scholarly journals Isolation, identification and 16S rRNA gene analysis of Yersinia enterocolitica strains isolated from the Gymnocypris przewalskii

2020 ◽  
Author(s):  
Hongjian Zhang ◽  
Qigang Cai ◽  
Jing Zhao ◽  
Yuxia Fan ◽  
Fanlin Kong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yersinia Enterocolitica ◽  
Animal Species ◽  
Lethal Effect ◽  
Trial Registration ◽  
Rrna Gene ◽  
Drug Resistant ◽  
Important Species ◽  
Gymnocypris Przewalskii

Abstract Background: Yersinia enterocolitica is a human-animal-fish-associated infectious diarrhea pathogen that has caused widespread international attention in recent years. Many strains of Yersinia enterocolitica were identified from different animal species, but there is no information reported Yersinia enterocolitica in Gymnocypris przewalskii. The Gymnocypris przewalskii is a very important species in the Qinghai Lake. They were listed in the China' s second-class protected animal species. Preliminary research on the distribution of Yersinia enterocolitica and the drug sensitive fauna test on Gymnocypris przewalskii was a urgent solving problem for which maintain the original ecological symbiotic system and restore Gymnocypris przewalskii resource. In order to solve these issues, we performed this research.Methods: Pathogen of Yersinia enterocolitica of 75 death Gymnocypris przewalskii was isolated by routine isolation culture and identification technique in fishing bank of Xining. At the same time, the drug sensitive fauna test had been detected. At the meantime, 16S rRNA gene of Yersinia enterocolitica was cloned and sequences identified.Results: The results showed that 5 strains Yersinia enterocolitica were obtained, positive ratio was 6.67% (5/75). 1 strains bacteria had lethal effect to mice by pathogenic test. The average drug-resistant of 5 strain Yersinia enterocolitica was 54.29% (38/70) to 14 kinds of antibiotic. The result of 16S rRNA gene of Yersinia enterocolitica identified showed that one piece of 1419 bp specific braid was obtained. The homologies of nucleotide of 16S rRNA were 91%-95% between 15 strains of Yersinia enterocolitica from GenBank by measuring sequence.Conclusion: Yersinia enterocolitica can infect Gymnocypris przewalskii. Some strains cause lethal effect to mice and have drug-resistant effect. The 16S rRNA gene matches 91%-95% with other strains nucleotides download from GenBank and forms a unique branch separated from them.Trial registration: During this research, we didn’t need to apply for trail and have no trial registration number.

scholarly journals Isolation, identification and 16S rRNA gene analysis of Yersinia enterocolitica strains isolated from the Gymnocypris Przewalskii

2020 ◽  
Author(s):  
Hongjian Zhang ◽  
Qigang Cai ◽  
Jing Zhao ◽  
Yuxia Fan ◽  
Fanlin Kong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yersinia Enterocolitica ◽  
Animal Species ◽  
Qinghai Lake ◽  
Rrna Gene ◽  
Drug Resistant ◽  
16S Rrna Gene Analysis ◽  
Important Species ◽  
Gymnocypris Przewalskii

Abstract Background: Yersinia enterocolitica is a human-animal-fish-associated infectious diarrhea pathogen that has caused widespread international attention in recent years. Many strains of Yersinia enterocolitica were identified from different animal species, but there is no information reported Yersinia enterocolitica in Gymnocypris przewalskii . The Gymnocypris przewalskii is a very important species in the Qinghai Lake. They were listed in the China' s second-class protected animal species. Preliminary research on the distribution of Yersinia enterocolitica and the drug sensitive fauna test on Gymnocypris przewalskii was a urgent solving problem for which maintain the original ecological symbiotic system and restore Gymnocypris przewalskii resource. In order to solve these issues, we performed this research.Results: The results showed that 5 strains Yersinia enterocolitica were obtained, positive ratio was 6.67% (5/75). The average drug-resistant of 5 strain Yersinia enterocolitica was 54.29% (38/70) to 14 kinds of antibiotic. The result of 16S rRNA gene of Yersinia enterocolitica identified showed that one piece of 1419 bp specific braid was obtained. The homologies of nucleotide of 16S rRNA were 91%-95% between 15 strains of Yersinia enterocolitica from GenBank by measuring sequence.Conclusion: Yersinia enterocolitica can infect Gymnocypris przewalskii . Some strains have drug-resistant effect. The 16S rRNA gene matches 91%-95% with other strains nucleotides download from GenBank and forms a unique branch separated from them.

scholarly journals 16S rRNA Gene Amplicon Sequence Data from Feces of Five Species of Wild Animals in Japan

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Kasumi Ishida-Kuroki ◽  
Nachiko Takeshita ◽  
Yoshihiro Nitta ◽  
Takehisa Chuma ◽  
Ken Maeda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Animal Species ◽  
Sequence Data ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Wild Animals ◽  
Wild Boars ◽  
Raccoon Dogs

ABSTRACT We report 16S rRNA amplicon sequence data from feces from 58 wild boars, 60 feral raccoons, 9 wild Japanese badgers, 21 wild masked palm civets, and 8 wild raccoon dogs in Japan. The predominant bacterial taxa in the fecal microbiota were similar in part but varied among the animal species.

scholarly journals Cutibacterium modestum and “Propionibacterium humerusii” represent the same species that is commonly misidentified as Cutibacterium acnes

2021 ◽  
Author(s):  
Daniel Goldenberger ◽  
Kirstine K. Søgaard ◽  
Aline Cuénod ◽  
Helena Seth-Smith ◽  
Daniel de Menezes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Correct Identification ◽  
Skin Microbiome ◽  
Isolation And Identification ◽  
Important Species ◽  
Cutibacterium Acnes ◽  
The 16S Rrna Gene

AbstractCutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12T (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named “Propionibacterium humerusii”. Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning “P. humerusii”. The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.

scholarly journals dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus

2007 ◽  
Vol 57 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Mohammad Monir Shah ◽  
Hirotoshi Iihara ◽  
Makiko Noda ◽  
Sun Xiao Song ◽  
Pham Hong Nhung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Important Species ◽  
Conserved Gene ◽  
Mean Similarity

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA–DNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.

scholarly journals 16S rRNA Gene Amplicon Sequencing of Gut Microbiota from Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China

2021 ◽  
Vol 10 (23) ◽  
Author(s):  
Fayan Wang ◽  
Yu Liu ◽  
Guangxin Li ◽  
Xi Yang ◽  
Qiang Gao
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Qinghai Lake ◽  
Second Grade ◽  
Rrna Gene ◽  
Content Type ◽  
Gymnocypris Przewalskii ◽  
State Protection

Naked carp ( Gymnocypris przewalskii ) is a second-grade animal under state protection of China. We report 16S rRNA gene amplicon analysis of the gut microbiota of Gymnocypris przewalskii . The three most abundant phyla are Tenericutes , Proteobacteria , and Fusobacteria , and the six most abundant genera are Aeromonas , Clostridium , Cetobacterium , Shewanella , Prochlorococcus , and Vibrio .

Yersinia enterocolitica 16S rRNA gene types belong to the same genospecies but form three homology groups

2000 ◽  
Vol 290 (1) ◽  
pp. 61-64 ◽  
Author(s):  
Heinrich Neubauer ◽  
Stojanka Aleksic ◽  
Andreas Hensel ◽  
Ernst-Jürgen Finke ◽  
Hermann Meyer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yersinia Enterocolitica ◽  
Rrna Gene ◽  
Homology Groups

scholarly journals 8.Animal Species Identification through High Resolution Melting Real Time PCR (HRM) of the Mitochondrial 16S rRNA Gene

2016 ◽  
Vol 16 (2) ◽  
pp. 415-424 ◽  
Author(s):  
Pitchayanipa Klomtong ◽  
Yupin Phasuk ◽  
Monchai Duangjinda
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Identification ◽  
Animal Species ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Universal Primer ◽  
Pcr Product ◽  
Mitochondrial 16S Rrna Gene

Abstract Animal species identification has received growing attention, regarding genetic diversity and food traceability. The objective of this study is to apply a universal primer of part of the mitochondrial 16S rRNA gene analysis using the PCR-RFLP and HRM methods for identification of species origin in cattle, chicken, horse, sheep, pig, buffalo, and goat. PCR product size was 512 bp. The PCR product of 16S rRNA was digested with two restriction enzymes (BclI and MseI); sufficient to easily generate analyzable species-specific restriction profiles that could distinguish the unambiguity of all targeted species. The HRM method successfully identified all species by shape of melting temperature, and proved to be of higher resolution, and a more cost effective, alternative method compared with other identification techniques.

Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene

2009 ◽  
Vol 11 ◽  
pp. S449-S450 ◽  
Author(s):  
Tomoaki Mitani ◽  
Atsushi Akane ◽  
Takuma Tokiyasu ◽  
Sumitaka Yoshimura ◽  
Yutaka Okii ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Animal Species ◽  
Rrna Gene ◽  
Mitochondrial 16S Rrna Gene

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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