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.

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 GENETIC DIVERGENCE AND GEOGRAPHIC DISTRIBUTION OF FROGS IN GENUS FEJERVARYA FROM INDONESIA INFERRED FROM MITOCHONDRIAL 16S rRNA GENE ANALYSIS

TREUBIA ◽  
2014 ◽  
Vol 41 ◽  
pp. 1 ◽  
Author(s):  
Nia Kurniawan ◽  
Tjong Hon Djong ◽  
Tesri Maideliza ◽  
Amir Hamidy ◽  
Mahmudul Hasan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Geographic Distribution ◽  
Genetic Divergence ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Indonesian Archipelago ◽  
Average Sequence Divergence ◽  
Mitochondrial 16S Rrna Gene

The Indonesian archipelago is an ideal setting for the study of speciation and biogeography. This archipelago is divided into three island groups based on zoogeography: Sundaland, Wallaceaand the Australian region. In this paper we used frogs in genus Fejervarya (Bolkay) to study biogeography and examine patterns of gene flow across proposed zoogeographic boundaries. Severalmolecular studies on Fejervarya species from Indonesia have been carried out, but comparative studies among members of the genus Fejervarya have yet to be performed. In order to elucidate genetic divergence and geographic distribution of these frogs, we conducted a molecular analysis of the mitochondrial 16S rRNA gene using 179 frogs from five Fejervarya species. In total we collected from 32 localities in Sumatra, Kalimantan (Indonesian part of Borneo), Java, Bali, Sulawesi and Lesser Sunda Islands in Indonesia. Molecular phylogenetic analysis recovered 35 haplotypes and showed that frogs in the genus Fejervarya were divided into two well-supported clades. The first group were of three species, F. limnocharis, F. iskandari and F. cf. verruculosa and the other group clade consisted of Fejervarya cancrivora and Fejervarya sp. (Sulawesi-type). The average sequence divergence among these four species ranged from 1.09 to 16.03% (mean = 11.29±2.83%). The present results clearly show that there are five Fejervarya species in the Indonesian archipelago. Fejervarya limnocharis and F. cancrivora are widely distributed and sympatric in Sumatra, Borneo and Java. Fejervarya iskandari is not endemic to Java and also occurs in the Lesser Sundas. Fejervarya cf. verruculosa and Fejervarya sp. (Sulawesi-type) are endemic to Lesser Sunda and Sulawesi Island, respectively. Key words: Fejervarya, genetic divergence, geographic distribution, 16S rRNA gene

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

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

2011 ◽  
Vol 61 (2) ◽  
pp. 400-412 ◽  
Author(s):  
Xianguang Guo ◽  
Xin Dai ◽  
Dali Chen ◽  
Theodore J. Papenfuss ◽  
Natalia B. Ananjeva ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Divergence Times ◽  
Rrna Gene ◽  
Mitochondrial 16S Rrna Gene
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