scholarly journals Genetic diversity of oral streptococci in the guinea pig as assessed by sequence analysis of the 16S rRNA and groEL genes

2021 ◽  
Author(s):  
Jarosław Król ◽  
Aneta Nowakiewicz ◽  
Alicja Błaszków ◽  
Maria Brodala ◽  
Adrianna Domagała ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Guinea Pig ◽  
Oral Streptococci ◽  
Human Pathogens ◽  
Vast Number ◽  
Gene Sequence Analysis ◽  
Streptococcal Species ◽  
Sequence Similarities ◽  
Rrna Sequences

AbstractThe aim of the present study was to characterize bacteria of the genus Streptococcus isolated from the oral cavity of the guinea pig as well as to assess the significance of these microorganisms as potential veterinary and human pathogens. Sixty-two streptococcal isolates recovered from 27 clinically healthy guinea pigs were examined genotypically by sequencing the 16S rRNA and groEL genes. Among these isolates, only 13 could be assigned to a species described previously (mainly Streptococcus parasanguinis, S. mitis and S. suis), and the majority of the remaining ones differed considerably from the streptococcal species known to date (16S rRNA and groEL sequence similarities were < 97% and < 87%, respectively). Based on 16S rRNA sequences, these unidentified isolates were divided into seven groups (clades), of which clades I through III comprised most of the isolates examined and had also the widest distribution among guinea pig colonies. Upon groEL gene sequence analysis, however, members of the three clades grouped together without forming such distinct clusters. The remaining clades distinguished by 16S rRNA sequencing could also be discerned by the second gene, and they contained only a few isolates often restricted to one or a few animal colonies. The present work reveals that the guinea pig mouth is inhabited by a vast number of phylogenetically diverse, so far unrecognized populations of streptococci, most of them being apparently host-specific genomospecies. On the contrary, S. parasanguinis and S. mitis are also common human commensals and S. suis is a well-recognized zoonotic pathogen.

Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4094-4099 ◽  
Author(s):  
Chun Tao Gu ◽  
Chun Yan Li ◽  
Li Jie Yang ◽  
Gui Cheng Huo
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of Lactobacillus nantensis , Lactobacillus mindensis , Lactobacillus crustorum , Lactobacillus futsaii , Lactobacillus farciminis and Lactobacillus kimchiensis . dnaK gene sequence similarities between S4-3T and Lactobacillus nantensis LMG 23510T, Lactobacillus mindensis LMG 21932T, Lactobacillus crustorum LMG 23699T, Lactobacillus futsaii JCM 17355T and Lactobacillus farciminis LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).

Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1012-1017 ◽  
Author(s):  
Chun Yan Li ◽  
Fen Tian ◽  
Ya Dong Zhao ◽  
Chun Tao Gu
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-stain-positive bacterial strain, 11097T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized using a polyphasic approach, including 16S rRNA gene sequence analysis, phenylalanyl-tRNA synthase (pheS) gene sequence analysis, RNA polymerase α subunit (rpoA) gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11097T was phylogenetically related to Enterococcus devriesei , E. pseudoavium , E. viikkiensis , E. avium , E. malodoratus , E. gilvus and E. raffinosus . Strain 11097T had 99.1–99.9 % 16S rRNA gene sequence similarities, 78.2–83.2 % pheS gene sequence similarities and 93.8–96.6 % rpoA gene sequence similarities with type strains of phylogenetically related species. Based upon polyphasic characterization data obtained in the present study, a novel species of the genus Enterococcus , Enterococcus xiangfangensis sp. nov., is proposed with the type strain 11097T ( = LMG 27495T = NCIMB 14834T).

scholarly journals Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group

2007 ◽  
Vol 57 (8) ◽  
pp. 1846-1850 ◽  
Author(s):  
Li-Ting Wang ◽  
Fwu-Ling Lee ◽  
Chun-Ju Tai ◽  
Hiroaki Kasai
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Phoenix 2: A locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface

2013 ◽  
Vol 167 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Jung Soh ◽  
Xiaoli Dong ◽  
Sean M. Caffrey ◽  
Gerrit Voordouw ◽  
Christoph W. Sensen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Large Scale ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Web Interface ◽  
Rrna Gene Sequence ◽  
Analysis Pipeline ◽  
Gene Sequence Analysis

scholarly journals Micrococcus lactis sp. nov., isolated from dairy industry waste

2011 ◽  
Vol 61 (12) ◽  
pp. 2832-2836 ◽  
Author(s):  
Chittpurna ◽  
Pradip K. Singh ◽  
Dipti Verma ◽  
Anil Kumar Pinnaka ◽  
Shanmugam Mayilraj ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Dairy Industry ◽  
Effluent Treatment ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A Gram-positive, yellow-pigmented, actinobacterial strain, DW152T, was isolated from a dairy industry effluent treatment plant. 16S rRNA gene sequence analysis indicated that strain DW152T exhibited low similarity with many species with validly published names belonging to the genera Micrococcus and Arthrobacter. However, phenotypic properties including chemotaxonomic markers affiliated strain DW152T to the genus Micrococcus. Strain DW152T had ai-C15 : 0 and i-C15 : 0 as major cellular fatty acids, and MK-8(H2) as the major menaquinone. The cell-wall peptidoglycan of strain DW152T had l-lysine as the diagnostic amino acid and the type was A4α. The DNA G+C content of strain DW152T was 68.0 mol%. In 16S rRNA gene sequence analysis, strain DW152T exhibited significant similarity with Micrococcus terreus NBRC 104258T, but the mean value of DNA–DNA relatedness between these strains was only 42.3 %. Moreover, strain DW152T differed in biochemical and chemotaxonomic characteristics from M. terreus and other species of the genus Micrococcus. Based on the above differences, we conclude that strain DW152T should be treated as a novel species of the genus Micrococcus, for which the name Micrococcus lactis sp. nov. is proposed. The type strain of Micrococcus lactis sp. nov. is DW152T ( = MTCC10523T  = DSM 23694T).

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