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).

Rhodococcus canchipurensis sp. nov., an actinomycete isolated from a limestone deposit site

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 114-118 ◽  
Author(s):  
Salam Nimaichand ◽  
Suchitra Sanasam ◽  
Liu-Qiang Zheng ◽  
Wen-Yong Zhu ◽  
Ling-Ling Yang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Sequence Similarities

A novel actinobacterial strain, MBRL 353T, was isolated from a sample collected from a limestone quarry at Hundung, Manipur, India. Comparison of 16S rRNA gene sequences of strain MBRL 353T and other members of the genus Rhodococcus showed sequence similarities ranging from 95.5 to 98.2 %, with strain MBRL 353T showing closest sequence similarity to Rhodococcus triatomae IMMIB RIV-085T (98.2 %) and Rhodococcus equi DSM 20307T (97.2 %). DNA–DNA hybridization results, however, revealed that DNA–DNA relatedness values between strain MBRL 353T and R. triatomae DSM 44892T (43.4 %) and R. equi DSM 20307T (33.4 %) were well below the 70 % limit for species identification. Strain MBRL 353T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose in the cell wall. Mycolic acids were present. The major fatty acids were C16 : 0 (45.7 %), C18 : 1ω9c (18.2 %) and 10-methyl C18 : 0 (11.3 %). The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 69.2 mol%. The phenotypic and genotypic data showed that strain MBRL 353T merits recognition as a representative of a novel species of the genus Rhodococcus for which the name Rhodococcus canchipurensis sp. nov. is proposed; the type strain is MBRL 353T ( = KCTC 19851T = JCM 17578T).

Spelaeicoccus albus gen. nov., sp. nov., an actinobacterium isolated from a natural cave

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3958-3963 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel Gram-stain-positive, non-endospore-forming, coccoid actinobacterium, designated strain D3-40T, was isolated from the soil of a natural cave and characterized by means of a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis showed that strain D3-40T is a member of the suborder Micrococcineae and forms a distinct branch at the base of a Brevibacteriaceae cluster. Its closest relative is the type strain of Brevibacterium samyangense (95.7 % sequence similarity). The chemotaxonomic characteristics were as follows: the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; the major menaquinone was MK-9(H2); the polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, an unknown glycolipid and an unknown phospholipid; the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and cyclohexyl-C17 : 0; mycolic acids were absent. The G+C content of the DNA was 64.3 mol%. On the basis of morphological, chemotaxonomic and phylogenetic data, it is suggested that the organism represents a novel species of a new genus within the family Brevibacteriaceae , for which the name Spelaeicoccus albus gen. nov., sp. nov. is proposed. The type strain of the type species is D3-40T ( = KCTC 29141T = DSM 26341T).

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).

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.

scholarly journals Microbacterium murale sp. nov., isolated from an indoor wall

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2669-2673 ◽  
Author(s):  
P. Kämpfer ◽  
J. Schäfer ◽  
N. Lodders ◽  
K. Martin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Diamino Acid ◽  
Unknown Phospholipid

A Gram-positive rod, designated 01-Gi-001T, was isolated from a wall colonized with moulds. The 16S rRNA gene sequence analysis clearly showed that the isolate belonged to the genus Microbacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain 01-Gi-001T was most closely related to Microbacterium hydrocarbonoxydans DSM 16089T (98.9 % sequence similarity), Microbacterium profundi Shh49T (98.7 %), Microbacterium phyllosphaerae DSM 13468T (98.3 %) and Microbacterium foliorum DSM 12966T (98.1 %). The diagnostic diamino acid of the peptidoglycan was ornithine. The major menaquinones detected were MK-13 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which were in agreement with those reported for other members of the genus Microbacterium . Physiological and biochemical characteristics and DNA–DNA relatedness between strain 01-Gi-001T and the type strains of its closest phylogenetic neighbours showed clear differences. For this reason, strain 01-Gi-001T ( = DSM 22178T = CCM 7640T) is proposed as the type strain of a novel species, Microbacterium murale sp. nov.

scholarly journals Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand

2020 ◽  
Vol 70 (10) ◽  
pp. 5296-5303 ◽  
Author(s):  
Kenika Lipun ◽  
Wee Fei Aaron Teo ◽  
Paweena Suksaard ◽  
Wasu Pathom-aree ◽  
Kannika Duangmal
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Whole Cell ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
Reference Strains

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).

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).

Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L.

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1037-1044 ◽  
Author(s):  
Bi He Kong ◽  
Qun Fang Liu ◽  
Min Liu ◽  
Yang Liu ◽  
Lei Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Typha Angustifolia ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
Unknown Phospholipid

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain xj7T, was isolated from roots of Typha angustifolia L. growing in Beijing Cuihu Wetland, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inference. The novel strain was spore-forming, motile, catalase-positive and oxidase-negative. Optimal growth of strain xj7T occurred at 28–30 °C and pH 7.0–7.5. Diphosphatidylglycerol was the most abundant polar lipid and occurred along with phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and three unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant isoprenoid quinone was MK-7. The major fatty acid components were anteiso-C15 : 0 (56.1 %), iso-C16 : 0 (9.1 %), C16 : 0 (8.0 %), iso-C14 : 0 (6.3 %) and iso-C15 : 0 (5.1 %). The G+C content of genomic DNA was 47.9 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain xj7T fell within the evolutionary radiation encompassed by the genus Paenibacillus , its closest neighbours were Paenibacillus borealis KK19T (97.5 %) and Paenibacillus durus DSM 1735T (97.1 %). However, the DNA–DNA relatedness values between strain xj7T and P. borealis KK19T and between strain xj7T and P. durus DSM 1735T, were both 35 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain xj7T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus typhae sp. nov. is proposed. The type strain is xj7T ( = CGMCC 1.11012T = DSM 25190T).

scholarly journals Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3010-3015 ◽  
Author(s):  
Avinash Sharma ◽  
Sunil Kumar Dhar ◽  
Om Prakash ◽  
Venkata Ramana Vemuluri ◽  
Vishal Thite ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Marine Sediment Sample

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111T that forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111T grew well on seawater agar at pH 6–10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Domibacillus robiginosus WS 4628T ( = DSM 25058T). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA–DNA relatedness to D. robiginosus DSM 25058T. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111T consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained meso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111T represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111T ( = MCC 2255T = DSM 28032T).

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).

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