scholarly journals Characterization a Novel Butyric Acid-Producing Bacterium Collinsella aerofaciens Subsp. Shenzhenensis Subsp. Nov.

2019 ◽  
Vol 7 (3) ◽  
pp. 78 ◽  
Author(s):  
Panpan Qin ◽  
Yuanqiang Zou ◽  
Ying Dai ◽  
Guangwen Luo ◽  
Xiaowei Zhang ◽  
...  
Keyword(s):  
Butyric Acid ◽  
Dna Hybridization ◽  
Type Strain ◽  
Inflammatory Diseases ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Human Gut ◽  
Positive Growth ◽  
The 16S Rrna Gene

Butyrate-producing bacteria can biosynthesize butyrate and alleviate inflammatory diseases. However, few studies have reported that the genus Collinsella has the ability to produce butyric acid. Here, our study depicts a Collinsella strain, which is a rod-shaped obligate anaerobe that is able to produce butyric acid. This microorganism was isolated from a human gut, and the optimal growth conditions were found to be 37 °C on PYG medium with pH 6.5. The 16S rRNA gene sequence demonstrated that this microorganism shared 99.93% similarity with C. aerofaciens ATCC 25986T, which was higher than the threshold (98.65%) for differentiating two species. Digital DNA–DNA hybridization and average nucleotide identity values also supported that this microorganism belonged to the species C. aerofaciens. Distinct phenotypic characteristics between TF06-26 and the type strain of C. aerofaciens, such as the fermentation of D-lactose, D-fructose and D-maltose, positive growth under pH 5 and 0.2% (w/v) cholate, suggested this strain was a novel subspecies. Comparative genome analysis revealed that butyric acid kinase and phosphate butyryltransferase enzymes were coded exclusively by this strain, indicating a specific butyric acid-producing function of this C. aerofaciens subspecies within the genus Collinsella. Thus, Collinsella aerofaciens subsp. shenzhenensis subsp. nov. was proposed, with set strain TF06-26T (=CGMCC 1.5216T = DSM 105138T) as the type strain.

scholarly journals Methanobacterium veterum sp. nov., from ancient Siberian permafrost

2010 ◽  
Vol 60 (2) ◽  
pp. 455-459 ◽  
Author(s):  
Kirill V. Krivushin ◽  
Viktoria A. Shcherbakova ◽  
Lada E. Petrovskaya ◽  
Elizaveta M. Rivkina
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Siberian Permafrost ◽  
The 16S Rrna Gene

A methanogenic archaeon, strain MK4T, was isolated from ancient permafrost after long-term selective anaerobic cultivation. The cells were rods, 2.0–8.0 μm long and 0.40–0.45 μm wide, and stained Gram-negative. Optimal growth was observed at 28 °C and pH 7.0–7.2 and in 0.05 M NaCl. The isolate used H2 plus CO2, methylamine plus H2 and methanol plus H2 as sources for growth and methanogenesis. Phylogenetic analysis of the 16S rRNA gene sequence of the strain showed close affinity with Methanobacterium bryantii (similarity >99 % to the type strain). On the basis of the level of DNA–DNA hybridization (62 %) between strain MK4T and Methanobacterium bryantii VKM B-1629T and phenotypic and phylogenetic differences, strain MK4T was assigned to a novel species of the genus Methanobacterium, Methanobacterium veterum sp. nov., with the type strain MK4T (=DSM 19849T =VKM B-2440T).

scholarly journals Kocuria koreensis sp. nov., isolated from fermented seafood

2010 ◽  
Vol 60 (1) ◽  
pp. 140-143 ◽  
Author(s):  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31T, was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0–15.0 % (w/v) NaCl, and at pH 5–10 and 15–37 °C. Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain P31T contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31T was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31T was most closely related to Kocuria kristinae DSM 20032T, with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA–DNA hybridization value between strain P31T and K. kristinae DSM 20032T was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31T represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31T (=KCTC 19595T=JCM 15915T).

scholarly journals Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China

2007 ◽  
Vol 57 (11) ◽  
pp. 2538-2542 ◽  
Author(s):  
A. M. Castillo ◽  
M. C. Gutiérrez ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Inner Mongolia ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Negative ◽  
Sequence Similarities

A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).

scholarly journals Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 1956-1959 ◽  
Author(s):  
Bing Li ◽  
Keiko Furihata ◽  
Lin-Xian Ding ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids ◽  
Rhodococcus Fascians ◽  
The 16S Rrna Gene ◽  
Is Strain

A polyphasic study was undertaken to establish the taxonomic position of an isolate, strain DS472T, from soil in Kyoto, Japan. Phylogenetic analysis, based on the 16S rRNA gene sequences, revealed that this strain constitutes a new subline within the genus Rhodococcus, with Rhodococcus yunnanensis YIM 70056T and Rhodococcus fascians DSM 20669T as its nearest phylogenetic neighbours (98.2 and 97.8 % sequence similarity, respectively). DNA–DNA hybridization experiments revealed 36 and 29 % relatedness between the isolate and its phylogenetic relatives, R. yunnanensis and R. fascians, respectively. Chemotaxonomic characteristics, including the major quinone MK-8(H2), predominant fatty acids C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0, the presence of cell-wall chemotype IV and mycolic acids, were consistent with the properties of members of the genus Rhodococcus. The DNA G+C content was 64.5 mol%. On the basis of both phenotypic and genotypic evidence, strain DS472T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus kyotonensis sp. nov. is proposed. The type strain is strain DS472T (=IAM 15415T=CCTCC AB206088T).

scholarly journals Chryseobacterium shandongense sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1860-1865 ◽  
Author(s):  
Fan Yang ◽  
Hong-ming Liu ◽  
Rong Zhang ◽  
Ding-bin Chen ◽  
Xiang Wang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Rrna Gene Sequence ◽  
Yellow Orange ◽  
The 16S Rrna Gene

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA–DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China

2005 ◽  
Vol 55 (6) ◽  
pp. 2539-2542 ◽  
Author(s):  
Xue-Wei Xu ◽  
Shuang-Jiang Liu ◽  
Dilbar Tohty ◽  
Aharon Oren ◽  
Min Wu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Extremely Halophilic Archaeon ◽  
Taxonomic Characterization ◽  
Derivatives Of ◽  
The 16S Rrna Gene ◽  
Haloterrigena Turkmenica

A novel extremely halophilic strain, isolated from Aibi salt lake, Xin-Jiang, China, was subjected to polyphasic taxonomic characterization. This strain, designated AB14T, is neutrophilic, motile and requires at least 10 % (w/v) NaCl for growth. Strain AB14T grows at 24–58 °C, with optimal growth at 42–45 °C. Mg2+ is not required, but growth is observed in MgCl2 concentrations as high as 1·0 M. Strain AB14T possesses the diphytanyl (C20C20) and phytanyl-sesterterpanyl diether (C20C25) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6 disulfate 1→2 glucose-glycerol diether. The genomic DNA G+C content is 66·6 mol%. The 16S rRNA gene sequence similarity values of strain AB14T with its nearest phylogenetic neighbours (Haloterrigena thermotolerans and Haloterrigena turkmenica) are 98·6 and 96·0 %, respectively. DNA–DNA hybridization revealed 54 % relatedness between strain AB14T and Haloterrigena thermotolerans JCM 11050T and 21 % between strain AB14T and Haloterrigena turkmenica JCM 9101T. It is therefore proposed that strain AB14T represents a novel species, for which the name Haloterrigena saccharevitans sp. nov. is proposed. The type strain is AB14T (=AS 1.3730T=JCM 12889T).

scholarly journals Vibrio oceanisediminis sp. nov., a nitrogen-fixing bacterium isolated from an artificial oil-spill marine sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3552-3557 ◽  
Author(s):  
Sang Rim Kang ◽  
Sathiyaraj Srinivasan ◽  
Sang-Seob Lee
Keyword(s):  
Oil Spill ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Gram Staining ◽  
Gene Sequence Analysis

A Gram-staining-negative, halophilic, facultatively anaerobic, motile, rod-shaped and nitrogen-fixing bacterium, designated strain S37T, was isolated from an artificial oil-spill sediment sample from the coast of Taean, South Korea. Cells grew at 10–37 °C and pH 5.0–9.0, with optimal growth at 28 °C and pH 6.0–8.0. Growth was observed with 1–9 % (w/v) NaCl in marine broth, with optimal growth with 3–5 % NaCl, but no growth was observed in the absence of NaCl. According to the results of 16S rRNA gene sequence analysis, strain S37T represents a member of the genus Vibrio of the class Gammaproteobacteria and forms a clade with Vibrio plantisponsor MSSRF60T (97.38 %), Vibrio diazotrophicus ATCC 33466T (97.31 %), Vibrio aestuarianus ATCC 35048T (97.07 %) Vibrio areninigrae J74T (96.76 %) and Vibrio hispanicus LMG 13240T (96.76 %). The major fatty acids were C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The DNA G+C content was 41.9 %. The DNA–DNA hybridization analysis results showed a 30.2 % association value with the closely related type strain V. plantisponsor DSM 21026T. On the basis of phenotypic and chemotaxonomic characteristics, strain S37T represents a novel species of the genus Vibrio, for which the name Vibrio oceanisediminis sp. nov., is proposed with the type strain S37T ( = KEMB 2255-005T = JCM 30409T).

scholarly journals Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3196-3202 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Chang Ho Kang ◽  
Jong-Pyo Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Ginseng Root ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100T, was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100T belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189T (97.9 %), Microbacterium lacus JCM 15575T (97.2 %) and Microbacterium invictum DSM 19600T (97.1 %). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA–DNA hybridization relatedness values between strain DCY100T and Microbacterium ginsengisoli KCTC 19189T, Microbacterium lacus JCM 15575T and Microbacterium invictum DSM 19600T were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100T is proposed. The type strain is DCY100T ( = KCTC 39529T = JCM 30598T).

scholarly journals Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater

2006 ◽  
Vol 56 (11) ◽  
pp. 2571-2574 ◽  
Author(s):  
Igor Tiago ◽  
Carlos Pires ◽  
Vítor Mendes ◽  
Paula V. Morais ◽  
Milton S. da Costa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Bootstrap Analysis ◽  
Groundwater Environment ◽  
The 16S Rrna Gene

A low-G+C-content Gram-positive bacterium, designated CV53T, phylogenetically related to species of the genus Bacillus, was isolated from a highly alkaline non-saline groundwater environment (pH 11.4). This organism comprised rod-shaped cells, was aerobic, did not display spore formation, was catalase- and oxidase-negative, had an optimum growth temperature of 40 °C and had an optimum pH of approximately 7.0–8.5. Optimal growth was observed in the absence of NaCl, but growth did occur at NaCl concentrations up to 3.0 %. The strain possessed an A1γ-type peptidoglycan cell wall and the major respiratory quinone was MK-7. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the DNA was 43.1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that the novel isolate is closely related to the type strain of Bacillus jeotgali, forming a coherent cluster supported by bootstrap analysis at a confidence level of 90 %. The pairwise similarity of the 16S rRNA gene sequences of the two strains is 97.7 %. On the basis of the phylogenetic analyses and the distinct phenotypic characteristics, strain CV53T represents a novel species within the genus Bacillus, for which we propose the name Bacillus foraminis sp. nov. The type strain is CV53T (=LMG 23174T=CIP 108889T).

scholarly journals Staphylococcus rostri sp. nov., a haemolytic bacterium isolated from the noses of healthy pigs

2010 ◽  
Vol 60 (9) ◽  
pp. 2042-2047 ◽  
Author(s):  
Andrea Riesen ◽  
Vincent Perreten
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Reference Strain ◽  
Novel Species ◽  
Teichoic Acid ◽  
Wall Structure ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Glucuronidase Activity ◽  
The 16S Rrna Gene

Twenty coagulase-negative Staphylococcus strains displaying α-haemolysis (δ-haemolysin) on sheep-blood agar were isolated from the noses of different pigs in Switzerland. The strains were Gram-stain-positive, non-motile cocci, catalase-positive and coagulase-negative. Sequence analysis of the 16S rRNA gene, sodA, rpoB, dnaJ and hsp60 and phylogenetic characteristics revealed that the strains showed the closest relatedness to Staphylococcus microti CCM 4903T and Staphylococcus muscae DSM 7068T. The strains can be differentiated from S. microti by the absence of mannose fermentation and arginine arylamidase and from S. muscae by the absence of β-glucuronidase activity and production of alkaline phosphatase. The chosen type strain ARI 262T shared 20.1 and 31.9 % DNA relatedness with S. microti DSM 22147T and S. muscae CCM 4903T, respectively, by DNA–DNA hybridization. iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 were the most common fatty acids. Cell-wall structure analysis revealed the peptidoglycan type A3α l-Lys–Gly2–l-Ser–Gly (type A11.3). The presence of teichoic acid was determined by sequencing the N-acetyl-β-d-mannosaminyltransferase gene tarA, which is involved in biosynthesis of ribitol teichoic acid. Menaquinone 7 (MK-7) was the predominant respiratory quinone. The G+C content of ARI 262T was 38.8 mol%. The isolated strains represent a novel species of the genus Staphylococcus, for which we propose the name Staphylococcus rostri sp. nov. The type strain is ARI 262T (=DSM 21968T =CCUG 57266T) and strain ARI 602 (=DSM 21969 =CCUG 57267) is a reference strain.

Sign in / Sign up

Export Citation Format

Share Document