Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.
ABSTRACT: Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50-66% of each individual genome. Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).
Project description:The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146T = DSM 2975T = CCUG 69503T = CIP 111191T) and Elizabethkingia ursingii sp. nov. (type strain, G4122T = DSM 2974T = CCUG 69496T = CIP 111192T), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070T = DSM 2976T = CCUG 69505T = CIP 111193T), is proposed.
Project description:A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191F<sup>T</sup>, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family <i>Chitinophagaceae</i> that was distinct from members of the genus <i>Pseudoflavitalea</i> (95.1-95.2 % sequence similarity) and <i>Pseudobacter ginsenosidimutans</i> (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191F<sup>T</sup> and <i>Pseudoflavitalea rhizosphaerae</i> T16R-265<sup>T</sup> and <i>Pseudobacter ginsenosidimutans</i> Gsoil 221<sup>T</sup> was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191F<sup>T</sup> was MK-7 and the major fatty acids were iso-C<sub>15 : 0</sub>, iso-C<sub>15 : 1</sub> G and summed feature 3 (C<sub>16:1</sub> ω7<i>c</i> and/or C<sub>16:1</sub> ω6<i>c</i>). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191F<sup>T</sup> calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191F<sup>T</sup> represents a novel species and genus for which the name <i>Parapseudoflavitalea muciniphila</i> gen. nov., sp. nov. is proposed. The type strain is PMP191F<sup>T</sup> (=DSM 104999<sup>T</sup>=ATCC BAA-2857<sup>T</sup> = CCUG 72691<sup>T</sup>). The phylogenetic analyses also revealed that <i>Pseudobacter ginsenosidimutans</i> shared over 98 % sequence similarly to members of the genus <i>Pseudoflavitalea</i>. However, the average nucleotide identity value between <i>Pseudoflavitalea rhizosphaerae</i> T16R-265<sup>T</sup>, the type species of the genus and <i>Pseudobacter ginsenosidimutans</i> Gsoil 221<sup>T</sup> was 86.8 %. Therefore, we also propose that <i>Pseudobacter ginsenosidimutans</i> be reclassified as <i>Pseudoflavitalea ginsenosidimutans</i> comb. nov.
Project description:Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3:22(T) and N1(T)) are described. Strain CD3:22(T) was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1(T) from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H(2)S, NH(3), butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98% sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/E. saburreum-like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae. While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089(T) confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3:22(T) and N1(T) represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales, class Clostridia, phylum Firmicutes]. Strain CD3:22(T) (=CCUG 58757(T) =DSM 23576(T)) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1(T) (=CCUG 60305(T)=DSM 24553(T)) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089(T) =ATCC 33271(T) =CIP 105341(T) =DSM 3986(T) =JCM 11021(T) =VPI 11763(T)).
Project description:Here, we report the annotated draft genome sequences of two type strains belonging to the family Eggerthellaceae within the class Coriobacteriia (phylum Actinobacteria), Adlercreutzia muris WCA-131-CoC-2 (= DSM 29508 = KCTC 15543) and Ellagibacter urolithinifaciens CEBAS 4A (= CCUG 70284 = DSM 104140).
Project description:We previously discovered a symbiotic lactic acid bacterial (LAB) microbiota in the honey stomach of the honeybee Apis mellifera. The microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus. 16S rRNA gene sequence analyses and phenotypic and genetic characteristics revealed that the phylotypes isolated represent seven novel species. One grouped with Lactobacillus kunkeei and the others belong to the Lactobacillus buchneri and Lactobacillus delbrueckii subgroups of Lactobacillus. We propose the names Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov. for these novel species, with the respective type strains being Fhon13N(T) (?=?DSM 26257(T)?=?CCUG 63287(T)), Bin4N(T) (?=?DSM 26254(T)?=?CCUG 63291(T)), Hon2N(T) (?=?DSM 26255(T)?=?CCUG 63289(T)), Hma8N(T) (?=?DSM 26256(T)?=?CCUG 63629(T)), Hma2N(T) (?=?DSM 26263(T)?=?CCUG 63633(T)), Bma5N(T) (?=?DSM 26265(T)?=?CCUG 63301(T)) and Biut2N(T) (?=?DSM 26262(T)?=?CCUG 63631(T)).
Project description:Comparative analysis of partial <i>gyrB</i>, <i>recA</i>, and <i>gltB</i> gene sequences of 84 <i>Pandoraea</i> reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The <i>gyrB</i>, <i>recA</i>, and <i>gltB</i> phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available <i>Pandoraea</i> genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA-DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel <i>Pandoraea</i> species among the strains analyzed, and allowed the identification of several unclassified <i>Pandoraea</i> strains reported in the literature. The genus <i>Pandoraea</i> has an open pan genome that includes many orthogroups in the 'Xenobiotics biodegradation and metabolism' KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel <i>Pandoraea</i> species as <i>P. anapnoica</i> sp. nov. (type strain LMG 31117<sup>T</sup> = CCUG 73385<sup>T</sup>), <i>P. anhela</i> sp. nov. (type strain LMG 31108<sup>T</sup> = CCUG 73386<sup>T</sup>), <i>P. aquatica</i> sp. nov. (type strain LMG 31011<sup>T</sup> = CCUG 73384<sup>T</sup>), <i>P. bronchicola</i> sp. nov. (type strain LMG 20603<sup>T</sup> = ATCC BAA-110<sup>T</sup>), <i>P. capi</i> sp. nov. (type strain LMG 20602<sup>T</sup> = ATCC BAA-109<sup>T</sup>), <i>P. captiosa</i> sp. nov. (type strain LMG 31118<sup>T</sup> = CCUG 73387<sup>T</sup>), <i>P. cepalis</i> sp. nov. (type strain LMG 31106<sup>T</sup> = CCUG 39680<sup>T</sup>), <i>P. commovens</i> sp. nov. (type strain LMG 31010<sup>T</sup> = CCUG 73378<sup>T</sup>), <i>P. communis</i> sp. nov. (type strain LMG 31110<sup>T</sup> = CCUG 73383<sup>T</sup>), <i>P. eparura</i> sp. nov. (type strain LMG 31012<sup>T</sup> = CCUG 73380<sup>T</sup>), <i>P. horticolens</i> sp. nov. (type strain LMG 31112<sup>T</sup> = CCUG 73379<sup>T</sup>), <i>P. iniqua</i> sp. nov. (type strain LMG 31009<sup>T</sup> = CCUG 73377<sup>T</sup>), <i>P. morbifera</i> sp. nov. (type strain LMG 31116<sup>T</sup> = CCUG 73389<sup>T</sup>), <i>P. nosoerga</i> sp. nov. (type strain LMG 31109<sup>T</sup> = CCUG 73390<sup>T</sup>), <i>P. pneumonica</i> sp. nov. (type strain LMG 31114<sup>T</sup> = CCUG 73388<sup>T</sup>), <i>P. soli</i> sp. nov. (type strain LMG 31014<sup>T</sup> = CCUG 73382<sup>T</sup>), and <i>P. terrigena</i> sp. nov. (type strain LMG 31013<sup>T</sup> = CCUG 73381<sup>T</sup>).
Project description:Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317(T) = CCUG 68412(T)), Burkholderia hypogeia sp. nov. (type strain LMG 29322(T) = CCUG 68407(T)), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326(T) = CCUG 68403(T)), Burkholderia glebae sp. nov. (type strain LMG 29325(T) = CCUG 68404(T)), Burkholderia pedi sp. nov. (type strain LMG 29323(T) = CCUG 68406(T)), Burkholderia arationis sp. nov. (type strain LMG 29324(T) = CCUG 68405(T)), Burkholderia fortuita sp. nov. (type strain LMG 29320(T) = CCUG 68409(T)), Burkholderia temeraria sp. nov. (type strain LMG 29319(T) = CCUG 68410(T)), Burkholderia calidae sp. nov. (type strain LMG 29321(T) = CCUG 68408(T)), Burkholderia concitans sp. nov. (type strain LMG 29315(T) = CCUG 68414(T)), Burkholderia turbans sp. nov. (type strain LMG 29316(T) = CCUG 68413(T)), Burkholderia catudaia sp. nov. (type strain LMG 29318(T) = CCUG 68411(T)) and Burkholderia peredens sp. nov. (type strain LMG 29314(T) = CCUG 68415(T)). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively.
Project description:Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).
Project description:The first complete genome sequence of the recently described Macrococcus canis species has been determined for the strain KM45013T (=DSM 101690T = CCOS 969T = CCUG 68920T = CCM 8748T). The strain was isolated from a dog with rhinitis and contains a putative ?-hemolysin and a mecB-carrying staphylococcal cassette chromosome mec element (SCCmecKM45013).