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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 M75 T , isolated from a Brazilian cocoa bean fermentation, had the highest 16S rRNA gene sequence similarity towards Weissella fabaria LMG 24289 T (97.7 %), W. ghanensis LMG 24286 T (93.3 %) and W. beninensis LMG 25373 T (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 M75 T (5LMG 26217 T 5CCUG 61472 T

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BackgroundPediococcus 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.ResultsThe 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.ConclusionsGenome 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1438-z) contains supplementary material, which is available to authorized users.

The novel, Gram-stain-positive, ovoid, lactic acid bacterial isolates LMG 27205, LMG 27206, LMG 27207 T and MRI-F 18 were obtained from throat samples of healthy humans. 16S rRNA gene sequence analyses indicated that these isolates belong to the genus Streptococcus, specifically the Streptococcus mitis group, with Streptococcus australis and Streptococcus mitis as the nearest neighbours (99.45 and 98.56 % 16S rRNA gene sequence similarity to the respective type strains). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE), DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA and atpA and physiological and biochemical tests revealed that these bacteria formed a taxon well separated from its nearest neighbours and other species of the genus Streptococcus with validly published names and, therefore, represent a novel species, for which the name Streptococcus rubneri sp. nov. is proposed, with LMG 27207 T (5DSM 26920 T ) as the type strain.The streptococci are lactic acid bacteria that belong to the phylum Firmicutes, class Bacilli, order Lactobacillales and family Streptococcaceae. Comparative 16S rRNA gene sequence analysis clusters species of the genus Streptococcus into six main species groups (Bentley et al., 1991;Kawamura et al., 1995) that are referred to as the anginosus, bovis, mitis, mutans, pyogenes and salivarius species groups (Kawamura et al., 1995). The mitis group currently includes Streptococcus australis, S. cristatus, S. gordonii, S. infantis, S. lactarius, S. massiliensis, S. mitis, S. oligofermentans, S. oralis, S. parasanguinis, S. peroris, S. pseudopneumoniae, S. pneumoniae, S. sanguinis, S. sinensis and S. tigurinus (Kawamura et al., 1999;Hoshino et al., 2005;Glazunova et al., 2006;Naser, 2006; Martín et al., 2011;Zbinden et al., 2012), and combines the Streptococcus mitis and Streptococcus sanguinis groups reported by Facklam (2002). However, assignment of Streptococcus massiliensis to the mitis group is based on partial sequences of housekeeping genes, and not on a 16S rRNA gene sequence comparison, which allocates it to the mutans group (Glazunova et al., 2006(Glazunova et al., , 2010.Isolates LMG 27205, LMG 27206, LMG 27207 T and MRI-F 18 were obtained during an investigation of the microbial populations associated with the throats of healthy human volunteers taking part in a probiotics study (Seifert et al., 2011). Isolates LMG 27205 and MRI-F 18 were taken from throat swabs of the same individual on different sampling occasions, while LMG 27206 and LMG 27207 T originated from throat swabs of different individuals participating in the study. Streptococci were isolated on Columbia CNA 5 % sheep blood agar (Becton Dickinson) and were purified by repeated streaking using the same medium. Cells were Gram-stained and and observed by microscopy.The nearly complete 16S rRNA gene sequences of all four isolates were determined as follows. DNA was extracted according to the method of Pitcher et al. (19...

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. The genus Carnobacterium was created to accommodate heterofermentative, facultatively anaerobic, psychrotolerant, rod-shaped lactic acid bacteria that produce L-lactic acid from glucose. At the time of writing, the genus Carnobacterium comprises 10 species with validly published names. Most of them were isolated from food of animal origin and/or living fish, except for Carnobacterium alterfunditum, Carnobacterium funditum and Carnobacterium pleistocenium which were isolated from cold environments with low nutrient contents, such as Antarctic ice lakes and permafrost ice (Franzmann et al., 1991;Pikuta et al., 2005). .2] at 4 u C for 10 days and 20 u C for 4 days, respectively. The clonality of these isolates was investigated by randomly amplified polymorphic DNA fingerprinting using primers and RAPD-272 (59-AGCGGGCCAA-39), as described by Mahenthiralingam et al. (1996). The fingerprints indicated that isolates LMG 26642 T , LMG 26896, R-37000 and R-36994 were genetically identical, as was the case for LMG 26641 and LMG 26897 (data not shown).Nearly complete 16S rRNA gene sequence analysis was performed as described by Vancanneyt et al. (2004) for strains LMG 26642T and LMG 26641. PCR products were purified using a Nucleofast 96 PCR clean up membrane system (Macherey-Nagel, Germany). The sequencing primers were Abbreviations: MLSA, multilocus sequence analysis; rep, repetitive element palindromic.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, pheS, rpoA and atpA sequences of strain LMG 26642T are HE583595 and HE578182-HE578184, respectively.

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767 T , that could not be assigned to a species with a validly published name. 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 to 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 26767 T represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767 T (5CCUG 62266 T ). Biochemically, L. porcinae can be distinguished from L. manihotivorans and L. camelliae by its carbohydrate fermentation profile, absence of growth at 45 6C, and production of D-and L-lactate as end products of glucose metabolism.