Lactobacillus porcinae sp. nov. isolated from traditional Vietnamese nem chua

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767T, that could not be assigned to a validly named species. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus Lactobacillus, with Lactobacillus manihotivorans and Lactobacillus camelliae as the closest relatives (98.9% and 96.9% gene sequence similarity towards the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767T (= CCUG 62266T) represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed. Biochemically, Lb. porcinae can be distinguished from Lb. manihotivorans and Lb. camelliae by its carbohydrate fermentation profile, absence of growth at 45°C, and production of D- and L- lactate as end products of glucose metabolism

Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment

Background: Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions. It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. The molecular mechanisms underlying its metabolic capabilities and niche adaptations were unknown up to now. In the present study, whole-genome sequencing and comparative genome analysis were used to investigate this strain's mechanisms to reside in the beer niche, with special focus on not only stress and hop resistances but also folate biosynthesis and exopolysaccharide (EPS) production. Results: The draft genome sequence of P. damnosus LMG 28219 harbored 183 contigs, including an intact prophage region and several coding sequences involved in plasmid replication. The annotation of 2178 coding sequences revealed the presence of many transporters and transcriptional regulators and several genes involved in oxidative stress response, hop resistance, de novo folate biosynthesis, and EPS production. Comparative genome analysis of P. damnosus LMG 28219 with Pediococcus claussenii ATCC BAA-344T (beer origin) and Pediococcus pentosaceus ATCC 25745 (plant origin) revealed that various hop resistance genes and genes involved in de novo folate biosynthesis were unique to the strains isolated from beer. This contrasted with the genes related to osmotic stress responses, which were shared between the strains compared. Furthermore, transcriptional regulators were enriched in the genomes of bacteria capable of growth in beer, suggesting that those cause rapid up-or down-regulation of gene expression. Conclusions: Genome sequence analysis of P. damnosus LMG 28219 provided insights into the underlying mechanisms of its adaptation to the beer niche. The results presented will enable analysis of the transcriptome and proteome of P. damnosus LMG 28219, which will result in additional knowledge on its metabolic activities

Characterization of strains of Weissella fabalis sp. nov. and Fructobacillus tropaeoli from spontaneous cocoa bean fermentations

Six facultatively anaerobic, non-motile lactic acid bacteria were isolated from spontaneous cocoa bean fermentations carried out in Brazil, Ecuador and Malaysia. Phylogenetic analysis revealed that one of these strains, designated M75T, isolated from a Brazilian cocoa bean fermentation, had the highest 16S rRNA gene sequence similarity towards Weissella fabaria LMG 24289T (97.7 %), W. ghanensis LMG 24286T (93.3 %) and W. beninensis LMG 25373T (93.4 %). The remaining lactic acid bacteria isolates, represented by strain M622, showed the highest 16S rRNA gene sequence similarity towards the type strain of Fructobacillus tropaeoli (99.9 %), a recently described species isolated from a flower in South Africa. pheS gene sequence analysis indicated that the former strain represented a novel species, whereas pheS, rpoA and atpA gene sequence analysis indicated that the remaining five strains belonged to F. tropaeoli; these results were confirmed by DNA–DNA hybridization experiments towards their respective nearest phylogenetic neighbours. Additionally, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry proved successful for the identification of species of the genera Weissella and Fructobacillus and for the recognition of the novel species. We propose to classify strain M75T ( = LMG 26217T  = CCUG 61472T) as the type strain of the novel species Weissella fabalis sp. nov

Leuconostoc rapi sp nov., isolated from sous-vide-cooked rutabaga

A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676(T), was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676(T) from all established species of the genus Leuconostoc. Strain LMG 27676(T) (=R-50029(T)=MHB 277(T)=DSM 27776(T)) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed

Vergelijkende studie van de diversiteit, stabiliteit en antibioticum resistentie in de predominante fecale microbiota van patiënten met mucovisidose en gezonde siblings. /

Master of Science in de biochemie en de biotechnologi

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642(T), could be assigned to a novel species, with Carnobacterium funditum DSM 5970(T) as its closest phylogenetic neighbour (99.2% 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA-DNA relatedness confirmed that strain LMG 26642(T) represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642(T) =CCUG 62000(T))