Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer.
ABSTRACT: Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15?:?0, anteiso-C17?:?0 and iso-C16?:?0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T?=?DSM 27160T?=?CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T?=?DSM 27160T?=?CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T?=?DSM 27158T?=?CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T?=?KACC 14220T?=?JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T?=?DSM 27159T?=?CIP 110720T), and to emend the description of Leucobacter celerShin et al. 2011.
Project description:"Leucobacter massiliensis" strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. "Leucobacter massiliensis" is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.
Project description:Ten strains, BG-AF3-A<sup>T</sup>, pH52_RY, WF-MT5-A<sup>T</sup>, BG-MG3-A, Lr3000<sup>T</sup>, RRLNB_1_1, STM3_1<sup>T</sup>, STM2_1, WF-MO7-1<sup>T</sup> and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as <i>Limosilactobacillus reuteri</i>. However, average nucleotide identity and digital DNA-DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names <i>Limosilactobacillus balticus</i> sp. nov. (type strain BG-AF3-A<sup>T</sup>=DSM 110574<sup>T</sup>=LMG 31633<sup>T</sup>), <i>Limosilactobacillus agrestis</i> sp. nov. (type strain WF-MT5-A<sup>T</sup>=DSM 110569<sup>T</sup>=LMG 31629<sup>T</sup>), <i>Limosilactobacillus albertensis</i> sp. nov. (type strain Lr3000<sup>T</sup>=DSM 110573<sup>T</sup>=LMG 31632<sup>T</sup>), <i>Limosilactobacillus rudii</i> sp. nov. (type strain STM3_1<sup>T</sup>=DSM 110572<sup>T</sup>=LMG 31631<sup>T</sup>) and <i>Limosilactobacillus fastidiosus</i> sp. nov. (type strain WF-MO7-1<sup>T</sup>=DSM 110576<sup>T</sup>=LMG 31630<sup>T</sup>). Core genome phylogeny and experimental evidence of host adaptation of strains of <i>L. reuteri</i> further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of <i>L. reuteri</i>: <i>L. reuteri</i> subsp. <i>kinnaridis</i> subsp. nov. (type strain AP3<sup>T</sup>=DSM 110703<sup>T</sup>=LMG 31724<sup>T</sup>), <i>L. reuteri</i> subsp. <i>porcinus</i> subsp. nov. (type strain 3c6<sup>T</sup>=DSM 110571<sup>T</sup>=LMG 31635<sup>T</sup>), <i>L. reuteri</i> subsp. <i>murium</i> subsp. nov. (type strain lpuph1<sup>T</sup>=DSM 110570<sup>T</sup>=LMG 31634<sup>T</sup>), <i>L. reuteri</i> subsp. <i>reuteri</i> subsp. nov. (type strain F 275<sup>T</sup>=DSM 20016<sup>T</sup>=ATCC 23272<sup>T</sup>), <i>L. reuteri</i> subsp. <i>suis</i> subsp. nov. (type strain 1063<sup>T</sup>=ATCC 53608<sup>T</sup>=LMG 31752<sup>T</sup>) and <i>L. reuteri</i> subsp. <i>rodentium</i> subsp. nov. (type strain 100-23<sup>T</sup>=DSM 17509<sup>T</sup>=CIP 109821<sup>T</sup>).
Project description:Cockle mortality events have been reported in northern France since 2012. In the present study, we describe and investigate the implication of a potential bacterial causative agent in cockle mortality. Bacteria isolated from five different cockle mortality events were characterized and studied. Using phenotypic analysis combined with DNA-DNA hybridization (DDH) and whole genome sequencing, the isolates were shown to belong to <i>Vibrio aestuarianus</i>, a species regularly detected in France during oyster mortality events. Comparison of the strains from cockles with strains from French oysters and the type strain showed that the strains from cockles were genetically different to those from oysters and also different to the <i>V. aestuarianus</i> type strain. Moreover, the cockle and oyster strains were classified into two different, but close, groups both separated from the type strain by: (1) analyses of the <i>ldh</i> gene sequences; (2) DDH assays between 12/122 3T3<sup>T</sup> (LMG 31436<sup>T</sup>=DSM 109723<sup>T</sup>), a representative cockle strain, 02/041<sup>T</sup> (CIP 109791<sup>T</sup>=LMG 24517<sup>T</sup>) representative oyster strain and <i>V. aestuarianus</i> type strain LMG 7909<sup>T</sup>; (3) average nucleotide identity values calculated on the genomes; and (4) phenotypic traits. Finally, results of MALDI-TOF analyses also revealed specific peaks discriminating the three representative strains. The toxicity of representative strains of these cockle isolates was demonstrated by experimental infection of hatchery-produced cockles. The data therefore allow us to propose two novel subspecies of <i>Vibrio aestuarianus</i>: <i>Vibrio aestuarianus</i> subsp. <i>cardii</i> subsp. nov. for the cockle strains and <i>Vibrio aestuarianus</i> subsp. <i>francensis</i> subsp. nov. for the Pacific oyster strains, in addition to an emended description of the species <i>Vibrio aestuarianus</i>.
Project description:Heckmann and Schmidt described the genus Polynucleobacter for bacterial endosymbionts of freshwater ciliates affiliated with the genus Euplotes, and the species Polynucleobacter necessarius for obligate endosymbionts living in the cytoplasm of Euplotes aediculatus. Pure cultures of the type strain could not be established due to the obligate nature of the symbiotic relationship between the endosymbionts and their hosts. Therefore, Polynucleobacter necessarius is one of a few bacterial species with validly published names that lack a deposited pure culture. Meanwhile, it was demonstrated that the endosymbionts used for the description of the type of Polynucleobacter necessarius are closely related to obligately free-living strains. Similarity values of the 16S rRNA gene sequences obtained from the endosymbionts in the ciliate culture and free-living isolates in the range 99.1-99.4% indicate that these organisms belong to the same species. Here, we have emended the description of Polynucleobacter necessarius by characterization of free-living strains maintained as pure cultures. The species Polynucleobacter necessarius was characterized as having low G+C contents of the DNA (44-46 mol%), small genome sizes (1.5-2.5 Mbp) and a lack of motility. Because of distinct differences in lifestyle and the genome size of Polynucleobacter necessarius strains, we propose that two novel subspecies should be established, Polynucleobacter necessarius subsp. necessarius subsp. nov. [with a type, which is a description based on endosymbionts in the culture 'stock 15' of the ciliate E. aediculatus (ATCC 30859)] and Polynucleobacter necessarius subsp. asymbioticus subsp. nov. [with the type strain QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T)], for the obligate endosymbionts of E. aediculatus and Euplotes harpa and obligately free-living strains, respectively.
Project description:The genus <i>Macrococcus</i> is a close relative of the genus <i>Staphylococcus</i>. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as <i>Macrococcus</i> sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus <i>Macrococcus</i>. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a <i>com</i> operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCC<i>mec</i>-like element containing a unique <i>mec</i> gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus <i>Macrococcus</i>, for which the names <i>Macrococcus caseolyticus</i> subsp. <i>hominis</i> subsp. nov. (type strain CCM 7927<sup>T</sup> = DSM 103682<sup>T</sup>), <i>Macrococcus goetzii</i> sp. nov. (type strain CCM 4927<sup>T</sup> = DSM 103683<sup>T</sup>), <i>Macrococcus epidermidis</i> sp. nov. (type strain CCM 7099<sup>T</sup> = DSM 103681<sup>T</sup>), and <i>Macrococcus bohemicus</i> sp. nov. (type strain CCM 7100<sup>T</sup> = DSM 103680<sup>T</sup>) are proposed. Moreover, a formal description of <i>Macrococcus caseolyticus</i> subsp. <i>caseolyticus</i> subsp. nov. and an emended description of the genus <i>Macrococcus</i> are provided.
Project description:Genome comparisons based on average nucleotide identity (ANI) values of four strains currently classified as Polynucleobacter necessarius subsp. asymbioticus resulted in ANI values of 75.7-78.4 %, suggesting that each of those strains represents a separate species. The species P. necessarius was proposed by Heckmann and Schmidt in 1987 to accommodate obligate endosymbionts of ciliates affiliated with the genus Euplotes. The required revision of this species is, however, hampered by the fact, that this species is based only on a description and lacks a type strain available as pure culture. Furthermore, the ciliate culture Euplotes aediculatus ATCC 30859, on which the description of the species was based, is no longer available. We found another Euplotes aediculatus culture (Ammermann) sharing the same origin with ATCC 30859 and proved the identity of the endosymbionts contained in the two cultures. A multilocus sequence comparison approach was used to estimate if the four strains currently classified as Polynucleobacternecessarius subsp. asymbioticus share ANI values with the endosymbiont in the Ammermann culture above or below the threshold for species demarcation. A significant correlation (R2 0.98, P<0.0001) between multilocus sequence similarity and ANI values of genome-sequenced strains enabled the prediction that it is highly unlikely that these four strains belong to the species P. necessarius. We propose reclassification of strains QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T), MWH-MoK4T (=DSM 21495T=CIP 110977T), MWH-JaK3T (=DSM 21493T=CIP 110976T) and MWH-HuW1T (=DSM 21492T=CIP 110978T) as Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., respectively.
Project description:Thirty-three Yersinia strains previously characterized by the French Yersinia National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7?%?and ANI values within each putative novel species were >97.5?%. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus Yersinia: Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp. nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).
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:Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the C. diphtheriae NCTC 11397T reference genome than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new C. diphtheriae subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: C. diphtheriae subsp. lausannense subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and C. diphtheriae subsp. diphtheriae subsp. nov, regrouping all other C. diphtheriae in the dataset (instead of lineage-1). Interestingly, members of subspecies lausannense displayed a larger genome size than subspecies diphtheriae and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks csn2 or cas4, which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.
Project description:The heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3(T), isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0-0.3?% (w/v). Whole-cell fatty acids were dominated by C(16?:?1)?7c (feature 3), C(18?:?1)?7c and straight-chain C(16?:?0); furthermore, the components C(12?:?0) and C(14?:?0) 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8?%. DNA-DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3(T) (?=?DSM 21994(T) ?=?CIP 110079(T)).