Pediococcus lolii DSM 19927T and JCM 15055T are strains of Pediococcus acidilactici

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3105-3108 ◽  
Author(s):  
Anneleen Wieme ◽  
Ilse Cleenwerck ◽  
Anita Van Landschoot ◽  
Peter Vandamme
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Pediococcus Acidilactici ◽  
Culture Collections ◽  
Ionization Time ◽  
Content Type ◽  
Link Type ◽  
Flight Mass Spectrometry ◽  
Gene Sequence Analysis

Strain NGRI 0510QT, isolated from ryegrass silage, was recently classified as a representative of a novel Pediococcus species, Pediococcus lolii Doi et al. 2009. It was deposited in the DSMZ and JCM culture collections as DSM 19927T and JCM 15055T, respectively. A polyphasic taxonomic study, including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, pheS and 16S rRNA gene sequence analysis, fluorescent amplified fragment length polymorphism and DNA–DNA hybridization, was used to prove that both subcultures of the type, and only, strain of this species are strains of Pediococcus acidilactici .

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

scholarly journals Streptomyces smaragdinus sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis

2020 ◽  
Vol 70 (11) ◽  
pp. 5806-5811 ◽  
Author(s):  
Jan W. Schwitalla ◽  
René Benndorf ◽  
Karin Martin ◽  
John Vollmers ◽  
Anne-Kristin Kaster ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
A Value ◽  
Gene Sequence Analysis

The taxonomic position of a novel aerobic, Gram-positive actinobacteria, designated strain RB5T, was determined using a polyphasic approach. The strain, isolated from the gut of the fungus-farming termite Macrotermes natalensis, showed morphological, physiological and chemotaxonomic properties typical of the genus Streptomyces . Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of RB5T was Streptomyces polyrhachis DSM 42102T (98.87 %). DNA–DNA hybridization experiments between strain RB5T and S. polyrhachis DSM 42102T resulted in a value of 27.4 % (26.8 %). The cell wall of strain RB5T contained ll-diaminopimelic acid as the diagnostic amino acid. Mycolic acids and diagnostic sugars in whole-cell hydrolysates were not detected. The strain produced the following major phospholipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannoside and phosphatidylserine. The menaquinone profile showed hexa- and octahydrogenated menaquinones containing nine isoprene units [MK-9(H6) and MK-9(H8)]. The strain exhibited a fatty acid profile containing the following major fatty acids: 12-methyltridecanoic acid (iso-C14 : 0) 12-methyltetradecanoic acid (anteiso-C15 : 0), 13-methyltetradecanoic acid (iso-C15 : 0) and 14-methylpentadecanoic acid (iso-C16 : 0). Here, we propose a novel species of the genus Streptomyces – Streptomyces smaragdinus with the type strain RB5T (=VKM Ac-2839T=NRRL B65539T).

Mycetocola miduiensis sp. nov., a psychrotolerant bacterium isolated from Midui glacier

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2661-2665 ◽  
Author(s):  
Lang Zhu ◽  
Qing Liu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Yuhua Xin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Psychrotolerant Bacterium ◽  
Sequence Similarities

An aerobic, asporous, flagellated, Gram-stain-positive, rod-shaped bacterium MD-T1-10-2T was isolated from the topsoil of Midui Glacier, Tibet Province, China. Phylogenetic analysis based on 16S rRNA gene sequence analysis placed the strain in a clade containing Mycetocola manganoxydans CCTCC AB 209002T, Mycetocola reblochoni DSM 18580T, Mycetocola tolaasinivorans JCM 11656T, Mycetocola lacteus JCM 11654T and Mycetocola saprophilus JCM 11655T, with the sequence similarities of 99.2, 98.1, 96.7, 96.6 and 96.4 %, respectively. DNA–DNA hybridization analysis indicated that strain MD-T1-10-2T represented a new member of this genus. The optimal ranges of temperature and pH for growth were 20–25 °C and 7.0–9.0, respectively; the strain could even grow at 0 °C. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinones were MK-10 and MK-11. The cell wall amino acids were lysine, alanine, glycine and glutamic acids. The DNA G+C content was 65.9 mol%. Based on the genotypic and phenotypic data, strain MD-T1-10-2T for which the name Mycetocola miduiensis sp. nov. is proposed; the type strain is MD-T1-10-2T ( = CGMCC 1.11101T = NBRC 107877T).

scholarly journals Bifidobacterium faecale sp. nov., isolated from human faeces

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3134-3139 ◽  
Author(s):  
Jung-Hye Choi ◽  
Kyung Min Lee ◽  
Myung-Ki Lee ◽  
Chang-Jun Cha ◽  
Geun-Bae Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Gene Sequence Analysis

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).

Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2690-2699 ◽  
Author(s):  
S. Wellner ◽  
N. Lodders ◽  
S. P. Glaeser ◽  
P. Kämpfer
Keyword(s):  
Fatty Acid ◽  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Leaf Surfaces

Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium . The closest relatives of strains C34T and T5 were Methylobacterium gnaphalii 23eT (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833T (97.0 and 97.2 %, respectively). Strain TA73T showed the highest sequence similarities to Methylobacterium marchantiae JT1T and Methylobacterium bullatum F3.2T (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27T and Methylobacterium brachiatum DSM 19569T (both 97.8 %), Methylobacterium cerastii C15T and Methylobacterium radiotolerans JCM 2831T (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73T and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34T and T5. Physiological and biochemical analysis, including DNA–DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA–DNA hybridization studies also showed high similarities between strains C34T and T5 (59.6–100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium , for which the names Methylobacterium trifolii sp. nov. (type strain TA73T = LMG 25778T = CCM 7786T) and Methylobacterium thuringiense sp. nov. (type strain C34T = LMG 25777T = CCM 7787T) are proposed.

Cohnella terricola sp. nov., isolated from soil

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Jiyoun Kim ◽  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Minchung Kang ◽  
Taegun Seo
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Phenotypic Tests ◽  
A New Species

A Gram-positive, aerobic, flagellated, endospore-forming, rod-shaped strain, designated as G13T, was isolated from soil. The results of 16S rRNA gene sequence analysis led to the conclusion that strain G13T was phylogenetically related to Cohnella boryungensis BR29T (97.5 %) and Cohnella phaseoli CECT 7287T (96.9 %) with digital DNA–DNA hybridization values of 21.0 and 21.4 %, and distantly related to Cohnella thermotolerans CCUG 47242T (94.8 %), type species of the genus Cohnella , at 19.0 %. The genome size of strain G13T was 5 387 258 bp, with 51.3 mol% G+C content. The predominant fatty acids were summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0, iso-C17 : 0 and iso-C15 : 0. The predominant quinone was menaquinone-7 and the major polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysylphosphatidylglycerol, three aminophospholipids, two phosphoglycolipids, three aminolipids and two unidentified lipids. Based on the data from phenotypic tests and the genotypic differences between strain G13T and its close phylogenetic relatives, strain G13T represents a new species belonging to the genus Cohnella , for which the name Cohnella terricola sp. nov. (=KACC 19905T=NBRC 113748T) is proposed.

Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya

2021 ◽  
Author(s):  
Peng Cao ◽  
Xi Xu ◽  
Chenxu Li ◽  
Liyuan Han ◽  
Wenhao Mu ◽  
...  
Keyword(s):  
Sandy Soil ◽  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China

A novel actinobacterium, designated strain NEAU-AAG5T, was isolated from sandy soil collected from Niuwang island in Sanya, Hainan Province, PR China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-AAG5T belongs to the genus Actinomadura and shared highest sequence similarity with Actinomadura macra NBRC 14102T (98.8 %). Strain NEAU-AAG5T grows at 20–40 °C (optimum, 28 °C), pH 6–10 (optimum, pH 7) and has NaCl tolerance of 0–3 %. The menaquinones were identified as MK-9(H4) (4.2 %), MK-9(H6) (49.2 %) and MK-9(H8) (46.5 %). The major fatty acids were C16 : 0 (31.4 %), 10-methyl C18 : 0 (21.3 %) and C18 : 1  ω9c (15.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain NEAU-AAG5T based on whole genome sequences was 72.8 mol%. Digital DNA–DNA hybridization between strain NEAU-AAG5T and its closest phylogenetic neighbour, A. macra NBRC 14102T, resulted in similarity value of 28.0 % (<70 %). Additionally, the average nucleotide identity was 84.2 % for A. macra NBRC 14102T. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-AAG5T can be characterized to represent a novel species of the genus Actinomadura , for which the name Actinomadura litoris sp. nov. is proposed. The type strain is NEAU-AAG5T (=JCM 33456T=CCTCC AA 2019043T).

scholarly journals Saccharothrix hoggarensis sp. nov., an actinomycete isolated from Saharan soil

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 549-553 ◽  
Author(s):  
Dalila Boubetra ◽  
Abdelghani Zitouni ◽  
Noureddine Bouras ◽  
Florence Mathieu ◽  
Ahmed Lebrihi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Saharan Soil ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains

An actinomycete, designated SA181T, was isolated from Saharan soil in the Hoggar region (south Algeria) and was characterized taxonomically by using a polyphasic approach. The morphological and chemotaxonomic characteristics of the isolate were consistent with the genus Saccharothrix , and 16S rRNA gene sequence analysis confirmed that strain SA181T was a novel member of the genus Saccharothrix . DNA–DNA hybridization values between strain SA181T and its closest phylogenetic neighbours, the type strains of Saccharothrix longispora , Saccharothrix texasensis and Saccharothrix xinjiangensis , were clearly below the 70 % threshold. The genotypic and phenotypic data showed that the isolate represents a novel species of the genus Saccharothrix , for which the name Saccharothrix hoggarensis sp. nov. is proposed, with the type strain SA181T ( = DSM 45457T  = CCUG 60214T).

Adlercreutzia hattorii sp. nov., an equol non-producing bacterium isolated from human faeces

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Nao Ikeyama ◽  
Masahiro Yuki ◽  
Takumi Murakami ◽  
Hiroshi Mori ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Related Species ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Healthy Humans ◽  
Gene Sequence Analysis ◽  
Faecal Samples

Two obligately anaerobic, Gram-stain-positive, rod-shaped bacteria were isolated from faecal samples of healthy humans in Japan. 16S rRNA gene sequence analysis indicated that these two strains (8CFCBH1T and 9CBH6) belonged to the genus Adlercreutzia , which is known as an equol-producing bacterium. The closest neighbours of strain 8CFCBH1T were Adlercreutzia equolifaciens subsp. equolifaciens DSM 19450T (98.6%), Adlercreutzia equolifaciens subsp. celatus do03T (98.4%), Adlercreutzia muris WCA-131-CoC-2T (96.6%), Parvibacter caecicola NR06T (96.4%), Adlercreutzia caecimuris B7T (95.3%) and Adlercreutzia mucosicola Mt1B8T (95.3%). The closest relatives to strain 9CBH6 were A. equolifaciens subsp. equolifaciens DSM 19450T (99.8%), A. equolifaciens subsp. celatus do03T (99.6%) and A. muris WCA-131-CoC-2T (96.8%). Strain 8CFCBH1T showed 22.3–53.5% digital DNA–DNA hybridization (dDDH) values with its related species. In addition, the average nucleotide identity (ANI) values between strain 8CFCBH1T and its related species ranged from 75.4 to 93.3%. On the other hand, strain 9CBH6 was considered as A. equolifaciens based on the dDDH and ANI values (>70% dDDH and >95–96% ANI). Strain 9CBH6 showed daidzein-converting activity, as expected from the result of genome analysis. The genome of strain 8CFCBH1T lacked four genes involved in equol production. Growing cells of strain 8CFCBH1T were not capable of converting daidzein. Based on the collected data, strain 8CFCBH1T represents a novel species in the genus Adlercreutzia , for which the name Adlercreutzia hattorii sp. nov. is proposed. The type strain of A. hattorii is 8CFCBH1T (=JCM 34083T=DSM 112284T).

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