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Additional file 5: Table S2. Extraction and sequencing information corresponding to the four newly sequenced Mucor isolates

Additional file 4: Table S1. Number of identified CAZyme encoding genes involved in the degradation of plant cell wall components (Cellulose active, Hemicellulose active and Pectin active). The presence of genes has been confirmed with manual annotation.

Additional material is published online only. To view please visit the journal online (http://dx.doi.org/10.1136/bmjresp-2018-000374).; International audience; Introduction : Pseudomonas aeruginosa pulmonary infections are the primary cause of morbi-mortality in patients with cystic fibrosis (CF). In this cohort study, the objective was to identify candidate biomarkers of P. aeruginosa infection within the airway microbiota. Methods : A 3-year prospective multicentre study (PYOMUCO study) was conducted in Western France and included patients initially P. aeruginosa free for at least 1year. A 16S-targeted metagenomics approach was applied on iterative sputum samples of a first set of patients (n=33). The composition of airway microbiota was compared according to their P. aeruginosa status at the end of the follow-up (colonised vs non-colonised), and biomarkers associated with P. aeruginosa were screened. In a second step, the distribution of a candidate biomarker according to the two groups of patients was verified by qPCR on a second set of patients (n=52) coming from the same cohort and its load quantified throughout the follow-up. Results : Porphyromonas (mainly P. catoniae) was found to be an enriched phylotype in patients uninfected by P. aeruginosa (pDiscussion : Further studies on replication cohorts are needed to validate this potential predictive biomarker, which may be relevant for the follow-up in the early years of patients with CF. The identification of infection candidate biomarkers may offer new strategies for CF prevision medicine.

Dichotomous keys based on morphological, cultural and biochemical tests have long been used to identify Bacillus species. The analysis of 16S rDNA is suggested to be used for identification that is more exact. The present study was carried out to compare a conventional phenotypic method with the analysis of the 16S rRNA and gyrB gene for better identification, to determine their phylogenetic relationships and to contribute to selecting starter cultures for Mbuja production. Twenty-six (26) Bacillus strains isolated from 12 samples of Mbuja formerly identified by phenotyping as representatives of eight species (licheniformis, polymyxa, laterosporus, cereus, circulans, subtilis, pumilus and brevis) were studied. Results of genotypic analyses were not concurrent with previous phenotypic identification. Bacillus from different species were able to cluster together to form phylogenetic groups. An insight of these groups revealed important genetic diversity between strains from the same species. Bacillus subtilis and close relatives were the most abundant and presented appreciable biochemical traits. This group could therefore be considered for starter selection.Keywords: Mbuja, Bacillus sp., phenotyping, genotyping, starterAfrican Journal of Biotechnology Vol. 12(12), pp. 1335-1343

Cadophora malorum Mo12 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. We present the draft genome sequence of this filamentous fungal strain, which has high biotechnological potentials as revealed by the presence of genes encoding biotechnologically important enzymes and genes involved in the synthesis of secondary metabolites.

International audience; This study describes the diversity and dynamics of bacterial communities in the fermentation of Hibiscus sabdariffa seeds to produce Mbuja, a traditional condiment from Cameroon, using culture-dependent and independent methods. The total aerobic mesophilic bacteria, lactic acid bacteria (LAB) and Bacillus spp. were numbered on specific culture media. The bacterial communities were characterized by PCR-SSCP, sequencing of 16S rRNA clone libraries and community-level physiological profiles. Viable cells counts evidenced the domination of Bacillus spp. during the process, and the continuous decrease of LAB. PCR-SSCP revealed three groups of bacteria succeeding with the first microorganism communities from day 2 to day 7 being similar. The two other groups were communities in day 8 and 9 and those from day 10. The sequencing of clone libraries showed that the first group communities was more diversified and consisted in Bacillus spp., Lactobacillus, Streptomyces and Staphylococcus . The last two groups of bacterial communities involved fewer genera but diverse Bacillus species different from those occurring at the first step. The early phase metabolism profile was exclusively oriented toward carbohydrates and the last targeted broad substrates with amino-acids and organic and carboxylic acids being the most important. This suggests a combination of species in starter formulation.

The definitive version is available at ww3.interscience.wiley.com. Post-print en libre-accès sur Archimer : http://archimer.ifremer.fr/doc/00006/11704/8475.pdf; International audience; Investigations of the diversity of culturable yeasts at deep-sea hydrothermal sites have suggested possible interactions with endemic fauna. Samples were collected during various oceanographic cruises at the Mid-Atlantic Ridge, South Pacific Basins and East Pacific Rise. Cultures of 32 isolates, mostly associated with animals, were collected. Phylogenetic analyses of 26S rRNA gene sequences revealed that the yeasts belonged to Ascomycota and Basidiomycota phyla, with the identification of several genera: Rhodotorula, Rhodosporidium, Candida, Debaryomyces and Cryptococcus. Those genera are usually isolated from deep-sea environments. To our knowledge, this is the first report of yeasts associated with deep-sea hydrothermal animals.