The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions

La fabrication microbiologique des fromages

La dénomination " fromage " s'applique aux produits, fermentés ou non, obtenus à partir de lait et d'autres matières d'origine laitière (lait plus ou moins écrémé, crème, babeurre), coagulé avant égouttage ou après élimination partielle de la phase aqueuse. La fabrication fromagère française se caractérise par sa très riche diversité car elle compte plus de 400 fromages fabriqués à partir de lait de vache mais aussi de chèvre ou de brebis dont plus d'une quarantaine d'A.O.C (Appellation d'origine contrôlée) répondant à des critères draconiens. Cette production correspond à deux discours opposés notamment sur la maîtrise des ferments et sous-entendant des rapports à la nature et à l'espace différents ; l'un revendiquant l'universalité de la production et de la consommation, l'autre les liens entre le fromage et son terroir. Le fromage, véritable écosystème bactérien, subit diverses modifications physico-chimiques au cours de trois étapes successives de fabrication (coagulation, égouttage, affinage) communes à tous les types de fromages. L'affinage représente une étape déterminante au cours de laquelle le fromage est soumis à une intense activité bactérienne et enzymatique correspondant à une transformation de la matière première en composés hydrosolubles et volatiles à l'origine des qualités aromatiques du produit nature. Au cours de cette étape vont intervenir de façon successive ou simultanée des bactéries lactiques, des levures ou des champignons filamenteux. L'ensemble de cette flore d'affinage constitue un équilibre microbien évoluant en fonction des conditions de milieu (température, pH de la pâte, activité de l'eau AW).The name "fromage" (cheese) applies to any product, fermented or not, processed from milk or other milk related product (skimmed or unskimmed milk, cream, dasher), clotted before draining or after partial elimination of the aqueous content. French cheese production is characterized by it's very rich diversity as it comprises more than 400 cheeses processed from cow's milk, but also from goat's or ewe's. More than 40 are labeled as AOC (guaranteed origin vintage), fulfilling harsh regulations. This production is a response to two opposite principles, that differ especially upon the mastering of ferments, and that are subtended by different relationships with Nature and Space. One is based on the universality of processing and consumption of cheese, the other on the strong links between cheese and its native tang.Cheese, a complex bacterial ecosystem, is submitted to various physico-chemical alterations along the three successive stages of its process (clotting, draining and maturing), common to all kinds of cheese. During maturing, a determinative stage of the process, cheese is submitted to an intense microbiological and enzymatic activity that converts elements of the raw material into water soluble and volatile compounds which give its aromatic qualities to the natural final product. Along this stage, lactic bacteria, yeasts or filamentous fungi will play their part, simultaneously or successively. The whole of this maturing flora constitutes a microbial equilibrium which evolves according to the medium's conditions (temperature, pH of the material, water activity).GRENOBLE1-BU Médecine pharm. (385162101) / SudocSudocFranceF

Modeling Copper Binding to the Amyloid‑β Peptide at Different pH: Toward a Molecular Mechanism for Cu Reduction

Oxidative stress, including the production of reactive oxygen species (ROS), has been reported to be a key event in the etiology of Alzheimer’s disease (AD). Cu has been found in high concentrations in amyloid plaques, a hallmark of AD, where it is bound to the main constituent amyloid-β (Aβ) peptide. Whereas it has been proposed that Cu-Aβ complexes catalyze the production of ROS via redox-cycling between the Cu­(I) and Cu­(II) state, the redox chemistry of Cu-Aβ and the precise mechanism of redox reactions are still unclear. Because experiments indicate different coordination environments for Cu­(II) and Cu­(I), it is expected that the electron is not transferred between Cu-Aβ and reactants in a straightforward manner but involves structural rearrangement. In this work the structures indicated by experimental data are modeled at the level of modern density-functional theory approximations. Possible pathways for Cu­(II) reduction in different coordination sites are investigated by means of first-principles molecular dynamics simulations in the water solvent and at room temperature. The models of the ligand reorganization around Cu allow the proposal of a preferential mechanism for Cu-Aβ complex reduction at physiological pH. Models reveal that for efficient reduction the deprotonated amide N in the Ala 2-Glu 3 peptide bond has to be protonated and that interactions in the second coordination sphere make important contributions to the reductive pathway, in particular the interaction between COO^– and NH₂ groups of Asp 1. The proposed mechanism is an important step forward to a clear understanding of the redox chemistry of Cu-Aβ, a difficult task for spectroscopic approaches as the Cu-peptide interactions are weak and dynamical in nature

Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates: Comparative genome analysis of Enterococcus cecorum

ABSTRACT Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum -related diseases

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

International audienceEnterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of diseaseassociated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases