Characterization of lactic acid bacteria isolated from a traditional Ivoirian beer process to develop starter cultures for safe sorghum-based beverages.

The present study aimed to characterize lactic acid bacteria involved in the different processing steps of tchapalo, a traditional Ivoirian beverage, for their potential application as starter cultures in food and beverages. Lactic acid bacteria (LAB) were therefore isolated and enumerated at different steps of the process on MRS and BEA agars. Of the 465 isolates, 27 produced bacteriocins that inhibit Lactobacillus delbrueckii F/31 strain. Of those, two also inhibited Listeria innocua ATCC 33090, while two others displayed inhibitory activity against L.innocua ATCC 33090, E. faecalis CIP 105042, E. faecalis ATCC 29212, Streptococcus sp. clinical LNSP, E. faecalis CIP 105042 and E. faecium ATCC 51558. The dominant species involved in tchapalo LAB fermentation, as determined by 16S rRNA gene sequencing, were Lactobacillus fermentum (64%), followed by Pediococcus acidilactici (14%). Two strains representing the two dominant species, L. fermentum S6 and P. acidilactici S7, and two potential bacteriocin producers, Weissella confusa AB3E41 and Enterococcus faecium AT1E22, were selected for further characterization. First, genome analysis showed that these strains do not display potential harmful genes such as pathogenic factors or transmissible antibiotic resistance genes. Furthermore, phylogenetic analyses were performed to assess evidence of eventual links to groups of strains with particular properties. They revealed that (i) L. fermentum S6 and P. acidilactici S7 are closely related to strains that ferment plants, (ii) E. faecium AT1E22 belongs to the environmental clade B of E. faecium, while W. confusa is quite similar to other strains also isolated from plant fermentations. Further genome analysis showed that E. faecium AT1E22 contains the Enterocin P gene probably carried by a megaplasmid, whereas no evidence of a bacteriocin gene was found in W. confusa AB3E41. The metabolic and the first step of the probiotic potentials of the different strains were analyzed. Lactobacillus fermentum S6 and P. acidilactici S7 are good candidates to develop starter cultures, and E. faecium AT1E22 should be further tested to confirm its potential as a probiotic strain in the production of sorghum wort.

Comparative genomics of extrachromosomal elements in Bacillus thuringiensis subsp. israelensis.

Bacillus thuringiensis subsp. israelensis is one of the most important microorganisms used against mosquitoes. It was intensively studied following its discovery and became a model bacterium of the B. thuringiensis species. Those studies focused on toxin genes, aggregation-associated conjugation, linear genome phages, etc. Recent announcements of genomic sequences of different strains have not been explicitly related to the biological properties studied. We report data on plasmid content analysis of four strains using ultra-high-throughput sequencing. The strains were commercial product isolates, with their putative ancestor and type B. thuringiensis subsp. israelensis strain sequenced earlier. The assembled contigs corresponding to published and novel data were assigned to plasmids described earlier in B. thuringiensis subsp. israelensis and other B. thuringiensis strains. A new 360 kb plasmid was identified, encoding multiple transporters, also found in most of the earlier sequenced strains. Our genomic data show the presence of two toxin-coding plasmids of 128 and 100 kb instead of the reported 225 kb plasmid, a co-integrate of the former two. In two of the sequenced strains, only a 100 kb plasmid was present. Some heterogeneity exists in the small plasmid content and structure between strains. These data support the perception of active plasmid exchange among B. thuringiensis subsp. israelensis strains in nature.

Detection of the cryptic prophage-like molecule pBtic235 in Bacillus thuringiensis subsp. israelensis.

Bacillus thuringiensis has long been recognized to carry numerous extrachromosomal molecules. Of particular interest are the strains belonging to the B. thuringiensis subsp. israelensis lineage, as they can harbor at least seven extrachromosomal molecules. One of these elements seems to be a cryptic molecule that may have been disregarded in strains considered plasmid-less. Therefore, this work focused on this cryptic molecule, named pBtic235. Using different approaches that included transposition-tagging, large plasmid gel electrophoresis and Southern blotting, conjugation and phage-induction experiments, in combination with bioinformatics analyses, it was found that pBtic235 is a hybrid molecule of 235,425 bp whose genome displays potential plasmid- and phage-like modules. The sequence of pBtic235 has been identified in all sequenced genomes of B. thuringiensis subsp. israelensis strains. Here, the pBtic235 sequence was considered identical to that of plasmid pBTHD789-2 from strain HD-789. Despite the fact that the pBtic235 genome possesses 240 putative CDSs, many of them have no homologs in the databases. However, CDSs coding for potential proteins involved in replication, genome packaging and virion structure, cell lysis, regulation of lytic-lysogenic cycles, metabolite transporters, stress and metal resistance, were identified. The candidate plasmidial prophage pBtic235 exemplifies the notable diversity of the extrachromosomal realm found in B. thuringiensis.

Sequence of the Bacillus subtilis genome region in the vicinity of the lev operon reveals two new extracytoplasmic function RNA polymerase sigma factors SigV and SigZ.

Two regions with sizes 18,900 and 25,400 bp, which join previously known contigs containing levRDEFG, aadK and blt genes near 235 degrees of the Bacillus subtilis chromosome, were sequenced. Among others, two genes, which encode proteins homologous to RNA polymerase sigma-factors, were identified within this region. The gene products designated SigV and SigZ, show the highest homology with sigma-factors encoded by the gene carQ of Myxococcus xanthus and sigX (formerly orfX20) of B. subtilis, correspondingly. All sigma-factors which show statistically significant homology to SigV and SigZ, belong to the ECF (extracytoplasmic functions) subfamily. SigV and SigZ do not have N-terminal sequence which prevents such proteins from binding to DNA without RNA polymerase core enzyme.