RESULTS:

Paenibacillus durus and Paenibacillus azotofixans both Gram-stain-positive and endospore-forming bacilli have been considered to be a single species. However a preliminary computation of their average nucleotide identity (ANI) values suggested that these species are not synonyms. Given this the taxonomic attributions of these species were evaluated through genomic and phylogenomic approaches. Although the identity of 16S rRNA gene sequences of P. durus DSM 1735T and P. azotofixans ATCC 35681T are above the circumscription species threshold genomic metrics analyses indicate otherwise. ANI gANI and OrthoANI values computed from their genome sequences were around 92 % below the species limits. Digital DNA–DNA hybridization and MUMi estimations also corroborated these observations. In fact in all metrics Paenibacillus zanthoxyli JH29T seemed to be more similar to Paenibacillus azotofixans . ATCC 35681T than P. durus DSM 1735T. Phylogenetic analyses based on concatenated core-proteome and concatenated gyrB recA recN and rpoB genes confirmed that P. zanthoxyli is the closest Paenibacillus species to P. azotofixans . A review of the phenotypic profiles from these three species revealed that their biochemical repertoires are very similar although P. azotofixans ATCC 35681T can be differentiated from P. durus DSM1735T in 13 among more than 90 phenotypic traits. Considering phylogenetic and genomic analyses Paenibacillus azotofixans should be considered as an independent species and not as a later synonym of Paenibacillus durus .

A comparative analysis of the two type strains of Pseudidiomarina maritima 908087T and Pseudidiomarina tainanensis PIN1T was performed to examine their taxonomic relationship. The 16S rRNA gene sequence of P. maritima 908087T shared a high similarity (99.8 %) with that of P. tainanensis PIN1T. The phylogenetic trees based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Pseudidiomarina . Whole genomic comparison between the two strains revealed a digital DNA–DNA hybridization estimate of 75.8 % and an average nucleotide identity value of 97.3 % strongly indicating that they represented a single species. In addition the strains did not display any striking differences in their metabolic physiological or chemotaxonomic features. Therefore we propose that Pseudidiomarina maritima is a later heterotypic synonym of Pseudidiomarina tainanensis .

Streptomyces rimosus is currently composed of two subspecies: Streptomyces rimosus subsp. rimosus and Streptomyces rimosus subsp. paromomycinus . The 16S rRNA gene similarity between type strains of these two subspecies is 99.03 % whereas that between S. rimosus subsp. paromomycinus and Streptomyces chrestomyceticus is 100 %. To assess the taxonomic status of S. rimosus subsp. paromomycinus genome sequencing was performed on the type strains of S. rimosus subsp. paromomycinus and S. chrestomyceticus . Digital DNA–DNA hybridization values between S. rimosus subsp. paromomycinus NBRC 15454T and S. rimosus subsp. rimosus ATCC 10970T and between S. rimosus subsp. paromomycinus NBRC 15454T and S. chrestomyceticus NBRC 13444T were 35.4 and 59.9 % respectively which are less than the thresholds for bacterial species delineation and indicate that S. rimosus subsp. paromomycinus is not S. rimosus but an independent species different from S. rimosus and S. chrestomyceticus . In addition phenotypic data also support that S. rimosus subsp. paromomycinus is distinct from S. chrestomyceticus . Therefore S. rimosus subsp. paromomycinus should be reclassified as a novel species for which we propose the name Streptomyces paromomycinus sp. nov. The type strain is NBRC 15454T (=ATCC 14827T=DSM 41429T=JCM 4541T=JCM 4871T=NRRL 2455T=VKM Ac-605T).

Flexibacter tractuosa [Lewin 1969] was reclassified as Marivirga tractuosa . Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic Gram-stain-negative slender rods which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0 iso-G-C15 : 1 C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine several unidentified aminolipids glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes . Levels of DNA–DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin as well as by α-glucosidase and β-glucosidase activity. On the basis of these results NBRC 15981T is proposed as representing a novel species of the genus Marivirga named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald) Germany by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria . Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia . These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia that this order should be split into two orders and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales . We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov. sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.

The type strains of four subspecies of Leuconostocmesenteroides L. mesenteroides subsp. mesenteroides L. mesenteroides subsp. cremoris L. mesenteroides subsp. dextranicum and L. mesenteroides subsp. suionicum and strain DRC1506T used as a starter culture for commercial kimchi production in Korea were phylogenetically analyzed on the basis of their complete genome sequences. Although the type strains of the four L. mesenteroides subspecies and strain DRC1506T shared very high 16S rRNA gene sequence similarities (>99.72 %) the results of analysis of average nucleotide identity (ANI) in silico DNA–DNA hybridization (DDH) and core-genome-based relatedness indicated that they could form five different phylogenetic lineages. The type strains of L. mesenteroides subsp. mesenteroides L. mesenteroides subsp. cremoris and L. mesenteroides subsp. dextranicum and DRC1506T shared higher ANI and in silico DDH values than the thresholds (95–96 % and 70 % respectively) generally accepted for different species delineation whereas the type strain of L. mesenteroides subsp. suionicum (DSM 20241T) shared lower ANI (<94.1 %) and in silico DDH values (<57.0 %) with the other four L. mesenteroides lineage strains indicating that DSM 20241T couldn be reclassified as representing a different species. Here we report that DRC1506T represents a novel subspecies within the species Leuconostoc mesenteroides for which the name Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. is proposed. The type strain is DRC1506T (=KCCM 43249T=JCM 31787T). In addition L. mesenteroides subsp. suionicum is also reclassified as Leuconostoc suionicum. sp. nov. (type strain DSM 20241T=ATCC 9135T=LMG 8159T=NCIMB 6992T).

The aim of the study was to reclarify the taxonomic status of four species Mameliella phaeodactyli Mameliella atlantica Ponticoccus lacteus and Alkalimicrobium pacificum by using a polyphasic taxonomic approach. A combination of physiological properties of the four type strains KD53T L6M1-5T JL351T and F15T was consistent with those of the closest type strain JLT354-WT of Mameliella alba . The 16S rRNA gene sequences of the five type strains shared 100 % identity. The close relationship between the five strains was underpinned by the results of chemotaxonomic characteristics including the fatty acids quinone and polar lipids. The pairwise digital DNA–DNA hybridization values among the five strains were well above 70 % considered the threshold value for species definition. In this case a further statement of Rule 24a applies in which priority of names is determined by the date of the original publication. Hence we propose that that Mameliella phaeodactyli Mameliella atlantica Ponticoccus lacteus and Alkalimicrobium pacificum should be regarded as later heterotypic synonyms of Mameliella alba .

A Gram-staining-negative strictly aerobic bacterial strain designated MA7-20T was isolated from a marine alga Porphyridium marinum in Korea. Cells showing oxidase-positive and catalase-positive activities were motile rods with bipolar flagella. Growth of strain MA7-20T was observed at 15–45 °C (optimum 30–37 °C) at pH 6.0–10.5 (optimum pH 7.0–8.0) and in the presence of 0–7 % (w/v) NaCl (optimum 2–3 %). Strain MA7-20T contained summed feature 8 (comprising C18 : 1ω7c/C18  : 1ω6c) 11-methyl C18 : 1ω7c and C18 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. The major polar lipids were phosphatidylcholine phosphatidylglycerol diphosphatidylglycerol phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. The G+C content of the genomic DNA was 61.5 mol%. Strain MA7-20T was most closely related to Hoeflea suaedae YC6898T Oricola cellulosilytica CC-AMH-0T and Nitratireductor basaltis J3T with 96.0 95.8 and 95.8 % 16S rRNA gene sequence similarities respectively but the strain formed a distinct phylogenetic lineage from them within the family Phyllobacteriaceae with a low bootstrap value. H. suaedae also formed a clearly distinct phylogenetic lineage from other members of the genus Hoeflea and closely related genera. On the basis of phenotypic chemotaxonomic and molecular properties strain MA7-20T represents a novel species of a new genus of the family Phyllobacteriaceae for which the name Roseitalea porphyridii gen. nov. sp. nov. is proposed. The type strain is MA7-20T (=KACC 18807T=JCM 31538T). In addition H. suaedae is also reclassified as Pseudohoeflea suaedae gen. nov. comb. nov. (type strain YC6898T=KACC 14911T=NBRC 107700T).

Lactobacillus bobalius Lactobacillus kimchii and Lactobacillus paralimentarius belong to the genus Lactobacillus and show close phylogenetic relationships. In a previous study L. bobalius and L. kimchii were proposed to be reclassified as later heterotypic synonyms of L. paralimentarius using high 16S rRNA gene sequence similarities (≥99.5 %) and DNA–DNA hybridization values (≥82 %). We determined high quality whole genome assemblies of the type strains of L. bobalius and L. kimchii which were then compared with that of L. paralimentarius . Average nucleotide identity values among three genomes ranged from 91.4 to 92.3 % which are clearly below 95~96 % the generally recognized cutoff value for bacterial species boundaries. On the basis of comparative genomic evidence L. bobalius L. kimchii and L. paralimentarius should stand as separate species in the genus Lactobacillus . We therefore suggest rejecting the previous proposal to combine these three species into a single species.

A polyphasic taxonomic approach was applied to strains of the species Staphylococcus sciuri in order to clarify the taxonomic legitimacy of the delineation of S. sciuri into S. sciuri subsp. sciuri S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium . A group of 81 S. sciuri isolates obtained from human (n=62) and veterinary (n=17) clinical materials and foods (n=2) and ten reference and type strains obtained from the Czech Collection of Microorganisms were characterized by extensive biotyping using conventional tests and commercial identification kits (ID 32 Staph STAPHYtest Biolog Microbial ID System) matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry automated ribotyping with EcoRI restriction enzyme 16S–23S rRNA gene intergenic transcribed spacer PCR fingerprinting and repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Selected strains representing different ribotypes were further characterized using sequencing of the β-subunit of RNA polymerase (rpoB) gene. Individual techniques revealed high heterogeneity within the analysed S. sciuri strains but differentiation of the investigated strains into groups corresponding to the aforementioned S. sciuri subspecies and supported by these techniques was not clearly revealed. Based on obtained results and data retrieved from literature we propose rejecting the separation of S. sciuri species into S. sciuri subsp. sciuri S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium and we suggest reclassification these subspecies as S. sciuri with the type strain W.E. Kloos SC 116T (=ATCC 29062T=BCRC 12927T=CCM 3473T=CCUG 15598T=CNCTC 5683T=DSM 20345T=JCM 2425T=NCTC 12103T).