caloric intake, body weight, glucose intolerance, and adiposity. The intestinal paracellular permeability, cytokine, and tight junction protein expression were assessed in the jejunum, cecum, and colon. In the cecum, the microbiota composition was determined. Glucose-fed mice developed a marked increase in total adiposity, glucose intolerance, and paracellular permeability in the jejunum and cecum while fructose absorption did not affect any of these parameters. Fructose-fed mice displayed increased circulation levels of IL6. In the cecum, both glucose and fructose intake were associated with an increase in Il13 , Ifnγ , and Tnfα mRNA and MLCK protein levels. To clarify the relationships between monosaccharides and barrier function, we measured the permeability of Caco-2 cell monolayers in response to IFNγ+TNFα in the presence of glucose or fructose. In vitro , IFNγ+TNFα-induced intestinal permeability increase was less pronounced in response to fructose than glucose. Mice treated with glucose showed an enrichment of Lachnospiracae and Desulfovibrionaceae while the fructose increased relative abundance of Lactobacillaceae. Correlations between pro-inflammatory cytokine gene expression and bacterial abundance highlighted the potential role of members of Desulfovibrio and Lachnospiraceae NK4A136 group genera in the inflammation observed in response to glucose intake. The increase in intestinal inflammation and circulating levels of IL6 in response to fructose was observed in the absence of intestinal permeability modification, suggesting that the intestinal permeability alteration does not precede the onset of metabolic outcome (low-grade inflammation, hyperglycemia) associated with chronic fructose consumption. The data also highlight the deleterious effects of glucose on gut barrier function along the GI tract and suggest that Desulfovibrionaceae and Lachnospiraceae play a key role in the onset of GI inflammation in response to glucose. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Designing bacterial co-cultures adapted to ferment mixes of vegetal and animal resources for food diversification and sustainability is becoming a challenge. Among bacteria used in food fermentation, lactic acid bacteria (LAB) are good candidates, as they are used as starter or adjunct in numerous fermented foods, where they allow preservation, enhanced digestibility, and improved flavor. We developed here a strategy to design LAB co-cultures able to ferment a new food made of bovine milk and lupin flour, consisting in: (i) in silico preselection of LAB species for targeted carbohydrate degradation; (ii) in vitro screening of 97 strains of the selected species for their ability to ferment carbohydrates and hydrolyze proteins from milk and lupin and clustering strains that displayed similar phenotypes; and (iii) assembling strains randomly sampled from clusters that showed complementary phenotypes. The designed co-cultures successfully expressed the targeted traits i.e., hydrolyzed proteins and degraded raffinose family oligosaccharides of lupin and lactose of milk in a large range of concentrations. They also reduced an off-flavor-generating volatile, hexanal, and produced various desirable flavor compounds. Most of the strains in co-cultures achieved higher cell counts than in monoculture, suggesting positive interactions. This work opens new avenues for the development of innovative fermented food products based on functionally complementary strains in the world-wide context of diet diversification. [ABSTRACT FROM AUTHOR]

A role of the gut microbiota in psychiatric disorders is supported by a growing body of literature. The effects of a probiotic mixture of four bacterial strains were studied in two models of anxiety and depression, naturally stress-sensitive Fischer rats and Long Evans rats subjected to maternal deprivation. Rats chronically received either the probiotic mixture (1.109 CFU/day) or the vehicle. Anxiety- and depressive-like behaviors were evaluated in several tests. Brain monoamine levels and gut RNA expression of tight junction proteins (Tjp) and inflammatory markers were quantified. The gut microbiota was analyzed in feces by 16S rRNA gene sequencing. Untargeted metabolite analysis reflecting primary metabolism was performed in the cecal content and in serum. Fischer rats treated with the probiotic mixture manifested a decrease in anxiety-like behaviors, in the immobility time in the forced swimming test, as well as in levels of dopamine and its major metabolites, and those of serotonin metabolites in the hippocampus and striatum. In maternally deprived Long Evans rats treated with the probiotic mixture, the number of entries into the central area in the open-field test was increased, reflecting an anxiolytic effect. The probiotic mixture increased Tjp1 and decreased Ifnγ mRNA levels in the ileum of maternally deprived rats. In both models, probiotic supplementation changed the proportions of several Operational Taxonomic Units (OTU) in the gut microbiota, and the levels of certain cecal and serum metabolites were correlated with behavioral changes. Chronic administration of the tested probiotic mixture can therefore beneficially affect anxiety- and depressive-like behaviors in rats, possibly owing to changes in the levels of certain metabolites, such as 21-deoxycortisol, and changes in brain monoamines. [ABSTRACT FROM AUTHOR]

Background: The development of high-throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high-throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g., individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: homogenization, DNA extraction, and DNA amplification. Results: Controls yielded a significant number of sequences (1,126–13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e., the percentage of sequences belonging to OTUs identified as contaminants) varied with tick instar and sex: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in homogenization and extraction reagent controls, highlighting the importance of carefully controlling these steps. Conclusion: Here, we showed that contaminant OTUs from sample laboratory processing steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples. [ABSTRACT FROM AUTHOR]

We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p -values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini–Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini–Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented. [ABSTRACT FROM AUTHOR]

Spring phenology of temperate trees has advanced worldwide in response to global warming. However, increasing temperatures may not necessarily lead to further phenological advance, especially in the warmer latitudes because of insufficient chilling and/or shorter day length. Determining the start of the forcing phase, that is, when buds are able to respond to warmer temperatures in spring, is therefore crucial to predict how phenology will change in the future. In this study, we used 4,056 leaf‐out date observations during the period 1969–2017 for clones of European beech (Fagus sylvatica L.) and pedunculate oak (Quercus robur L.) planted in 63 sites covering a large latitudinal gradient (from Portugal ~41°N to Norway ~63°N) at the International Phenological Gardens in order to (a) evaluate how the sensitivity periods to forcing and chilling have changed with climate warming, and (b) test whether consistent patterns occur along biogeographical gradients, that is, from colder to warmer environments. Partial least squares regressions suggest that the length of the forcing period has been extended over the recent decades with climate warming in the colder latitudes but has been shortened in the warmer latitudes for both species, with a more pronounced shift for beech. We attribute the lengthening of the forcing period in the colder latitudes to earlier opportunities with temperatures that can promote bud development. In contrast, at warmer or oceanic climates, the beginning of the forcing period has been delayed, possibly due to insufficient chilling. However, in spite of a later beginning of the forcing period, spring phenology has continued to advance at these areas due to a faster satisfaction of heat requirements induced by climate warming. Overall, our results support that ongoing climate warming will have different effects on the spring phenology of forest trees across latitudes due to the interactions between chilling, forcing and photoperiod. [ABSTRACT FROM AUTHOR]

Gut microbiota is involved in the development of several chronic diseases, including diabetes, obesity, and cancer, through its interactions with the host organs. It has been suggested that the cross talk between gut microbiota and skeletal muscle plays a role in different pathological conditions, such as intestinal chronic inflammation and cachexia. However, it remains unclear whether gut microbiota directly influences skeletal muscle function. In this work, we studied the impact of gut microbiota modulation on mice skeletal muscle function and investigated the underlying mechanisms. We determined the consequences of gut microbiota depletion after treatment with a mixture of a broad spectrum of antibiotics for 21 days and after 10 days of natural reseeding. We found that, in gut microbiota-depleted mice, running endurance was decreased, as well as the extensor digitorum longus muscle fatigue index in an ex vivo contractile test. Importantly, the muscle endurance capacity was efficiently normalized by natural reseeding. These endurance changes were not related to variation in muscle mass, fiber typology, or mitochondrial function. However, several pertinent glucose metabolism markers, such as ileum gene expression of short fatty acid chain and glucose transporters G protein-coupled receptor 41 and sodium-glucose cotransporter 1 and muscle glycogen level, paralleled the muscle endurance changes observed after treatment with antibiotics for 21 days and reseeding. Because glycogen is a key energetic substrate for prolonged exercise, modulating its muscle availability via gut microbiota represents one potent mechanism that can contribute to the gut microbiota-skeletal muscle axis. Taken together, our results strongly support the hypothesis that gut bacteria are required for host optimal skeletal muscle function. [ABSTRACT FROM AUTHOR]

Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multiaffiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. [ABSTRACT FROM AUTHOR]

Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α- and β-diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering ( SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α- and β-community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates. [ABSTRACT FROM AUTHOR]

Abundance and specificity are two key characteristics of species distribution and biodiversity. Theories of species assembly aim to reproduce the empirical joint patterns of specificity and abundance, with the goal to explain patterns of biodiversity across habitats. The specialist-generalist paradigm predicts that specialists should have a local advantage over generalists and thus be more abundant. We developed a specificity index to analyse abundance-specificity relationships in microbial ecosystems. By analysing microbiota spanning 23 habitats from three very different data sets covering a wide range of sequencing depths and environmental conditions, we find that habitats are consistently dominated by specialist taxa, resulting in a strong, positive correlation between abundance and specificity. This finding is consistent over several levels of taxonomic aggregation and robust to errors in abundance measures. The relationship explains why shallow sequencing captures similar β-diversity as deep sequencing, and can be sufficient to capture the habitat-specific functions of microbial communities. [ABSTRACT FROM AUTHOR]

Background: Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow on a variety of carbon and nitrogen sources. The aim of this work was to discover the genetic basis for strain-dependent traits related to its ability to use specific carbon sources. High-throughput sequencing technologies were ideal for this purpose as they have the potential to decipher genomic diversity at a moderate cost. Results: 21 strains of PF were sequenced and the genomes were assembled de novo. Scaffolds were ordered by comparison with the complete reference genome CIRM-BIA1, obtained previously using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either the core genome or an accessory genome. The ability of the 21 strains to degrade 50 different sugars was evaluated. Thirty-three sugars were degraded by none of the sequenced strains whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were only used by some strains. In this case, the presence/absence of genes responsible for carbon uptake and degradation correlated well with the phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence of these genes was in line the metabolic pathways described previously in other species. We also considered the genetic origin (transduction, rearrangement) of the corresponding genomic islands. Ribose and gluconate were degraded to a greater or lesser extent (quantitative phenotype) by some strains. For these sugars, the phenotypes could not be explained by the presence/absence of a gene but correlated with the premature appearance of a stop codon interrupting protein synthesis and preventing the catabolism of corresponding carbon sources. Conclusion: These results illustrate (i) the power of correlation studies to discover the genetic basis of binary strain-dependent traits, and (ii) the plasticity of PF chromosomes, probably resulting from horizontal transfers, duplications, transpositions and an accumulation of mutations. Knowledge of the genetic basis of nitrogen and sugar degradation opens up new strategies for the screening of PF strain collections to enable optimum cheese starter, probiotic and white biotechnology applications. [ABSTRACT FROM AUTHOR]

Several probiotic bacteria have been proposed for treatment or prevention of inflammatory bowel diseases (IBD), showing a protective effect in animal models of experimental colitis and for some of them also in human clinical trials. While most of these probiotic bacteria are isolated from the digestive tract, we recently reported that a Lactobacillus strain isolated from cheese, L. delbrueckii subsp. lactis CNRZ327 (Lb CNRZ327), also possesses anti-inflammatory effects in vitro and in vivo, demonstrating that common dairy bacteria may be useful in the treatment or prevention of IBD. Here, we studied the mechanisms underlying the protective effects of Lb CNRZ327 in vivo, in a mouse dextran sodium sulfate (DSS) colitis model. During colitis, Lb CNRZ327 modulated the production of TGF-β, IL-6, and IL-12 in colonic tissue and of TGF-β and IL-6 in the spleen, and caused an expansion of CD4+Foxp3+ regulatory T cells in the cecal lymph nodes. Moreover, a strong tendency to CD4+Foxp3+ expansion was also observed in the spleen. The results of this study for the first time show that orally administered dairy lactobacilli can not only modulate mucosal but also systemic immune responses and constitute an effective treatment of IBD. [ABSTRACT FROM AUTHOR]

Background: Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results: We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed "advanced" phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions: We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the evolutionary affinities between double-stranded RNA and positive strand RNA viruses. In particular, we were able to show that there exists a good statistical support for the claims that dsRNA viruses are not monophyletic and that viruses with permuted RdRps belong to a common evolution lineage as previously proposed by other groups. We also propose a tree topology with a good statistical support describing the evolutionary relationships between the Picornaviridae, Caliciviridae, Flaviviridae families and a group including the Alphatetraviridae, Nodaviridae, Permutotretraviridae, Birnaviridae, and Cystoviridae families. [ABSTRACT FROM AUTHOR]

Background: The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. It was proposed that the corresponding genes in the phage genomes were transferred from the bacterial hosts. Recently new SSB proteins encoded by the virulent lactococcal bacteriophages (Orf14bIL67-like proteins) have been identified and characterized structurally and biochemically. Methodology/Principal Findings: This study focused on the determination of phylogenetic relationships between Orf14bIL67-like proteins and other SSBs. We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. The results show that, in remarkable contrast to other phage SSBs, the Orf14bIL67-like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14bIL67 protein complements the conditional lethal ssb-1 mutation of Escherichia coli. Conclusions/Significance: Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. Our findings suggest that unlike other phages, the virulent lactococcal phages carry ssb genes that were not acquired from their hosts, but transferred from an archaeal genome. This represents a unique example of a horizontal gene transfer between Archaea and bacterial phages. [ABSTRACT FROM AUTHOR]

Motivation De novo comparative metagenomics is one of the most straightforward ways to analyze large sets of metagenomic data. Latest methods use the fraction of shared k -mers to estimate genomic similarity between read sets. However, those methods, while extremely efficient, are still limited by computational needs for practical usage outside of large computing facilities. Results We present SimkaMin, a quick comparative metagenomics tool with low disk and memory footprints, thanks to an efficient data subsampling scheme used to estimate Bray-Curtis and Jaccard dissimilarities. One billion metagenomic reads can be analyzed in <3 min, with tiny memory (1.09 GB) and disk (≈0.3 GB) requirements and without altering the quality of the downstream comparative analyses, making of SimkaMin a tool perfectly tailored for very large-scale metagenomic projects. Availability and implementation https://github.com/GATB/simka. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Gut microbiota, a major contributor to human health, is influenced by physical activity and diet, and displays a functional cross-talk with skeletal muscle. Conversely, few data are available on the impact of hypoactivity, although sedentary lifestyles are widespread and associated with negative health and socio-economic impacts. The study aim was to determine the effect of Dry Immersion (DI), a severe hypoactivity model, on the human gut microbiota composition. Stool samples were collected from 14 healthy men before and after 5 days of DI to determine the gut microbiota taxonomic profiles by 16S metagenomic sequencing in strictly controlled dietary conditions. The α and β diversities indices were unchanged. However, the operational taxonomic units associated with the Clostridiales order and the Lachnospiraceae family, belonging to the Firmicutes phylum, were significantly increased after DI. Propionate, a short-chain fatty acid metabolized by skeletal muscle, was significantly reduced in post-DI stool samples. The finding that intestine bacteria are sensitive to hypoactivity raises questions about their impact and role in chronic sedentary lifestyles. [ABSTRACT FROM AUTHOR]

• Grey junglefowls from zoological parks are admixed with domestic chicken. • Two topology scenarios identified but one more probable based on gene flow analyses. • The red, rather than the green, junglefowl is basal to the genus Gallus tree. • Gallus gallus subspecies have limited genomic divergence. The genus Gallu s is distributed across a large part of Southeast Asia and has received special interest because the domestic chicken, Gallus gallus domesticus , has spread all over the world and is a major protein source for humans. There are four species: the red junglefowl (G. gallus), the green junglefowl (G. varius), the Lafayette's junglefowl (G. lafayettii) and the grey junglefowl (G. sonneratii). The aim of this study is to reconstruct the history of these species by a whole genome sequencing approach and resolve inconsistencies between well supported topologies inferred using different data and methods. Using deep sequencing, we identified over 35 million SNPs and reconstructed the phylogeny of the Gallus genus using both distance (BioNJ) and maximum likelihood (ML) methods. We observed discrepancies according to reconstruction methods and genomic components. The two most supported topologies were previously reported and were discriminated by using phylogenetic and gene flow analyses, based on ABBA statistics. Terminology fix requested by the deputy editor led to support a scenario with G. gallus as the earliest branching lineage of the Gallus genus, instead of G. varius. We discuss the probable causes for the discrepancy. A likely one is that G. sonneratii samples from parks or private collections are all recent hybrids, with roughly 10% of their autosomal genome originating from G. gallus. The removal of those regions is needed to provide reliable data, which was not done in previous studies. We took care of this and additionally included two wild G. sonneratii samples from India, showing no trace of introgression. This reinforces the importance of carefully selecting and validating samples and genomic components in phylogenomics. [ABSTRACT FROM AUTHOR]

Interactions of diet, gut microbiota, and host genetics play essential roles in the development of metabolic diseases. A/J and C57BL/6J (C57) are two mouse strains known to display different susceptibilities to metabolic disorders. In this context, we analyzed gut microbiota composition in A/J and C57 mice, and assessed its responses to high-fat diet (HFD) and antibiotic (AB) treatment. We also exchanged the gut microbiota between the two strains following AB treatment to evaluate its impact on the metabolism. We showed that A/J and C57 mice have different microbiome structure and composition at baseline. Moreover, A/J and C57 microbiomes responded differently to HFD and AB treatments. Exchange of the gut microbiota between the two strains was successful as recipients' microbiota resembled donor-strain microbiota. Seven weeks after inoculation, the differences between recipients persisted and were still closer from the donor-strain microbiota. Despite effective microbiota transplants, the response to HFD was not markedly modified in C57 and A/J mice. Particularly, body weight gain and glucose intolerance in response to HFD remained different in the two mouse strains whatever the changes in microbiome composition. This indicated that genetic background has a much stronger impact on metabolic responses to HFD than gut microbiome composition. [ABSTRACT FROM AUTHOR]

Spring phenology of temperate trees has advanced worldwide in response to global warming. However, increasing temperatures may not necessary lead to further phenological advance, especially in the southern part of tree species distribution because bud development may be delayed by the combination of warmer winters (insufficient chilling) and short photoperiod during the early season. Consequently, a focus on the start of the ecodormancy, i.e. when buds start to respond to warmer temperatures in early spring, is crucial to understand and predict how phenology will evolve in the future warmer climate as well as to improve carbon cycle models. Yet, the beginning of this period is not visible in the field and can so far only be derived statistically. In this study, we used leaf-out date observations of several clones of European beech (Fagus sylvatica L.) and pedonculate oak (Quercus robur L.) planted over a large latitudinal gradient (from Portugal to Sweden) at the International Phenological Gardens (IPGs) during the period 1969-2017 (>13'000 observations). The IPGs offers a unique opportunity to test the phenological plasticity of trees to contrasted climatic conditions without being affected by genetic adaptations (clones). We used Partial Least Squares Regression analyses to identify the sensitivity periods when leaf-out dates are mostly regulated by low (chilling) and warm temperatures (forcing) through space (>22° of latitudes) and time (~5 decades). We aimed (i) to evaluate how the periods of sensitivity to forcing and chilling have changed over the last decades, and (ii) to test whether consistent patterns can be found from colder to warmer environment.Our results suggest that the beginning of the period of sensitivity to forcing has been delayed over time and under lower (warmer) latitudes for beech, whereas no change has been detected for oak over the spatial and temporal scales. We attributed the shift of the forcing phase for beech to insufficient chilling which may have progressively delayed the dormancy release, whereas the lack of change for oak would indicate low chilling requirements. Our result suggest that global warming will likely affect the time sequence when tree species start their growing season due to substantial differences in chilling and forcing requirements among co-existing species. [ABSTRACT FROM AUTHOR]

Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 109 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]