Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Acinetobacter geminorum sp. nov., isolated from human throat swabs.

ABSTRACT: Two isolates of a non-fermenting, Gram-negative bacterial strain were cultured from two throat swabs that were taken from a pair of twins during routine microbiological surveillance screening. As these isolates could not be unambiguously identified using routine diagnostic methods, whole genome sequencing was performed followed by phylogenetic analysis based on the rpoB gene sequence and by whole genome datasets. The two strains compose a separate branch within the clade formed by the Acinetobacter calcoaceticus-baumannii (ACB) complex with Acinetobacter pittii CIP 70.29^T as the most closely related species. The average nucleotide identity compared to all other species of the ACB complex was below 94.2% and digital DNA-DNA hybridization values were less than 60%. Biochemical characteristics confirm affiliation to the ACB complex with some specific phenotypic differences. As a result of the described data, a new Acinetobacter species is introduced, for which the name Acinetobacter geminorum sp. nov. is proposed. The type strain is J00019^T with a G+C DNA content of 38.8 mol% and it is deposited in the DSMZ Germany (DSM 111094^T) and CCUG Sweden (CCUG 74625^T).

SUBMITTER: Wolf S

PROVIDER: S-EPMC8604166 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Description of Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., three new bacteria isolated from human blood.

Project description:Blood is precious tissue that is normally sterile. With the aim of diagnosing the cause of bacteremia, three bacterial strains were isolated from three different individuals. Strains Marseille-P7157T and Marseille-Q2854T are Gram-stain positive, non-spore-forming rod-shaped bacteria, while strain Marseille-P8049T is a Gram-stain negative, motile, non-spore-forming and rod-shaped bacterium. The major fatty acids found (>30%) were hexadecanoic acid for strain Marseille-P8049T and 12-methyl tetradecanoic acid for both strains Marseille-P7157T and Marseille-P2854T. The 16S rRNA gene sequence analysis shows that strains Marseille-P8049 and Marseille-Q2854T have sequence similarity of 96.8%, 99.04%, and 98.3% with Acinetobacter ursingii strain LUH3792 (NR_025392.1), Gulosibacter faecalis strain B187 (NR_041812.1), and Schaalia canis strain CCUG 41706 (NR_025366.1), respectively. In addition, strains Marseille-Q2854T, Marseille-P8049T and Marseille-P7157T shared with their closely related species cited above the following DDH values: 19.5%, 24.4%, and 20.2%, respectively. Based on these phenotypic and genomic findings, we consider that strains Marseille-P8049T (= CSUR P8049 = CECT 30350), Marseille-P2854T ( = CSUR Q2854 = CECT 30120) and Marseille-P7157T ( = CSUR P7157 = CECT 30048) are new bacterial species, for which the names Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., are proposed.

| S-EPMC9126734 | biostudies-literature

Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples.

Project description:Nine independent Gram-negative bacterial strains were isolated from rectal swabs or stool samples of immunocompromised patients from two different wards of a university hospital. All isolates were phylogenetically analysed based on their 16S rRNA gene sequence, housekeeping gene recN, multilocus sequence analysis of concatenated partial fusA, leuS, pyrG and rpoB sequences, and by whole genome sequencing data. The analysed strains of the new species cluster together and form a separate branch with Citrobacter werkmanii NBRC105721T as the most closely related species. An average nucleotide identity value of 95.9-96% and computation of digital DNA-DNA hybridization values separate the new species from all other type strains of the genus Citrobacter. Biochemical characteristics further delimit the isolates from closely related Citrobacter type strains. As a result of the described data, a new Citrobacter species is introduced, for which the name Citrobacter cronae sp. nov. is proposed. The type strain is Tue2-1T with a G+C DNA content of 52.2 mol%.

| S-EPMC7395625 | biostudies-literature

'Rothia nasisuis' sp. nov., 'Dermabacter porcinasus' sp. nov., 'Propionibacterium westphaliense' sp. nov. and 'Tessaracoccus nasisuum' sp. nov., isolated from porcine nasal swabs in the Munster region, Germany.

Project description:We report the core features of 'Rothia nasisuis' strain 1a5R-CH16 sp. nov., 'Dermabacter porcinasus' strain 2a1I-BL09 sp. nov., 'Propionibacterium westphaliense' strain 1a7I-CH12an sp. nov. and 'Tessaracoccus nasisuum' strain 1a6R-CH11an sp. nov. In 2016, these isolates were cultured from porcine nasal swabs taken from healthy pigs from farms in the region around Münster, Germany.

| S-EPMC6197708 | biostudies-literature

Acinetobacter pullorum sp. nov., Isolated from Chicken Meat.

Project description:A bacterial strain, designated B301T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30°C, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603T and A. sichuanensis WCHAc060041T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:0, and C18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301T (=KACC 21653T = JCM 33942T).

| S-EPMC9728200 | biostudies-literature

Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women.

Project description:Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.

| S-EPMC6656688 | biostudies-literature

'Acidaminococcus timonensis' sp. nov. and 'Acidaminococcus massiliensis' sp. nov. isolated from human gut.

Project description:We report here the main characteristics of 'Acidaminococcus timonensis' strain Marseille-P2764T, isolated from human right colon, and 'Acidaminococcus massiliensis' strain Marseille-P2828T, isolated from human duodenum.

| S-EPMC5175988 | biostudies-literature

'Merdibacter massiliensis' gen. nov., sp. nov., isolated from human ileum.

Project description:We report here the main characteristics of 'Merdibacter massiliensis' strain Marseille-P3254T (= CSUR P3254 = DSM 103475), which was isolated from human ileum.

| S-EPMC5192474 | biostudies-literature

"Ihuprevotella massiliensis" gen. nov., sp. nov., isolated from human gut.

Project description:We report here the main characteristics of "Ihuprevotella massiliensis" strain Marseille-P2826(T) (CSURP 2826) that was isolated from a human right colon lavage sample.

| S-EPMC5008045 | biostudies-literature

Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. isolated from human clinical infections.

Project description:One hundred eight isolates were previously identified in our laboratory as Clostridium clostridioforme by colonial and cellular morphology, as well as biochemical tests. Recent studies have indicated that there are actually three different species in this C. clostridioforme group: C. hathewayi, C. bolteae, and C. clostridioforme. Our isolates were reexamined using biochemical and enzymatic tests and molecular methods. Forty-six isolates were reidentified as C. hathewayi, 34 as C. bolteae, five as C. clostridioforme, and one as C. symbiosum. Twenty-two strains were identified only to the genus level by 16S rRNA gene sequencing, and although they are microscopically and morphologically indistinguishable from the above-mentioned three species, they are phenotypically different and only 96 to 98% similar by gene sequencing. Twenty of these 22 strains were indole positive and formed two novel species. We propose Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. as names for these new species. They are differentiated from each other by results for raffinose, rhamnose, alpha-galactosidase, and beta-galactosidase: positive, negative, positive, and positive, respectively, for the former species and negative, positive, negative, and negative, respectively, for the latter species. The type strain of C. aldenense is RMA 9741 (ATCC BAA-1318; CCUG 52204), and the type strain of C. citroniae is RMA 16102 (ATCC BAA-1317; CCUG 52203).

| S-EPMC1489485 | biostudies-literature

Enterococcus gilvus sp. nov. and Enterococcus pallens sp. nov. isolated from human clinical specimens.

Project description:Light yellow-pigmented (strain PQ1) and yellow-pigmented (strain PQ2), gram-positive, non-spore-forming, nonmotile bacteria consisting of pairs or chains of cocci were isolated from the bile of a patient with cholecystitis (PQ1) and the peritoneal dialysate of another patient with peritonitis (PQ2). Morphologically and biochemically, the organisms phenotypically belonged to the genus Eterococcus. Whole-cell protein (WCP) analysis and sequence analysis of a segment of the 16S rRNA gene suggested that they are new species within the genus Enterococcus. PQ1 and PQ2 displayed less than 70% identities to other enterococcal species by WCP analysis. Sequence analysis showed that PQ1 shared the highest level of sequence similarity with Enterococcus raffinosus and E. malodoratus (sequence similarities of 99.8% to these two species). Sequence analysis of PQ2 showed that it had the highest degrees of sequence identity with the group I enterococci E. malodoratus (98.7%), E. raffinosus (98.6%), E. avium (98.6%), and E. pseudoavium (98.6%). PQ1 and PQ2 can be differentiated from the other Enterococcus spp. in groups II, III, IV, and V by their phenotypic characteristics: PQ1 and PQ2 produce acid from mannitol and sorbose and do not hydrolyze arginine, placing them in group I. The yellow pigmentation differentiates these strains from the other group I enterococci. PQ1 and PQ2 can be differentiated from each other since PQ1 does not produce acid from arabinose, whereas PQ2 does. Also, PQ1 is Enterococcus Accuprobe assay positive and pyrrolidonyl-beta-naphthylamide hydrolysis positive, whereas PQ2 is negative by these assays. The name Enterococcus gilvus sp. nov. is proposed for strain PQ1, and the name Enterococcus pallens sp. nov. is proposed for strain PQ2. Type strains have been deposited in culture collections as E. gilvus ATCC BAA-350 (CCUG 45553) and E. pallens ATCC BAA-351 (CCUG 45554).

| S-EPMC140378 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data