scholarly journals Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species

2005 ◽  
Vol 55 (6) ◽  
pp. 2309-2315 ◽  
Author(s):  
Yuichi Nogi ◽  
Hideto Takami ◽  
Koki Horikoshi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Industrial Applications ◽  
Rrna Gene ◽  
Bacterial Strains

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).

scholarly journals Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.

2010 ◽  
Vol 60 (10) ◽  
pp. 2430-2440 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Stephanus N. Venter ◽  
Katrien Engelbeen ◽  
Paul De Vos ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Enterobacter Agglomerans ◽  
Bacterial Strains ◽  
Separate Species

Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola–Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), 45–55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA–DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345T =BD 874T =CDC 3123-70T), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781T =BD 872T =CDC 1741-71T =LMG 5346T), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 5343T =BD 873T =CDC 3482-71T) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 24534T =BD 805T =CDC 3527-71T) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657T =ATCC 29267T =DSM 3873T =LMG 2655T).

scholarly journals Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes

2006 ◽  
Vol 56 (7) ◽  
pp. 1465-1473 ◽  
Author(s):  
S. Shivaji ◽  
P. Chaturvedi ◽  
K. Suresh ◽  
G. S. N. Reddy ◽  
C. B. S. Dutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Air Samples ◽  
Bacillus Altitudinis ◽  
Bacillus Sonorensis

Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24KT, 28KT, 41KF2aT and 41KF2bT, were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24KT, 28KT and 41KF2aT, are very similar to one another (>98 % sequence similarity) and show a similarity of 98–99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA–DNA hybridization studies showed that strains 24KT, 28KT and 41KF2aT exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2bT showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA–DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24KT=MTCC 7303T=JCM 13348T), Bacillus aerophilus sp. nov. (type strain, 28KT=MTCC 7304T=JCM 13347T), Bacillus stratosphericus sp. nov. (type strain, 41KF2aT=MTCC 7305T=JCM 13349T) and Bacillus altitudinis sp. nov. (type strain, 41KF2bT=MTCC 7306T=JCM 13350T) are proposed.

scholarly journals Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China

2006 ◽  
Vol 56 (2) ◽  
pp. 459-463 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Wen-Jun Li ◽  
Ke-Yun Zhang ◽  
Xin-Peng Tian ◽  
Yi Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis

Four Gram-negative, motile, rod-shaped bacterial strains were isolated from soil samples collected from south-east China. A taxonomic study including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics was performed. DNA G+C contents of the four strains were 63–66 mol%. Their predominant ubiquinone was Q-8. The fatty acid profiles contained C16 : 1 ω7c (36·9–54·7 %) and C16 : 0 (22·8–25·5 %) as the major components. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and DNA–DNA hybridization results, the four isolates are considered to represent four novel species of the genus Massilia, for which the names Massilia dura sp. nov. (type strain 16T=CCTCC AB 204070T=KCTC 12342T), Massilia albidiflava sp. nov. (type strain 45T=CCTCC AB 204071T=KCTC 12343T), Massilia plicata sp. nov. (type strain 76T=CCTCC AB 204072T=KCTC 12344T) and Massilia lutea sp. nov. (type strain 101T=CCTCC AB 204073T=KCTC 12345T) are proposed.

scholarly journals Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2903-2907 ◽  
Author(s):  
Ana I. Vela ◽  
Encarna Casas-Díaz ◽  
Santiago Lavín ◽  
Lucas Domínguez ◽  
Jose F. Fernández-Garayzábal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences

Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03T (96.9  % 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03T (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9  %, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796BT ( = CECT 8754T = CCUG 66496T).

scholarly journals Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2

2010 ◽  
Vol 60 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Geert Huys ◽  
Margo Cnockaert ◽  
Sharon L. Abbott ◽  
J. Michael Janda ◽  
Peter Vandamme
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Reference Strains ◽  
Sequence Similarities

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2209-2213 ◽  
Author(s):  
Zubair Aslam ◽  
Wan-Taek Im ◽  
Leonid N. Ten ◽  
Myung-jin Lee ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Optimum Growth Temperature ◽  
Range Of Values

The taxonomic position of two lactic-acid-producing bacterial strains, isolated from wheat sourdough in South Korea, was studied using a polyphasic approach. Phylogenetic analysis on the basis of 16S rRNA gene sequences and biochemical and physiological characteristics indicated these two strains to be members of the genus Lactobacillus. They had high 16S rRNA gene sequence similarity (98.5 %) with Lactobacillus rossiae DSM 15814T and very low (<94.0 %) similarity with any other recognized species of the genus Lactobacillus. These two strains (designated M1-212T and M2-236) were heterofermentative, facultatively anaerobic, Gram-positive, non-spore-forming, non-motile, short rod-shaped bacteria. The optimum growth temperature for these strains was 30 °C (no growth at 15 or 45 °C) and they were able to tolerate 5 % (w/v) NaCl. The G+C content of the genomic DNA of the two strains was 45.5 mol%, within the range of values reported for the genus Lactobacillus (32–53 mol%). The peptidoglycan was of the A3α (l-lys–d-glu–l-Ala) type. Physiological, biochemical and genotypic data, as well as results of DNA–DNA hybridization of the genomic DNA with one of the closest phylogenetic relatives, L. rossiae DSM 15814T, indicated that the strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus siliginis sp. nov. is proposed. The type strain is M1-212T (=KCTC 3985T=NBRC 101315T).

scholarly journals Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

2011 ◽  
Vol 61 (7) ◽  
pp. 1606-1611 ◽  
Author(s):  
Enrico Tortoli ◽  
Erik C. Böttger ◽  
Anna Fabio ◽  
Enevold Falsen ◽  
Zoe Gitti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Mycobacterium Simiae

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T  = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.

scholarly journals Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3885-3893 ◽  
Author(s):  
Sandra Baumgardt ◽  
Igor Loncaric ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Established Species

Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).

scholarly journals Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).

scholarly journals Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae

2004 ◽  
Vol 54 (5) ◽  
pp. 1669-1676 ◽  
Author(s):  
Yi-Chueh Lin ◽  
Kazunori Uemori ◽  
Dominique A. de Briel ◽  
Vallapa Arunpairojana ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Hexadecanoic Acid ◽  
16S Rrna Gene Analysis ◽  
Separate Branch ◽  
The Family ◽  
Diamino Acid

Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).

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