scholarly journals Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1092-1097 ◽  
Author(s):  
Herbert Seiler ◽  
Verena Schmidt ◽  
Mareike Wenning ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Food Sources ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

Three Gram-staining-positive, strictly aerobic, motile, catalase-positive, endospore-forming rods, designated WCC 4582T, WCC 4581 and WCC 4583, were isolated from two different food sources and a pharmaceuticals production site. The three isolates were highly similar in their 16S rRNA gene sequences (100 % similarity) and groEL sequences (99.2–100 % similarity), Fourier-transform infrared spectroscopic fingerprints and other features tested. The isolates were most closely related to Bacillus horneckiae ; the isolates and the type strain of B. horneckiae shared 97.6 % and 89.6 % 16S rRNA gene and groEL sequence similarities, respectively. The organisms grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. The cell-wall peptidoglycan of WCC 4582T contained meso-diaminopimelic acid (A1γ) and the genomic DNA G+C content was 36.4 mol%. DNA–DNA relatedness between strain WCC 4582T and B. horneckiae NRRL B-59162T was 17 %. The three isolates are considered to represent a novel species of the genus Bacillus , for which the name Bacillus kochii sp. nov. is proposed. The type strain is WCC 4582T ( = DSM 23667T = CCUG 59877T = LMG 25855T).

scholarly journals Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2437-2441 ◽  
Author(s):  
Xiao-Xue Han ◽  
Xiao-Xia Luo ◽  
Li-Li Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipid ◽  
Type Strain ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Lipid Pattern

Two actinomycete strains, designated TRM 49117T and TRM 49136T, were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117T had 93.93 % similarity with the type strain Glycomyces halotolerans TRM 40137T (GenBank accession no. HQ651156) and TRM 49136T had 94.32 % similarity with G. halotolerans TRM 40137T. The 16S rRNA gene sequence similarity between the two new isolates was 93 %. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136T also contained arabinose. The polar lipid pattern of strain TRM 49117T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136T comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117T and TRM 49136T represent two novel species, clearly different from related species of the genus Glycomyces , for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117T = CCTCC AA 2013003T = NRRL B-59998T = KACC 17682T) and Glycomyces albus sp. nov. (type strain TRM 49136T = CCTCC AA 2013004T = NRRL B-24927T = KACC 17681T) are proposed.

scholarly journals Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2047-2052 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Fen-Fen Gong ◽  
Xiang Wang ◽  
Gang Hu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

The taxonomic status of a carbendazim-degrading strain, mbc-2T, isolated from soil under the long-term application of carbendazim in China was determined by means of a polyphasic study. The cells were Gram-stain-positive, motile and rod-shaped. Strain mbc-2T grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain mbc-2T fell within the genus Nocardioides , forming a coherent cluster with the type strain of Nocardioides hankookensis , with which it exhibited 16S rRNA gene sequence similarity values of 97.9 %. The chemotaxonomic properties of strain mbc-2T were consistent with those of the genus Nocardioides : the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8 (H4) and the major fatty acid was iso-C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unknown phospholipids and an unknown aminolipid. The DNA G+C content was 72 mol%. Strain mbc-2T exhibited DNA–DNA relatedness values of 12.5±1.5 %, 23.7±2.7 % and 26.3±3.2 % with respect to Nocardioides hankookensis DS-30T, Nocardioides aquiterrae GW-9T and Nocardioides pyridinolyticus OS4T. On the basis of the data obtained, strain mbc-2T represents a novel species of the genus Nocardioides , for which the name Nocardioides soli sp. nov. is proposed. The type strain is mbc-2T ( = KACC 17152T = CCTCC AB 2012934T).

scholarly journals Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2703-2709 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Giho Park ◽  
Hyejin Yang ◽  
Supyong Hwang ◽  
Yoonjung Bae ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sewage Disposal ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32T) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32T. Strain MJ32T showed highest 16S rRNA gene sequence similarity to Gordonia hirsuta DSM 44140T (98.1 %) and Gordonia hydrophobica DSM 44015T (97.0 %); levels of sequence similarity to the type strains of other recognized Gordonia species were less than 97.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32T belonged to the clade formed by members of the genus Gordonia in the family Gordoniaceae . The G+C content of the genomic DNA of strain MJ32T was 69.2 mol%. Chemotaxonomically, strain MJ32T showed features typical of the genus Gordonia . The predominant respiratory quinone was MK-9(H2), the mycolic acids present had C56–C60 carbon atoms, and the major fatty acids were C16 : 0 (34.6 %), tuberculostearic acid (21.8 %), C16 : 1ω7c (19.5 %) and C18 : 1ω9c (12.7 %). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32T is considered to represent a novel species of the genus Gordonia , for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32T ( = KCTC 19771T = JCM 16923T).

scholarly journals Rhodococcus cavernicola sp. nov., isolated from a cave, and Rhodococcus degradans is a later heterosynonym of Rhodococcus qingshengii

2020 ◽  
Vol 70 (7) ◽  
pp. 4409-4415 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Young-Ju Kim ◽  
Yochan Joung
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Developmental Cycle ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Link Type

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24T, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus Rhodococcus and formed a distinct sublineage at the base of the radiation including a Rhodococcus enclensis–Rhodococcus kroppenstedtii–Rhodococcus corynebacterioides–Rhodococcus trifoli cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to Rhodococcus corynebacterioides . The closest relatives were Rhodococcus qingshengii (98.01 % 16S rRNA gene sequence similarity) and Rhodococcus degradans (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1  ω9c, C16 : 1  ω7c and/or C16 : 1  ω6c and 10-methyl C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24T (=KACC 19964T=DSM 109484T) represents a new species of the genus Rhodococcus , for which Rhodococcus cavernicola sp. nov. is proposed. Also, it is proposed that R. degradans is a later heterosynonym of R. qingshengii based on analyses of 16S rRNA gene and whole-genome sequences.

scholarly journals Paenibacillus apii sp. nov., a novel nifH gene-harbouring species isolated from the rhizospheres of vegetable plants grown in different regions of northern China

2020 ◽  
Vol 70 (10) ◽  
pp. 5531-5538 ◽  
Author(s):  
Shuai Tong ◽  
Li-wei Wang ◽  
Yu-chen Sun ◽  
Mohammad Sayyar Khan ◽  
Jun-lian Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Nifh Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Separate Branch

Two nifH gene-harbouring bacterial strains were isolated from rhizospheres of different vegetable plants grown in different regions of northern PR China. The two strains possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.21 and 93.6% respectively, suggesting they belong to one species. Based on 16S rRNA gene phylogeny, the two strains were clustered together with Paenibacillus rhizophilus 7197T, Paenibacillus sabinae T27T and Paenibacillus forsythiae T98T, but on a separate branch. Novelty of the species was confirmed by ANI and dDDH comparisons between the type strain 7124T and its closest relatives, since the obtained values were considerably below the proposed thresholds for the species delineation. The genome size of strain 7124T was 5.40 Mb, comprising 5050 predicted genes with a DNA G+C content of 52.3 mol%. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The major cellular fatty acids were anteiso-C15  :  0 (52.9%) and C16  :  0 (23.4 %). Menaquinone-7 was reported as the major respiratory quinone. The diamino acid in the cell-wall peptidoglycan was found to be meso-diaminopimelic acid. Based on phylogenetic, genomic, chemotaxonomic and phenotypic data, the two isolates are considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus apii sp. nov. is proposed, with 7124T (=DSM 103172T=CGMCC 1.15689T) as type strain.

scholarly journals Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2217-2222 ◽  
Author(s):  
Xiaoyang Fan ◽  
Yanlu Qiao ◽  
Xin Gao ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Seafloor Sediment

A Gram-stain-positive, strictly aerobic, rod-shaped, non-motile bacterium, designated strain XH274T, was isolated from a deep sub-seafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH274T belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides kribbensis KSL-2T (96.81 %), Nocardioides daedukensis MDN22T (96.74 %) and Nocardioides psychrotolerans RHLT2-1T (96.61 %). The DNA G+C content of strain XH274T was 74.6 mol%. The cell wall of strain XH274T contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose, galactose and mannose as the major whole-cell sugars. The major fatty acids were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. The major respiratory quinone was menaquinone-8(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. On the basis of data from the polyphasic analysis, strain XH274T is considered to represent a novel species in the genus Nocardioides , for which the name Nocardioides pacificus sp. nov. is proposed. The type strain is XH274T ( = DSM 27278T = JCM 19260T).

scholarly journals Bacillus salinus sp. nov., isolated from commercial solar salt

2020 ◽  
Vol 70 (4) ◽  
pp. 2696-2702 ◽  
Author(s):  
Heeyoung Kang ◽  
Jinkyeong Kang ◽  
Inseong Cha ◽  
Haneul Kim ◽  
Yochan Joung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

Two strains of Gram-stain-positive, strictly aerobic, motile, spore-forming, rod-shaped, moderately halotolerant bacteria, designated as HMF5848T and HME7618, were isolated from salt/brine and subjected to a polyphasic taxonomic investigation. Growth of both yellow-coloured strains occurred in the presence of 1–9 % NaCl (w/v; optimum, 2–3 %), at 15–45 °C (optimum, 37 °C) and pH 6–9 (optimum, pH 7). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The cell-wall peptidoglycan was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, four unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. DNA G+C content was 37.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strains HMF5848T and HME7618 clustered with Bacillus luteolus YIM 93174T. Strains HMF5848T showed the highest 16S rRNA gene sequence similarities to Bacillus humi LMG 22167T (96.1 %), Bacillus isabeliae CVS-8T (96.0 %) and Bacillus luteolus YIM 93174T (96.0 %). The values of in silico DNA–DNA hybridization and average nucleotide identity between strains HMF5848T and B. humi DSM 16318T were 25.8 and 69.7 %, respectively. On the basis of phylogenetic, physiological and chemotaxonomic properties, strain HMF5848T represents a novel species, Bacillus salinus sp. nov. The type strain is HMF5848T (=KCTC 43010T=CECT 9695T).

Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Hai-Tao Wang ◽  
Lian Xu ◽  
Ji-Quan Sun
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Indole Acetic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–14.0 % NaCl (optimum, 5.0–8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain HU2P27T with A. koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

scholarly journals Bacillus iranensis sp. nov., a moderate halophile from a hypersaline lake

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 811-816 ◽  
Author(s):  
M. Bagheri ◽  
M. Didari ◽  
M. A. Amoozegar ◽  
P. Schumann ◽  
C. Sánchez-Porro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Moderate Halophile ◽  
Content Type ◽  
Link Type

A Gram-positive, moderately halophilic rod, designated X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a central-subterminal position in non-swollen sporangia. The isolate grew at pH 7.0–10.0 (optimum pH 7.5), at 25–45 °C (optimum 35 °C) and with 2.5–15 % (w/v) NaCl (optimum 5–7.5 %). On the basis of 16S rRNA gene sequences, strain X5BT belonged to the genus Bacillus and showed highest similarity with Bacillus persepolensis HS136T (95.6 % 16S rRNA gene sequence similarity) and Bacillus salarius BH169T (95.5 %). The DNA G+C content was 42.4 mol%. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and two glycolipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the isoprenoid quinones were MK-7 (92 %), MK-6 (6 %) and MK-5 (2 %). On the basis of phylogenetic, chemotaxonomic and phenotypic data, a novel species of the genus Bacillus is proposed, with the name Bacillus iranensis sp. nov. The type strain is X5BT ( = IBRC 10446T  = DSM 23995T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

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