scholarly journals Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae : characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prévot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2685-2690 ◽  
Author(s):  
Maria E. Hedberg ◽  
Edward R. B. Moore ◽  
Liselott Svensson-Stadler ◽  
Per Hörstedt ◽  
Vladimir Baranov ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T 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 H2S, NH3, 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 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T 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 : 22T ( = CCUG 58757T  = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T  = ATCC 33271T  = CIP 105341T  = DSM 3986T  = JCM 11021T  = VPI 11763T).

Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Yajun Ge ◽  
Bin Wang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Gui Zhang ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Major Fatty Acid ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family

Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051T and Pragia fontium DSM 5563T, while strain CF-1111T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273T and Pectobacterium punjabense SS95T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458T and CF-917) and group Ⅱ (CF-1111T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia . Summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c, 23.9 and 17.2 %, respectively), C16 : 0 (21.8 and 22.1 %, respectively) and C14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c, 12.3 %) was also a major fatty acid for strain CF-458T while cyclo-C17 : 0 (13.1%) was for strain CF-1111T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458T and CF-1111T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458T=CGMCC 1.16483T=GDMCC 1.1586T=JCM 33489T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111T=CGMCC 1.16786T=GDMCC 1.1587T=JCM 33490T), respectively.

Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2146-2154 ◽  
Author(s):  
Kathryn Bernard ◽  
Ana Luisa Pacheco ◽  
Ian Cunningham ◽  
Navdeep Gill ◽  
Tamara Burdz ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Single Test ◽  
Content Type ◽  
Link Type ◽  
Corynebacterium Pseudodiphtheriticum ◽  
Rrna Gene Sequencing

Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99 % sequence similarity) to Corynebacterium pseudodiphtheriticum . The two species are very similar biochemically, commonly differentiated by a single test, the detection of urease, where strains of C. propinquum are described as being urease-non-producing and strains of C. pseudodiphtheriticum are described as urease-producing. In this study, historical and contemporary strains of C. propinquum and C. pseudodiphtheriticum from this laboratory were definitively characterized, which included use of rpoB sequencing. Urease-producing strains of C. propinquum as well as typical urease-non-producing isolates were identified after rpoB sequencing, with six of these being originally identified as C. pseudodiphtheriticum . Based on these observations, we propose emendation of the description of C. propinquum to include strains which produce urease. MALDI-TOF analysis may be a useful tool to differentiate these taxa. Existing commercial databases should be updated to include urease-positive strains of C. propinquum .

scholarly journals Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1486-1490 ◽  
Author(s):  
Dominique Clermont ◽  
Laurence Motreff ◽  
Virginie Passet ◽  
José-Carlos Fernandez ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).

scholarly journals Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007

2020 ◽  
Vol 70 (12) ◽  
pp. 6313-6322
Author(s):  
Kathryn A. Bernard ◽  
Alicia Vachon ◽  
Ana Luisa Pacheco ◽  
Tamara Burdz ◽  
Deborah Wiebe ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cystic Fibrosis ◽  
Type Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73–98.29 % to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi . Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA–DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster. Pseudoxanthomonas spadix DSM 18855T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.

scholarly journals Arcanobacterium bovis sp. nov., isolated from the milk of a cow with mastitis

2020 ◽  
Vol 70 (7) ◽  
pp. 4105-4110 ◽  
Author(s):  
Osama Sammra ◽  
Geoffrey Foster ◽  
Abdulwahed Ahmed Hassan ◽  
Mazen Alssahen ◽  
Christoph Lämmler ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Wet Lab ◽  
Rrna Gene Sequencing

A polyphasic taxonomic study was performed on an unidentified Arcanobacterium -like Gram-stain-positive bacterium designated strain C605018/01/1T isolated from a milk sample collected from the udder of a cow at post mortem. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strain of Arcanobacterium pluranimalium (99.76 %); sequence similarities to all other Arcanobacterium species were below 97 %. The wet-lab DNA–DNA hybridization values among strain C605018/01/1T and A. pluranimalium DSM 13483ᵀ were low, 16.9 % (reciprocal, 49.8 %). Pertaining to the whole genome sequence with a total length of 2.02 Mb and 1654 protein counts, the novel strain C605018/01/01T displayed a G+C content of 51.6 % mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium . The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside and unidentified glycolipid and aminophospholipids. Based on these results it is proposed that strain C605018/01/1T should be classified as representing a novel species, Arcanbacterium bovis sp. nov. The type strain C605018/01/1T (CCUG 45425T=DSM 107286T=BCCM/LMG 30783T)

scholarly journals Mucilaginibacter gotjawali sp. nov., isolated from soil of a lava forest

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 952-958 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Mi Kyung Eom ◽  
Jong-Shik Kim ◽  
Dae-Shin Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A novel bacterial strain, designated SA3-7T, was isolated from soil of a lava forest located in Jeju, Republic of Korea. Cells of strain SA3-7T were Gram-stain-negative, oxidase- and catalase-positive, non-motile rods and produced creamy white colonies on ten-fold-diluted R2A agar. The isolate contained menaquinone-7 (MK-7) as the predominant isoprenoid quinone and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain SA3-7T was related most closely to Mucilaginibacter frigoritolerans FT22T (96.7 % sequence similarity) and that it formed a separate lineage in the genus Mucilaginibacter . Combined phenotypic, chemotaxonomic and phylogenetic characteristics supported the conclusion that strain SA3-7T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter gotjawali sp. nov. is proposed; the type strain is SA3-7T ( = KCTC 32515T = CECT 8628T = DSM 29289T).

scholarly journals Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017

2020 ◽  
Vol 70 (5) ◽  
pp. 3534-3540 ◽  
Author(s):  
K. A. Bernard ◽  
A. L. Pacheco ◽  
T. Burdz ◽  
D. Wiebe ◽  
Anne-Marie Bernier
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Rrna Gene Sequencing

Seven strains of an unidentifiable Corynebacterium species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from Corynebacterium imitans by 16S rRNA gene and partial rpoB gene sequencing, were studied. In November 2017, Atasayar et al. described a blood culture isolate as Corynebacterium gottingense sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani et al. described Corynebacterium godavarianum sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/rpoB sequencing to the Canadian strains and C. gottingense. In May 2018, Wei et al. described Corynebacterium hadale recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to C. gottingense , C. godavarianum and the Canadian strains. C. gottingense DSM 103494T and C. godavarianum LMG 29598T were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from C. hadale (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA–DNAhybridization, average nucleotide identity using blastn and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that C. godavarianum and C. hadale are later heterotypic synonyms of, and the Canadian isolates are identifiable as, C. gottingense . We provide an emended description of Corynebacterium gottingense Atasayar et al. 2017; genomes ranged from 2.48 to 2.69 Mb ( C. gottingense DSM 103494T, 2.62 Mb) with G+C content of 65.1–65.6 mol% (WGS), recovered from clinical and environmental sites.

scholarly journals Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1457-1464 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Lorinda van der Westhuizen ◽  
Stephanus N. Venter ◽  
Teresa A. Coutinho ◽  
...  
Keyword(s):  
South Africa ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa , Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.

scholarly journals Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member

2019 ◽  
Vol 69 (4) ◽  
pp. 1142-1148 ◽  
Author(s):  
Nisha B. Patel ◽  
Alexandra J. Obregón-Tito ◽  
Raul Y. Tito ◽  
Omar Trujillo-Villaroel ◽  
Luis Marin-Reyes ◽  
...  
Keyword(s):  
Fecal Sample ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
The Family ◽  
Diamino Acid ◽  
Rrna Gene Sequencing

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella , Finegoldia , Gallicola and Parvimonas . The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).

Imtechella halotolerans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from estuarine water

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2624-2630 ◽  
Author(s):  
Vikram Surendra ◽  
Pant Bhawana ◽  
Korpole Suresh ◽  
T. N. R. Srinivas ◽  
Pinnaka Anil Kumar
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Estuarine Water ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Pairwise Sequence Similarity

A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia , Coenonia and Capnocytophaga , being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).

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