scholarly journals Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.

2010 ◽  
Vol 60 (3) ◽  
pp. 664-674 ◽  
Author(s):  
C. Merabet ◽  
M. Martens ◽  
M. Mahdhi ◽  
F. Zakhia ◽  
A. Sy ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Medicago Sativa ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Reconstruction ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Reconstruction Method

Nine isolates from Argyrolobium uniflorum, Lotus creticus, Medicago sativa (Tunisia) and Lotus arabicus (Senegal) were analysed by multilocus sequence analysis (MLSA) of five housekeeping genes (recA, atpD, glnA, gltA and thrC), the 16S rRNA gene and the nodulation gene nodA. Analysis of the individual and concatenated gene sequences demonstrated that the nine new strains constituted three stable, well-supported (bootstrap and gene sequence similarity values) monophyletic clusters, A, B and C, all belonging to the branch of the genus Ensifer, regardless of the phylogenetic reconstruction method used (maximum likelihood, maximum-parsimony, neighbour-joining). The three groups were further characterized by API 100 auxanographic tests, host specificity and nodA gene sequence analysis. On the basis of these data, clusters A and C are suggested as representing two novel species within the genus Ensifer, for which the names Ensifer numidicus sp. nov. (type strain ORS 1407T=LMG 24690T=CIP 109850T) and Ensifer garamanticus sp. nov. (type strain ORS 1400T=LMG 24692T=CIP 109916T) are proposed. The cluster B strains were assigned to Ensifer adhaerens genomovar A.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

scholarly journals Identification and classification of the genus Bacteroides by multilocus sequence analysis

Microbiology ◽  
2011 ◽  
Vol 157 (12) ◽  
pp. 3388-3397 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Single Gene ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene

Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5 % gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.

scholarly journals Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2586-2590 ◽  
Author(s):  
Ulrike Lyhs ◽  
Isabel Snauwaert ◽  
Seija Pihlajaviita ◽  
Luc De Vuyst ◽  
Peter Vandamme
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sous Vide

A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676T, was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8 % 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676T from all established species of the genus Leuconostoc. Strain LMG 27676T ( = R-50029T = MHB 277T = DSM 27776T) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.

scholarly journals Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkongensis sp. nov.

2006 ◽  
Vol 56 (4) ◽  
pp. 781-786 ◽  
Author(s):  
Peter Kämpfer ◽  
Ramon Rosselló-Mora ◽  
Enevold Falsen ◽  
Hans-Jürgen Busse ◽  
Brian J. Tindall
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A Gram-positive, rod-shaped, endospore-forming organism, strain CCUG 47242T, was isolated from a sample of industrial starch production in Sweden. 16S rRNA gene sequence analysis demonstrated that this isolate was moderately related to species of the genus Paenibacillus, with <94·4 % sequence similarity to all other hitherto described Paenibacillus species. Strain CCUG 47242T showed the greatest sequence similarity (96·5 %) to ‘Paenibacillus hongkongensis’ HKU3, a strain with a name that has not yet been validly published. Chemotaxonomic data [major menaquinone, MK-7 (98 %); major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, two unknown phospholipids, four unknown aminophospholipids; major fatty acids, iso-C16 : 0 and anteiso-C15 : 0] showed some significant differences when compared with the type species of the genus Paenibacillus, Paenibacillus polymyxa. Physiological and biochemical tests allowed clear phenotypic differentiation of strain CCUG 47242T from strain HKU3. On the basis of 16S rRNA gene sequence analysis, in combination with chemotaxonomic data, strains CCUG 47242T and HKU3 represent two novel species of a new genus of endospore-forming bacteria for which we propose the names Cohnella thermotolerans gen. nov., sp. nov. (type strain CCUG 47242T=CIP 108492T=DSM 17683T) and Cohnella hongkongensis sp. nov. (type strain HKU3T=CCUG 49571T=CIP 107898T=DSM 17642T).

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 Gibbsiella papilionis Kim et al. 2013 is a later heterotypic synonym of Gibbsiella dentisursi Saito et al. 2013

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4788-4791 ◽  
Author(s):  
Carrie Brady ◽  
Tomohiro Irisawa ◽  
Takao Iino ◽  
Moriya Ohkuma ◽  
Dawn Arnold ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Polyphasic Approach ◽  
Multilocus Sequence Analysis ◽  
Taxonomic Relationship ◽  
Type Strains

Synonymy of Gibbsiella dentisursi DSM 23818T ( = NUM 1720T) and Gibbsiella papilionis JCM 18389T ( = LEN33T) was suspected following multilocus sequence analysis (MLSA) of both type strains in a previous classification study, where they were found to share >99.6 % gene sequence similarity. The taxonomic relationship between these two strains was re-examined here using a polyphasic approach. A DNA–DNA hybridization value of 98 % confirmed that the two type strains belong to a single taxon, while the phenotypic profiles were found to be nearly identical. Therefore we propose Gibbsiella papilionis as a later heterotypic synonym of Gibbsiella dentisursi, with the type strain as NUM 1720T ( = DSM 23818T = JCM 17201T).

scholarly journals Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4093-4099 ◽  
Author(s):  
Peter Kämpfer ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

A beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA–DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA–DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

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