The effects of the administration of Escherichia coli endotoxin (lipopolysaccharide, LPS) into the airways of C57Bl/6 mice were studied. Neutrophil sequestration in the lungs and their enrichment, together with tumor necrosis factor (TNF)-alpha, in bronchoalveolar lavage fluid (BALF) were associated with bronchoconstriction and bronchopulmonary hyperreactivity (BHR) to methacholine and alveolocapillary dysfunction. Granulocyte depletion by the myelotoxic drug vinblastine failed to modify TNF-alpha production and prevented LPS-induced neutrophil recruitment to lungs and BALF, bronchoconstriction, and BHR. Neutrophils were again sequestered in the lungs when LPS was administered 4 to 5 d after vinblastine, whereas inhibition of their passage to BALF persisted. Under those conditions, bronchoconstriction and BHR by LPS also recovered, showing that these functional effects are independent from BALF neutrophil enrichment but require lung sequestration. Administration of granulocyte colony-stimulating factor after vinblastine counteracted its effects and allowed the recovery of lung neutrophil sequestration by LPS and a partial recovery of bronchoconstriction under conditions where neutrophils still failed to migrate to BALF. Dexamethasone (the phosphate salt and its free base) suppressed LPS-induced TNF-alpha generation in BALF and its neutrophil enrichment, whereas neutrophil lung sequestration, bronchoconstriction, BHR, and alveolocapillary dysfunction were marginally reduced and only so at low doses of dexamethasone, higher doses being inactive or aggravating. In situ neutrophil activation could account for LPS-induced bronchoconstriction and BHR, both of which are refractory to steroids and appear to be mediated by unrelated mechanisms, which may be relevant for acute respiratory distress syndrome, a condition for which LPS administration is used as a model.

Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov. Species of the genus Citrobacter are considered to be inhabitants of human and other animal guts and can be found in varied environmental habitats (Borenshtein & Schauer, 2006). In humans, several species of the genus Citrobacter are regarded as opportunistic pathogens and have been associated with various infections, including urinary tract infections, wound infections, pneumonia, abscesses, septicaemia, meningitis, endocarditis and diarrhoea (Lipsky et al., 1980;Doran, 1999;Mohanty et al., 2007;Samonis et al., 2009;Vaz Marecos et al., 2012;Chowdhry & Cohen, 2012). Citrobacter rodentium can cause colitis and transmissible colonic hyperplasia in mice (Luperchio & Schauer, 2001) and uses molecular mechanisms of pathogenesis similar to those observed for enteropathogenic and enterohaemorrhagic strains of the species Escherichia coli causing diarrhoea and haemolytic uraemic syndrome in humans (Petty et al., 2011). At the time of writing, the genus Citrobacter comprises 11 species: Citrobacter freundii (the type species of the genus), Citrobacter amalonaticus, Citrobacter braakii, Citrobacter farmeri, Citrobacter gillenii, Citrobacter koseri, Citrobacter murliniae, C. rodentium, Citrobacter sedlakii, Citrobacter werkmanii and Citrobacter youngae (Brenner et al., 1993;Frederiksen, 2005). Since the large DNA hybridization study of Brenner and colleagues (Brenner et al., 1993), only three novel species have been described: C. rodentium (Schauer et al., 1995), C. gillenii and C. murliniae (Brenner et al., 1999). Identification of isolates of species of the genus Citrobacter can be tentatively achieved using biochemical profiles or matrixassisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF) (Richter et al., 2013; Kolinská et al., 2014). Phylogenetic relationships based on 16S rRNA sequences distinguished three groups (Warren et al., 2000): group I (C. freundii, C. youngae, C. braakii, C. werkmanii, C. gillenii and C. murliniae); group II (C. amalonaticus, C. farmeri, C. sedlakii and C. rodentium); and group III (C. koseri). 16S rRNA gene sequence variation provides limitedAbbreviations: ANI, average nucleotide identity; MALDI-TOF, matrixassisted laser desorption/ionization time-of-flight mass spectroscopy; MLSA, multilocus sequence analysis.The GenBank/EMBL/DDBJ accession numbers for the gene sequences of the type strains of species of the genus Citrobacter resulting from this study are KM515966 to KM515975, KP728117 and KP057683 for rrs, KM515976 to KM515985 for fusA, KM516006 to KM516012 for rpoB, KM515996 to KM516005 for pyrG, and KM515986 to KM5159 95 for leuS.The annotated genomic sequence of strain CIP 55.13

Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

Two strains of non-spore-forming, rod-shaped, Gram-positive bacteria, CIP 101303 T and CIP 102116, were isolated from human blood in 1976 and 1977, respectively. These strains had chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-10, MK-11 and MK-12 as the major menaquinones, predominant iso-and anteiso-branched cellular fatty acids, galactose, mannose and rhamnose as the cell-wall sugars and ornithine as the diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 70-72 mol%. Comparative 16S rRNA gene sequence studies revealed that strains CIP 101303 T and CIP 102116 belonged to the genus Microbacterium and that they were related closely to Microbacterium halotolerans. The level of DNA-DNA relatedness showed that the two isolates represented a separate genomic species. Based on phenotypic and genotypic results, it is proposed that strains CIP 101303 T and CIP 102116 be assigned to a novel species, Microbacterium binotii sp. nov. The type strain is CIP 101303 T (5DSM 19164 T ).

In the early 1980s, a facultatively anaerobic, non-motile, short rod, designated 202 T , was isolated from a chicken crop and identified as a homofermentative lactic acid bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was affiliated with the genus Lactobacillus, clustering within the Lactobacillus acidophilus-delbrueckii group. In this analysis, strain 202 T appeared to be most closely related to the type strains of Lactobacillus intestinalis and Lactobacillus amylolyticus, with gene sequence similarities of 96.1 and 96.2 %, respectively. Strain 202 T was found to differ from these two species, however, when investigated by multilocus sequence analysis, and it also differed in terms of some of its metabolic properties. On the basis of these observations, strain 202 T is considered to represent a novel species in the genus Lactobacillus, for which the name Lactobacillus gigeriorum sp. nov. is proposed; the type strain is 202 T (5CRBIP 24.85