scholarly journals Corynebacterium urogenitale sp. nov. isolated from the genital tract of a cow

2020 ◽  
Vol 70 (6) ◽  
pp. 3625-3632 ◽  
Author(s):  
Panagiotis Ballas ◽  
Christian Rückert ◽  
Karen Wagener ◽  
Marc Drillich ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Type Species ◽  
Functional Group ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Link Type ◽  
Lipids Profile

A Gram-stain-positive bacterial isolate, designated LMM-1652T, was isolated from an intrauterine cytobrush sample originating from a postpartum Holstein Friesian dairy cow. The strain had a rod to coccoid-shape, was catalase-positive and oxidase-negative. 16S rRNA gene sequence similarity analyses revealed that its closest relatives were Corynebacterium falsenii (97.05 % similarity), Corynebacterium jeikeium (96.83 %) and Corynebacterium urealyticum (96.82 %). Subsequent whole genome analysis showed that the genome-to-genome distance of strain LMM-1652T to its closest relatives was in the range of 23.2–24.8 %, while the average nucleotide identity values ranged from 73.7 to 74.3%, thus confirming that this isolate represents a novel species. Strain LMM-1652T was characterized by a quinone system mainly consisting of MK-9(H2) and MK-10(H2). The polar lipids profile of the strain consisted mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol-mannoside, as well as one unidentified lipid lacking any functional group. Smaller amounts of four unidentified phospholipids, four unidentified glycolipids, β-gentiobiosyl diacylglycerol and four unidentified lipids lacking a functional group were also found. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The fatty acid profile was mainly composed of C18 : 1 ω9c, C18 : 0 and C16 : 0. We propose a novel species of the genus Corynebacterium with the name Corynebacterium urogenitale LMM-1652T (=LMG 31163T=DSM 108747T).

scholarly journals Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring

2020 ◽  
Vol 70 (3) ◽  
pp. 1977-1981 ◽  
Author(s):  
Manik Prabhu Narsing Rao ◽  
Zhou-Yan Dong ◽  
Yu Kan ◽  
Lei Dong ◽  
Shuai Li ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Springs ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type

China is a hotspot for hot springs and during microbial diversity analysis of Tengchong hot spring, Yunnan province, south-west PR China, two strains designated SYSU G01001T and SY-13 were isolated. SYSU G01001T and SY-13 were Gram-stain-positive, motile and spore-forming. Colonies were white, circular, raised and punctiform. SYSU G01001T and SY-13 grew at pH 6.0–9.0 (optimum pH 8.0) and at 23–37 °C (optimum 28 °C). The 16S rRNA gene sequence similarity between SYSU G01001T and SY-13 was 99.6 % but these strains shared low sequence similarity with Paenibacillus azotifigens (97.5 %) indicating that they represented a novel species. On the basis of the results, SYSU G01001T was selected for further investigations and SY-13 was considered to represent a second strain of the species. The cell wall peptidoglycan of SYSU G01001T was meso-2,6-diaminopimelic acid and MK-7 was the only respiratory quinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified aminolipids (AL), two unidentified amino phospholipids (APL), an unidentified phospholipid (PL) and an unidentified polar lipid (L). The G+C content of the genomic DNA was 53.9 mol%. The average nucleotide identity (ANIb and ANIm) values between SYSU G01001T and Paenibacillus azotifigens LMG 29963T were below the cut-off level (95–96 %) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. On the basis of the above results strain SYSU G01001T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus tepidiphilus sp. nov. is proposed. The type strain is SYSU G01001T (=KCTC 33952T=CGMCC 1.13870T).

scholarly journals Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2693-2697 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Shan-Kun Tang ◽  
Srinivasan Krishnamurthi ◽  
V. Venkata Ramana ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterial strain, designated, NIO-1009T, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009T and other members of the genus Rhodococcus revealed that strain NIO-1009T had the closest sequence similarity to Rhodococcus kroppenstedtii DSM 44908T and Rhodococcus corynebacterioides DSM 20151T with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009T, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009T forms a stable clade with and R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T with 100 % bootstrap values. Strain NIO-1009T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C16 : 0, C18 : 1ω9c, C16 : 1(ω6c and/or ω7c) and 10-methyl C18 : 0. The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009T warrants recognition as a novel species of the genus Rhodococcus for which the name Rhodococcus enclensis sp. nov., is proposed; the type strain is NIO-1009T ( = NCIM 5452T = DSM 45688T).

scholarly journals Paenibacillus relictisesami sp. nov., isolated from sesame oil cake

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1534-1539 ◽  
Author(s):  
Takefumi Shimoyama ◽  
Nurziha Binti Johari ◽  
Atsuki Tsuruya ◽  
Arun Nair ◽  
Toru Nakayama
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Sesame Oil ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid

A facultatively anaerobic, Gram-stain-positive, rod-shaped bacterium, designated strain KB0549T, was isolated from sesame oil cake. Cells were motile, round-ended rods, and produced central or terminal spores. The cell wall peptidoglycan contained meso-diaminopimelic acid as the diamino acid. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain KB0549T was 51.9 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain KB0549T was affiliated with the genus Paenibacillus in the phylum Firmicutes and was most closely related to Paenibacillus cookii with 97.4 % sequence similarity. Strain KB0549T was physiologically differentiated from P. cookii by the high content of anteiso-C17 : 0, inability to grow at 50 °C, spore position, and negative Voges–Proskauer reaction. Based on these unique physiological and phylogenetic characteristics, it is proposed that the isolate represents a novel species, Paenibacillus relictisesami sp. nov.; the type strain is KB0549T ( = JCM 18068T = DSM 25385T).

Lactobacillus curieae sp. nov., isolated from stinky tofu brine

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2501-2505 ◽  
Author(s):  
Xiao Lei ◽  
Guipeng Sun ◽  
Jingli Xie ◽  
Dongzhi Wei
Keyword(s):  
Related Species ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genomic Markers ◽  
Physiological And Biochemical

A lactic acid bacterium, strain CCTCC M 2011381T, isolated from the brine of the traditional Chinese snack, stinky tofu, was studied to determine its taxonomic position. It was a Gram-stain-positive, non-motile, facultatively anaerobic rod-shaped bacterium that did not exhibit catalase activity. The DNA G+C content of the strain was 44.1 % and its peptidoglycan was characterized by the presence of meso-diaminopimelic acid. Levels of 16S rRNA gene sequence similarity between strain CCTCC M 2011381T and the most closely related species Lactobacillus senioris JCM 17472T, Lactobacillus parafarraginis JCM 14109T and Lactobacillus diolivorans JCM 12183T were 96.5, 96.4 and 96.4 %, respectively. Combined with data from high-resolution genomic markers recA, rpoA and pheS, strain CCTCC M 2011381T was classified as representing a novel species. The strain could also be distinguished from other related species of the genus Lactobacillus by its physiological and biochemical characteristics. Based on the phylogenetic, physiological and biochemical data, it is proposed that the new isolate can be classified as representing a novel species of the genus Lactobacillus , for which the name Lactobacillus curieae sp. nov. (type strain CCTCC M 2011381T = S1L19T = JCM 18524T) is proposed.

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

scholarly journals Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1370-1375 ◽  
Author(s):  
Isabel Snauwaert ◽  
Bart Hoste ◽  
Katrien De Bruyne ◽  
Karolien Peeters ◽  
Luc De Vuyst ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Littoral Zone ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642T, could be assigned to a novel species, with Carnobacterium funditum DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T  = CCUG 62000T).

scholarly journals Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov

2020 ◽  
Vol 70 (6) ◽  
pp. 3656-3664 ◽  
Author(s):  
Nao Ikeyama ◽  
Atsushi Toyoda ◽  
Sho Morohoshi ◽  
Tadao Kunihiro ◽  
Takumi Murakami ◽  
...  
Keyword(s):  
In Silico ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Faecal Samples

Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with ‘ Absiella argi ’ strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, ‘ A. argi ’ JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7–99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA–DNA hybridization (DDH) values among three strains were 88.4–90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5–24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for ‘ A. argi ’ strains identified because the name ‘ A. argi ’ has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).

scholarly journals Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).

Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 867-872 ◽  
Author(s):  
Herbert Seiler ◽  
Mareike Wenning ◽  
Verena Schmidt ◽  
Siegfried Scherer
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acid Type

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2T, Bacillus infantis SMC 4352-1T, Bacillus firmus NCIMB 9366T, Bacillus circulans ATCC 4513T and Bacillus horneckiae DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).

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