scholarly journals Lactobacillus secaliphilus sp. nov., isolated from type II sourdough fermentation

2007 ◽  
Vol 57 (4) ◽  
pp. 745-750 ◽  
Author(s):  
Matthias A. Ehrmann ◽  
Markus Brandt ◽  
Peter Stolz ◽  
Rudi F. Vogel ◽  
Maher Korakli
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Lactobacillus Reuteri ◽  
Rrna Gene ◽  
The Novel ◽  
Type Ii ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Two strains of Gram-positive, catalase-negative, lactic acid bacteria, strains TMW 1.1309T and TMW 1.1313, were isolated at an interval of several years from an industrial type II sourdough. They occurred at cell numbers of 8×108 c.f.u. g−1 and therefore were considered to be one of the dominant members of the microbiota in this type of fermentation. Cells of both strains grow exclusively on modified MRS containing trypsin-digested rye-bran extract. Both strains possessed identical 16S rRNA gene sequences, but could be discriminated by RAPD fingerprints. Comparative 16S rRNA and tuf gene sequence analyses positioned strain TMW 1.1309T as part of the Lactobacillus reuteri phylogenetic group within the genus Lactobacillus. The 16S rRNA gene sequence similarities to the closest related species, Lactobacillus coleohominis and Lactobacillus ingluviei were 97.1 and 95.4 %, respectively. The DNA G+C content of strain TMW 1.1309T was 48 mol%. Growth characteristics, biochemical features and DNA–DNA hybridization values below 70 % with all the nearest neighbours demonstrated that the isolates represent a novel Lactobacillus species. The name Lactobacillus secaliphilus sp. nov. is proposed for the novel isolates, with the type strain TMW 1.1309T (=DSM 17896T=CCUG 53218T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

scholarly journals Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2803-2809 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Jia Xu ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Panicum Virgatum ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow, nitrogen-fixing bacterial strain, NXU-44T, isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9 %), Flavobacterium phragmitis (97.6 %) and Flavobacterium anhuiense (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5 %. The fatty acid profile of strain NXU-44T consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44T represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44T ( = LMG 28694T = CIP 110894T).

scholarly journals Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4508-4513 ◽  
Author(s):  
Ji-Quan Sun ◽  
Min Liu ◽  
Xin-Ying Wang ◽  
Lian Xu ◽  
Xiao-Lei Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Northern China ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene ◽  
Sequence Similarities ◽  
Suaeda Corniculata

A Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).

scholarly journals Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3666-3673 ◽  
Author(s):  
Anand Kumar ◽  
Abhay Bajaj ◽  
Rajendran Mathan Kumar ◽  
Gurwinder Kaur ◽  
Navjot Kaur ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Sequence ◽  
Gene Sequence ◽  
Draft Genome ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA–DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp).

Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems

2010 ◽  
Vol 60 (8) ◽  
pp. 1765-1769 ◽  
Author(s):  
Peter Kämpfer ◽  
A. B. Arun ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen ◽  
K. R. Sridhar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Closely Related Species ◽  
The 16S Rrna Gene ◽  
Sequence Similarities ◽  
Chryseobacterium Gleum

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).

scholarly journals Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences

2010 ◽  
Vol 60 (12) ◽  
pp. 2697-2704 ◽  
Author(s):  
Byoung Jun Kim ◽  
Hee-Youn Kim ◽  
Yeo-Jun Yun ◽  
Bum-Joon Kim ◽  
Yoon-Hoh Kook
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rna Polymerase ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum–Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum–Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum–Bifidobacterium pullorum–Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

scholarly journals Flavobacterium fluvii sp. nov., isolated from stream sediment

2010 ◽  
Vol 60 (2) ◽  
pp. 353-357 ◽  
Author(s):  
Se Hee Lee ◽  
Jeong Myeong Kim ◽  
Jung Ro Lee ◽  
Woojun Park ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Gram Staining ◽  
Sequence Similarities

An aerobic, yellow-pigmented, Gram-staining-negative bacterium, designated strain H7T, was isolated from sediment of Gazwa stream in Jinju city, South Korea. Cells of strain H7T were non-motile, straight rods that produced flexirubin pigments and showed catalase- and oxidase activities. Strain H7T contained iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the main fatty acids and menaquinone-6 (MK-6) as the major isoprenoid quinone. The DNA G+C content of strain H7T was 37.2 mol%. Comparative 16S rRNA gene sequence analysis showed that strain H7T formed a distinct phyletic line within the genus Flavobacterium. Based on 16S rRNA gene sequence similarities, the novel strain was most closely related to Flavobacterium limicola ST-82T and Flavobacterium resistens BD-b365T with 97.2 % and 97.0 % gene sequence similarities, respectively. The DNA–DNA relatedness of the novel strain with these species was only 18 % and 14 %, respectively. On the basis of phenotypic data and molecular properties, strain H7T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium fluvii sp. nov. is proposed. The type strain is H7T (=KACC 12818T=DSM 19978T).

scholarly journals Chryseobacterium arachidiradicis sp. nov., isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2179-2186 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Arachis Hypogaea ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow-pigmented bacterial strain, 91A-612T, isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea) in Alabama, USA, was studied for its taxonomic position. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Chryseobacterium, showing the highest sequence similarities to the type strains of Chryseobacterium molle (98.4 %), C. pallidum (98.3 %) and C. hominis (97.8 %). The 16S rRNA gene sequence similarities to the type strains of all other species of the genus Chryseobacterium were below 97.0 %. The fatty acid profile of strain 91A-612T consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids, including two lipids that did not contain a sugar moiety, an amino group or a phosphate group (L3, L8), and an aminolipid (AL1). The quinone system was composed mainly of MK-6. The polyamine pattern contained sym-homospermidine as the major compound and moderate amounts of spermidine and spermine. DNA–DNA hybridizations between strain 91A-612T and the type strains of C. molle, C. pallidum and C. hominis resulted in relatedness values well below 70 %. These data and the differentiating biochemical and chemotaxonomic properties showed that isolate 91A-612T represents a novel species of the genus Chryseobacterium, for which we propose the name Chryseobacterium arachidiradicis sp. nov. (type strain 91A-612T = LMG 27814T = CCM 8490T = CIP 110647T).

scholarly journals Fontibacillus aquaticus gen. nov., sp. nov., isolated from a warm spring

2010 ◽  
Vol 60 (2) ◽  
pp. 422-428 ◽  
Author(s):  
P. Saha ◽  
S. Krishnamurthi ◽  
A. Bhattacharya ◽  
R. Sharma ◽  
T. Chakrabarti
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Warm Spring ◽  
The 16S Rrna Gene

A novel facultatively anaerobic strain, designated GPTSA 19T, was isolated from a warm spring and characterized using a polyphasic approach. The strain behaved as Gram-negative in the Gram staining procedure but showed a Gram-positive reaction in the aminopeptidase test. The novel strain was a mesophilic rod with ellipsoidal endospores. On the basis of 16S rRNA gene sequence analysis, the strain showed closest similarity (96.0 %) with Paenibacillus motobuensis MC10T. The gene sequence similarity of the novel strain with other species of the genus Paenibacillus was <95.8 %. The novel strain also had PAEN 515F and 682F signature sequence stretches in the 16S rRNA gene that are usually found in most species of the genus Paenibacillus. The strain possessed anteiso-C15 : 0 as the major fatty acid and MK-7 as the predominant menaquinone. Polar lipids included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), six unknown phospholipids (PLs), one aminophospholipid (PN), three glycolipids (GLs), two aminolipids (ALs), one aminophosphoglycolipid (APGL) and three unknown lipids (ULs). The polar lipid profile of the novel strain, especially as regards ALs, GLs and PLs, distinguished it from the recognized type species of the genus Paenibacillus, Paenibacillus polymyxa, as well as from its closest relative P. motobuensis. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the new strain merits the rank of a novel genus for which the name Fontibacillus gen. nov. is proposed. The type species of the new genus is Fontibacillus aquaticus gen. nov., sp. nov. with the type strain GPTSA 19T (=MTCC 7155T=DSM 17643T).

scholarly journals Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs

2011 ◽  
Vol 61 (4) ◽  
pp. 716-721 ◽  
Author(s):  
Joachim Spergser ◽  
Stefan Langer ◽  
Simone Muck ◽  
Kathrin Macher ◽  
Michael Szostak ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Intergenic Spacer Region ◽  
Pcr Rflp ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Fourteen Mycoplasma strains were isolated from the oral cavity and genital tract of asymptomatic dogs. Isolates had been preliminarily identified by conventional serological testing as Mycoplasma bovigenitalium, but in 16S–23S rRNA intergenic spacer PCR-RFLP assays the isolates exhibited an RFLP pattern distinct from M. bovigenitalium PG11T. Analysis of the 16S rRNA gene placed a representative of the isolates (strain 1642T) in the M. bovigenitalium subcluster of the Mycoplasma bovis cluster of mycoplasmas, with the highest sequence similarities to Mycoplasma californicum ST-6T (96.4 %), M. bovigenitalium PG11T (96.3 %) and Mycoplasma phocirhinis 852T (96.2 %). 16S rRNA gene sequence similarities almost equidistant from three recognized species and results obtained by sequence analysis of the 16S–23S rRNA intergenic spacer region, polar lipid profiles and serological reactions indicated that this organism represents a novel species of the genus Mycoplasma for which the name Mycoplasma mucosicanis sp. nov. is proposed, with strain 1642T ( = ATCC BAA-1895T  = DSM 22457T) as the type strain.

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