scholarly journals Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1140-1144 ◽  
Author(s):  
Yimin Cai ◽  
Huili Pang ◽  
Maki Kitahara ◽  
Moriya Ohkuma
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two strains of lactic acid bacteria, designated SU 18T and SU 83, were isolated from silage prepared with Sudan grass [Sorghum sudanense (Piper) Stapf.]. The isolates were Gram-stain-positive, catalase-negative, facultatively anaerobic rods that did not produce gas from glucose. The isolates exhibited ≥93.5 % DNA–DNA relatedness to each other and shared the same phenotypic characteristics, which indicated that they belonged to a single species. The DNA G+C content was 58.5–59.2 mol%. On the basis of 16S rRNA gene sequence analysis, the isolates were placed in the genus Lactobacillus . Their closest phylogenetic neighbours were Lactobacillus manihotivorans JCM 12514T and Lactobacillus camelliae JCM 13995T (95.9 and 96.8 % 16S rRNA gene sequence similarity, respectively, with strain SU 18T). Ribotyping revealed that strain SU 18T was well separated from L. manihotivorans JCM 12514T and L. camelliae JCM 13995T. Strain SU 18T exhibited ≤23.7 % DNA–DNA relatedness with its closest phylogenetic neighbours. The isolates represent a novel species in the genus Lactobacillus , for which the name Lactobacillus nasuensis sp. nov. is proposed. The type strain is SU 18T ( = JCM 17158T  = CGMCC 1.10801T). The description of the genus Lactobacillus is also amended.

Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1776-1781 ◽  
Author(s):  
Jian Zhang ◽  
Zi-Ting Wang ◽  
Hui-Min Yu ◽  
Yuchao Ma
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A bacterial strain, designated D75T, was isolated from the rhizosphere soil of Catalpa speciosa. Phylogenetic analysis based on the complete 16S rRNA gene sequence revealed that strain D75T was a member of the genus Paenibacillus . High levels of 16S rRNA gene sequence similarity were found between strain D75T and Paenibacillus glycanilyticus DS-1T (99.2 %), Paenibacillus xinjiangensis B538T (97.5 %) and Paenibacillus castaneae Ch-32T (97.2 %). The chemotaxonomic properties of strain D75T were consistent with those of the genus Paenibacillus : the cell-wall peptidoglycan type was based on meso-diaminopimelic acid (A1γ), the predominant menaquinone was MK-7, and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. However, levels of DNA–DNA relatedness between strain D75T and P. glycanilyticus NBRC 16618T, P. xinjiangensis DSM 16970T and P. castaneae DSM 19417T were 35, 20 and 18 %, respectively. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic data and DNA–DNA relatedness values, strain D75T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus catalpae sp. nov. is proposed. The type strain is D75T ( = DSM 24714T = CGMCC 1.10784T).

scholarly journals Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Ngoc-Lan Nguyen ◽  
Yeon-Ju Kim ◽  
Van-An Hoang ◽  
Bao-Tram Tran ◽  
Huong-Son Pham ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A novel bacterial strain, designated DCY94T, was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94T was closely related to Paracoccus sphaerophysae Zy-3T (97.5 % 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17T (96.9 %). The fatty acid profile of strain DCY94T contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4 %) and moderate to small quantities of C8 : 0 3-OH (1.0 %), C10 : 0 3-OH (2.8 %) and C18 : 0 (5.2 %). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94T within the genus Paracoccus . Levels of DNA–DNA relatedness between strain DCY94T and P. sphaerophysae HAMBI 3106T and P. caeni KCTC 22480T were 52 and 50 %, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA–DNA relatedness studies distinguished strain DCY94T from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94T ( = KCTC 42086T = JCM 30337T).

scholarly journals Streptomyces albiflavescens sp. nov., an actinomycete isolated from soil

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1467-1473 ◽  
Author(s):  
Xiufang Han ◽  
Jimei Zheng ◽  
Di Xin ◽  
Yuhua Xin ◽  
Xuexin Wei ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two actinobacterial strains, m20T and z8, were isolated from soil taken from rainforest areas/tropic forest region, Yunnan Province, south-west China. The 16S rRNA gene sequence similarities and DNA–DNA relatedness values between strains m20T and z8 were 100 and 88.2 %, respectively, which indicated that these two strains should be classified as the same species. The taxonomic position of the strains was determined by a polyphasic approach. Morphological and chemotaxonomic features of the strains were consistent with those of the genus Streptomyces . A phylogenetic tree based on 16S rRNA gene sequences showed that strains m20T and z8 formed an evolutionary branch within the genus Streptomyces and shared relatively high 16S rRNA gene sequence similarity values with other members of this genus, including ‘Streptomyces siamensis’ NBRC 108799 (98.95 %), Streptomyces graminilatus NBRC 108882T (98.25 %), Streptomyces seoulensis NBRC 16668T (98.11 %), Streptomyces peucetius ATCC 29050T (98.11 %) and Streptomyces hygroscopicus subsp. ossamyceticus ATCC 15420T (98.11 %). DNA–DNA relatedness values between strain m20T and the five above-mentioned strains were 56.3, 55.1, 52.8 , 50.1 and 48.4 %, respectively. On the basis of phenotypic, genotypic and phylogenetic properties, strains m20T and z8 could be distinguished from phylogenetically related members of the genus Streptomyces . The isolates thus merit species status within the genus Streptomyces , for which the name http://dx.doi.org/10.1601/nm.6817 Streptomyces albiflavescens sp. nov. is proposed. The type strain is m20T ( = CGMCC 4.7111T = KCTC 29196T). Strain z8 ( = CGMCC 4.7112 = KCTC 29197) is a reference strain.

Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2160-2162 ◽  
Author(s):  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
Somboon Tanasupawat ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Halobacterium Salinarum ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Halobacterium piscisalsi was proposed by Yachai et al. (2008), with a single strain, HPC1-2T ( = BCC 24372T  = JCM 14661T  = PCU 302T), which was isolated from fermented fish (pla-ra) in Thailand. According to Yachai et al. (2008), the strain was closely related to Halobacterium salinarum based on 16S rRNA gene sequence comparisons and could be differentiated by low DNA–DNA relatedness values and different biochemical profiles compared with other species of the genus. The reanalysis of the 16S rRNA gene sequences and the DNA–DNA relatedness among H. piscisalsi JCM 14661T and H. salinarum strains JCM 8978T, R1 and NRC-1 revealed that they all had exactly the same 16S rRNA gene sequence and shared more than 70 % DNA–DNA relatedness. In addition, the full-length DNA-dependent RNA polymerase subunit B (RpoB) protein sequence of H. piscisalsi JCM 14661T (607 amino acids) was the same as that of H. salinarum JCM 8978T and showed 94.7 and 96.7 % similarities with those of Halobacterium noricense JCM 15102T and Halobacterium jilantaiense JCM 13558T, respectively. Despite the different biochemical properties described by Yachai et al. (2008), the characteristic phenotypic properties of H. piscisalsi agreed with those in the description of H. salinarum emended by Gruber et al. (2004). Therefore, H. piscisalsi Yachai et al. (2008) should be regarded as a later heterotypic synonym of H. salinarum Elazari-Volcani 1957.

Oceanobacillus polygoni sp. nov., a facultatively alkaliphile isolated from indigo fermentation fluid

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3307-3312 ◽  
Author(s):  
Kikue Hirota ◽  
Yoshiko Hanaoka ◽  
Yoshinobu Nodasaka ◽  
Isao Yumoto
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SA9T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample prepared in a laboratory. The 16S rRNA gene sequence phylogeny suggested that strain SA9T was a member of the genus Oceanobacillus with the closest relative being Oceanobacillus profundus KCCM 42318T (99.3 % 16S rRNA gene sequence similarity). Cells of strain SA9T stained Gram-positive and were facultative anaerobic straight rods that were motile by peritrichous flagella. The strain grew between 5 and 48 °C (optimum, 35 °C) and at pH 7–12 (optimum, pH 9). The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 40.6±0.9 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. DNA–DNA hybridization with Oceanobacillus profundus DSM 18246T revealed a DNA–DNA relatedness value of 23±2 %. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from recognized species of the genus Oceanobacillus , strain SA9T merits classification as a representative of a novel species of the genus Oceanobacillus , for which the name Oceanobacillus polygoni sp. nov. is proposed. The type strain is SA9T ( = JCM 17252T = NCIMB 14684T). An emended description of the genus Oceanobacillus is also provided.

Lentisphaera marina sp. nov., and emended description of the genus Lentisphaera

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1540-1544 ◽  
Author(s):  
Ahyoung Choi ◽  
Seung-Jo Yang ◽  
Kwang-Hyun Rhee ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two Gram-stain-negative, non-motile, non-pigmented cocci, designated IMCC11369T and IMCC11389, were isolated from surface seawater of the East Sea of Korea by high-throughput cultivation based on dilution to extinction. Strains IMCC11369T and IMCC11389 shared 99.9 % 16S rRNA gene sequence similarity and >86.3 % DNA–DNA relatedness, which suggested that they belong to the same genomic species. The isolates were most closely related to Lentisphaera araneosa HTCC2155T (99.0 % 16S rRNA gene sequence similarity). Phylogenetic analysis revealed that the isolates formed a robust cluster with L. araneosa HTCC2155T. DNA–DNA relatedness values, however, showed that the isolates were distantly related to L. araneosa HTCC2155T (2.0–18.6 %), which suggested that they represent a separate genomic species in the genus Lentisphaera . The two isolates were phenotypically differentiated from their closest relative by several characteristics, including degradation of macromolecules and carbon source utilization. The DNA G+C content was 44.5–45.2 mol% and the predominant cellular fatty acids were C14 : 0, C16 : 1ω9c and C16 : 0. Strain IMCC11369T contained MK-7 as the respiratory quinone and phosphatidylethanolamine and an unknown lipid as the major polar lipids. On the basis of data obtained in this study, a novel species is proposed to accommodate the isolates, Lentisphaera marina sp. nov. The type strain is IMCC11369T ( = KCTC 23780T = NBRC 108776T).

scholarly journals Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2902-2906 ◽  
Author(s):  
Tomohiro Irisawa ◽  
Naoto Tanaka ◽  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains of lactic acid bacteria, Nu27T and Nu29, were isolated from Nukadoko, rice bran paste for Japanese pickles. The isolates were Gram-stain-positive, rod-shaped, catalase-negative, non-motile and facultatively anaerobic lactic acid bacteria. The isolates showed identical 16S rRNA gene sequences. The closest relatives to strain Nu27T based on 16S rRNA gene sequence similarities were Lactobacillus versmoldensis KU-3T (98.9 % 16S rRNA gene sequence similarity), Lactobacillus nodensis iz4bT (96.3 %) and Lactobacillus tucceti CECT 5290T (97.2 %). DNA–DNA relatedness values revealed genotype separation of the two isolates from the above three species. Based on the physiological, biochemical and genotypic characteristics provided, the isolates represent a novel species of the genus Lactobacillus , for which name is Lactobacillus furfuricola proposed. The type strain is Nu 27T ( = JCM 18764T = NRIC 0900T = DSM 27174T).

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

scholarly journals Pseudomonas piscis sp. nov., isolated from the profound head ulcers of farmed Murray cod (Maccullochella peelii peelii)

2020 ◽  
Vol 70 (4) ◽  
pp. 2732-2739 ◽  
Author(s):  
Yang Liu ◽  
Qiuhua Rao ◽  
Jochen Blom ◽  
Qiu Lin ◽  
Tuyan Luo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Murray Cod

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagella, designated as MC042T, was isolated from the profound head ulcers of farmed Murray cod sampled from Zhejiang Province, China. Analysis of its 16S rRNA gene sequence and multilocus sequence analysis phylogeny showed that strain MC042T belonged to the genus Pseudomonas , showing the highest 16S rRNA gene sequence similarity to Pseudomonas juntendi BML3T (98.9 %), and less than 98.8 % similarity to other Pseudomonas species with validly published names. Whole-genome sequencing and phylogenetic reconstruction based on a core set of 1563 Pseudomonas genes further indicated that strain MC042T was most closely related to the clade formed by Pseudomonas protegens CHA0T and Pseudomonas saponiphila DSM 975T and distantly related to any of the validly published species of the genus Pseudomonas . Furthermore, strain MC042T could be distinguished from its closely related species of the genus Pseudomonas by its ability to assimilate maltose, d-xylose and melibiose, but not d-mannitol. The principal fatty acids were C16 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinone was Q-9. Polar lipids of strain MC042T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified glycolipids, an unidentified lipid, an unknown glycolipid and aminolipid. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain MC042T is considered to represent a novel species, for which the name Pseudomonas piscis sp. nov. is proposed. The type strain is MC042T (=KCTC 72033T=MCCC 1K03575T).

scholarly journals Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1001-1008 ◽  
Author(s):  
Yuanyuan Tian ◽  
Chuanyu Han ◽  
Jiangmeihui Hu ◽  
Junwei Zhao ◽  
Chen Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain NEAU-TCZ24T, was isolated from soil and characterized using a polyphasic approach. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Cellulomonas and formed a stable clade with its closest relatives Cellulomonas terrae JCM 14899T (98.4 % 16S rRNA gene sequence similarity), Cellulomonas xylanilytica JCM 14281T (97.9 %) and Cellulomonas humilata JCM 11945T (97.7 %). The major menaquinones were identified as MK-9(H4) and MK-8(H4). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositolmannoside, a ninhydrin-positiveglycolipid, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15 : 0, C18 : 1ω9c, C16 : 0 and anteiso-C17 : 0. Moreover, morphological and chemotaxonomic properties of NEAU-TCZ24T also confirmed the affiliation of the isolate to the genus Cellulomonas . However, multilocus sequence analysis based on five other house-keeping genes (gyrB, rpoB, recA, relA and atpD), DNA–DNA relatedness, physiological and biochemical data indicated that NEAU-TCZ24T could be distinguished from its closest relatives. Therefore, it is proposed that NEAU-TCZ24T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas rhizosphaerae sp. nov. is proposed. The type strain is NEAU-TCZ24T (=CCTCC AA 2018042T=JCM 32383T).

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