scholarly journals Streptococcus oriloxodontae sp. nov., isolated from the oral cavities of elephants

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3755-3759 ◽  
Author(s):  
Noriko Shinozaki-Kuwahara ◽  
Masanori Saito ◽  
Masatomo Hirasawa ◽  
Kazuko Takada
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Streptococcal Species

Two strains were isolated from oral cavity samples of healthy elephants. The isolates were Gram-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequence analysis suggested classification of these organisms in the genus Streptococcus with Streptococcus criceti ATCC 19642T and Streptococcus orisuis NUM 1001T as their closest phylogenetic neighbours with 98.2 and 96.9 % gene sequence similarity, respectively. When multi-locus sequence analysis using four housekeeping genes, groEL, rpoB, gyrB and sodA, was carried out, similarity of concatenated sequences of the four housekeeping genes from the new isolates and Streptococcus mutans was 89.7 %. DNA–DNA hybridization experiments suggested that the new isolates were distinct from S. criceti and other species of the genus Streptococcus . On the basis of genotypic and phenotypic differences, it is proposed that the novel isolates are classified in the genus Streptococcus as representatives of Streptococcus oriloxodontae sp. nov. The type strain of S. oriloxodontae is NUM 2101T ( = JCM 19285T = DSM 27377T).

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

Parabacteroides faecis sp. nov., isolated from human faeces

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1342-1346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Yoshiki Tanaka ◽  
Yoshimi Benno ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Sequence Analysis

A bacterial strain, designated 157T, isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20 % (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157T was closely related to Parabacteroides gordonii JCM 15724T (96 % sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157T was different from P. gordonii JCM 15724T, with a hsp60 gene sequence similarity of 96.1 %. The major cellular fatty acids of strain 157T were anteiso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and anteiso-C17 : 0 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157T was 41.8 mol%. On the basis of these data, strain 157T represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157T ( = JCM 18682T = CCUG 66681T).

Stappia taiwanensis sp. nov., isolated from a coastal thermal spring

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1350-1354 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
A. Frischmann ◽  
H.-J. Busse ◽  
Chiu-Chung Young ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia , showing 98.3 % sequence similarity to Stappia indica B106T and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621T . Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1–L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1T could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10T represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 T ( = CCUG 59208T = LMG 25538 T = CCM 7757T).

Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3807-3811 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
Eun-Ji Yi ◽  
YongJin Park ◽  
Kyung-Hwa Won ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Physiological And Biochemical

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53T (98.7 % similarity), Dyella terrae JS14-6T (98.0 %), Dyella koreensis BB4T (96.9 %), Dyella soli JS12-10T (96.9 %) and Dyella thiooxydans ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus Dyella . The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus Dyella , and represents a novel species of this genus. The name Dyella kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).

scholarly journals Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1754-1759 ◽  
Author(s):  
Doan Thi Lam Nguyen ◽  
Margo Cnockaert ◽  
Koenraad Van Hoorde ◽  
Evie De Brandt ◽  
Isabel Snauwaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Fermentation Profile

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767T, that could not be assigned to a species with a validly published name. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus Lactobacillus , with Lactobacillus manihotivorans and Lactobacillus camelliae as the closest relatives (98.9 % and 96.9 % gene sequence similarity to the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA–DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767T represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767T ( = CCUG 62266T). Biochemically, L. porcinae can be distinguished from L. manihotivorans and L. camelliae by its carbohydrate fermentation profile, absence of growth at 45 °C, and production of d- and l-lactate as end products of glucose metabolism.

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.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

Thauera humireducens sp. nov., a humus-reducing bacterium isolated from a microbial fuel cell

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 873-878 ◽  
Author(s):  
Gui-Qin Yang ◽  
Jun Zhang ◽  
Soon-Wo Kwon ◽  
Shun-Gui Zhou ◽  
Lu-Chao Han ◽  
...  
Keyword(s):  
Fuel Cell ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Fuel Cell ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated SgZ-1T, was isolated from the anode biofilm of a microbial fuel cell. The strain had the ability to grow under anaerobic condition via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Growth occurred in TSB in the presence of 0–5.5 % (w/v) NaCl (optimum 0–1 %), at 10–45 °C (optimum 25–37 °C) and at pH 6.0–10.0 (optimum 8.0–8.5). Based on 16S rRNA gene sequence similarity, strain SgZ-1T belonged to the genus Thauera . The highest level of 16S rRNA gene sequences similarity (96.7 %) was found to be with Thauera aminoaromatica S2 T and Thauera selenatis AXT, and lower values were obtained when compared with other recognized Thauera species. Chemotaxonomic analysis revealed that strain SgZ-1T contained Q-8 as the predominant quinone, and putrescine and 2-hydroxyputrescine as the major polyamines. The major cellular fatty acids (>5 %) were C16 : 1ω6c and/or C16 : 1ω7c (44.6 %), C16 : 0 (18.8 %), and C18 : 1ω6c and/or C18 : 1ω7c (12.7 %). Based on its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-1T ( = KACC 16524T = CCTCC M 2011497T) was designated the type strain of a novel species of the genus Thauera , for which the name Thauera humireducens sp. nov. was proposed.

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3823-3828 ◽  
Author(s):  
Chokchai Kittiwongwattana ◽  
Chitti Thawai
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Low Levels ◽  
Sequence Similarity Analysis ◽  
Ph Range

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

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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