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

A new species of the processid shrimp genus Nikoides Paul’son, 1875 (Decapoda: Caridea) from Japan

Zootaxa ◽  
2021 ◽  
Vol 5057 (1) ◽  
pp. 114-126
Author(s):  
TOMOYUKI KOMAI ◽  
ISAO HIRABAYASHI
Keyword(s):  
New Species ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genetic Divergence ◽  
Identification Key ◽  
Rrna Gene ◽  
Characteristic Shape ◽  
Mitochondrial 16S Rrna Gene ◽  
A New Species

A new species of the processid shrimp genus Nikoides Paul’son, 1875, N. subdistalis, is described and illustrated on the basis of five specimens collected from Kushimoto, Wakayama Prefecture, Japan, at depths of 7–12 m. The new species appears most similar to N. maldivensis Borradaile, 1915 among the 10 known congeners, but is notable in the unique dentition of the rostrum and the characteristic shape of the antennular stylocerite. A partial segment of the mitochondrial 16S rRNA gene was sequenced from one of the paratypes of the new species, and genetic divergence among four congeneric taxa, of which three was downloaded from the GenBank database, is shown. An identification key to 11 species of Nikoides, including the new species, is given.  

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 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

scholarly journals Clinical Relevance of the Microbiome in Odontogenic Abscesses

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 916
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Molecular Methods ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Cultural Methods ◽  
Odontogenic Abscess ◽  
Polymicrobial Infections

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

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