scholarly journals Sporolactobacillus shoreae sp. nov. and Sporolactobacillus spathodeae sp. nov., two spore-forming lactic acid bacteria isolated from tree barks in Thailand

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1220-1226 ◽  
Author(s):  
Tanatip Thamacharoensuk ◽  
Maki Kitahara ◽  
Moriya Ohkuma ◽  
Nuttha Thongchul ◽  
Somboon Tanasupawat

Two Gram-stain-positive, endospore-forming lactic acid bacteria, designated BK92T and BK117-1T, were isolated from tree barks in Thailand. Cells were catalase-negative and facultatively anaerobic rods. 16S rRNA gene sequence analysis indicated that these strains belonged to the genus Sporolactobacillus . Strains BK92T and BK117-1T showed the highest 16S rRNA gene sequence similarity to Sporolactobacillus putidus QC81-06T with 97.7 % and 97.1 % similarity, respectively. Analysis of phylogenetic relationships based on 16S rRNA and gyrB gene sequencing revealed that the positions of strains BK92T and BK117-1T were clearly separated from all related species of the genus Sporolactobacillus . Strains BK92T and BK117-1T had low DNA–DNA relatedness between each other and also with S. putidus QC81-06T and Sporolactobacillus vineae SL153T. The DNA G+C content of strains BK92T and BK117-1T was 46.6 mol% and 47.4 mol%, respectively. The major fatty acids of strains BK92T and BK117-1T were anteiso-C17 : 0 and anteiso-C15 : 0. They contained meso-diaminopimelic acid in cell-wall peptidoglycan and had menaquinone with seven isoprene units (MK-7) as the predominant menaquinone. Based on evidence including phenotypic, genotypic and chemotaxonomic studies, strains BK92T and BK117-1T should be classified as representatives of novel species of the genus Sporolactobacillus , for which the names Sporolactobacillus shoreae sp. nov. and Sporolactobacillus spathodeae sp. nov. are proposed, respectively. The type strains are BK92T ( = JCM 19541T = LMG 28365T = PCU 336T = TISTR 2234T) and BK117-1T ( = JCM 19542T = LMG 28366T = PCU 337T = TISTR 2235T).

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2902-2906 ◽  
Author(s):  
Tomohiro Irisawa ◽  
Naoto Tanaka ◽  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
...  

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).


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1140-1144 ◽  
Author(s):  
Yimin Cai ◽  
Huili Pang ◽  
Maki Kitahara ◽  
Moriya Ohkuma

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.


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  

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.


Author(s):  
Yuxin Chen ◽  
Arisa Nishihara ◽  
Takao Iino ◽  
Moriya Ohkuma ◽  
Shin Haruta

A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31–91.10 %), average amino acid identity (91.45–92.10 %) and <70 % digital DNA–DNA hybridization value (41.8–44.2 %) with the three related species of the genus Caldicellulosiruptor . Strain YA01T grew at 50–78 °C (optimum, 70 °C) and at pH 5.0–9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2732-2739 ◽  
Author(s):  
Yang Liu ◽  
Qiuhua Rao ◽  
Jochen Blom ◽  
Qiu Lin ◽  
Tuyan Luo

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).


2019 ◽  
Vol 69 (4) ◽  
pp. 1001-1008 ◽  
Author(s):  
Yuanyuan Tian ◽  
Chuanyu Han ◽  
Jiangmeihui Hu ◽  
Junwei Zhao ◽  
Chen Zhang ◽  
...  

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).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 303-308 ◽  
Author(s):  
Laurent Urios ◽  
Laurent Intertaglia ◽  
Michel Magot

A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10T within the genus Pedobacter , family Sphingobacteriaceae . Pedobacter composti TR6-06T and Pedobacter oryzae DSM 19973T were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10T represents a novel species of the genus Pedobacter , for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10T ( = DSM 23085T = CIP 110085T = MOLA 820T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1017-1023 ◽  
Author(s):  
Hong Chen ◽  
Mareike Jogler ◽  
Brian J. Tindall ◽  
Hans-Peter Klenk ◽  
Manfred Rohde ◽  
...  

A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382T were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6–9 (optimum, pH 7) and temperatures of 10–37 °C (optimum, 28 °C). The genomic G+C content of strain 382T was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382T belongs to the family Sphingomonadaceae and clusters within the genus Sphingomonas . Sphingomonas histidinilytica UM 2T and Sphingomonas wittichii DSM 6014T were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively). Sphingomonas paucimobilis DSM 1098T (the type species of the genus Sphingomonas ) exhibited 95.3 % sequence similarity. This affiliation of strain 382T to the genus Sphingomonas is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382T were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus Sphingomonas and its unusually high C16 : 1ω7c content, strain 382T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas starnbergensis is proposed. The type strain is 382T ( = DSM 25077T  = LMG 26763T).


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.


Author(s):  
Ji Young Choi ◽  
Seung-Hyeon Choi ◽  
Jam-Eon Park ◽  
Ji-Sun Kim ◽  
Jiyoung Lee ◽  
...  

An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces of a 2-week-old piglet raised at the National Institute of Animal Science in Wanju, Republic of Korea. Growth of strain AGMB03916T occurred at 30–45 °C (optimum, 37 °C), at pH 6–9 (optimum, pH 8) and in the presence of 0.5–1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence analyses, strain AGMB03916T was closely related to two validly published species of the genus Phocaeicola , Phocaeicola plebeius and Phocaeicola coprocola . The 16S rRNA gene sequence similarity of strain AGMB03916T compared to P. plebeius M12T (=KCTC 5793T) and P. coprocola M16T (=KCTC 5443T) were 96.3 and 95.0 %, respectively. The genomic DNA G+C content of strain AGMB03916T was 46.4 mol%. The average nucleotide identity values between strain AGMB03916T and the reference strains were 74.9–78.5 %. Cells were able to utilize d-glucose, lactose, sucrose, maltose, salicin, aesculin hydrolysis, cellobiose and raffinose. The major end product of metabolism was acetate. The major cellular fatty acids (>10 %) of the isolate were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, C16 : 0 3-OH and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA). On the basis of the genotypic, biochemical, chemotaxonomic, phenotypic and phylogenetic data, strain AGMB03916T represents a novel species of the genus Phocaeicola , for which the name Phocaeicola faecicola sp. nov. is proposed. The type strain is AGMB03916T (=KCTC 25014T=GDMCC 1.2574T).


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