scholarly journals Molecular species identification of red shrimp (Crustacea: Decapoda: Barbouriidae) from Tanjung Sanjangan (Tolitoli, Central Sulawesi) through 16S rRNA mitochondrial gene

2020 ◽  
Author(s):  
Retno Sari ◽  
Tuty Arisuryanti
Keyword(s):  
16S Rrna ◽  
Species Identification ◽  
Molecular Species ◽  
Mitochondrial Gene ◽  
Molecular Species Identification ◽  
Central Sulawesi

scholarly journals Antimicrobial susceptibility and molecular species identification of clinical carbapenem-resistant bacteria

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
MAULIN INGGRAINI ◽  
SITI NURFAJRIAH ◽  
JEPRI AGUNG PRIYANTO ◽  
Noor Andryan Ilsan
Keyword(s):  
16S Rrna ◽  
Species Identification ◽  
Antimicrobial Susceptibility ◽  
Molecular Species ◽  
Resistant Bacteria ◽  
Drug Resistant ◽  
E Coli ◽  
Molecular Species Identification ◽  
Carbapenem Resistant ◽  
Insight Into

Abstract. Inggraini M, Nurfajriah S, Priyanto JA, Ilsan NA. 2021. Antimicrobial susceptibility and molecular species identification of clinical carbapenem-resistant bacteria. Biodiversitas 22: 555-562. Antibiotic is the first option treatment for infectious diseases both in human and animal. However, the excessive usage and misuse of antibiotics have driven antibacterial resistances worldwide and the increasing case of antibiotic resistance leads to limited options for treatment. This study aimed to observe antimicrobial susceptibility and molecular identification of carbapenem-resistant human clinical bacteria. A total of nine isolates in this study were collected in 2020 from a teaching hospital in Indonesia. All isolates were originated from various human clinical specimens, including urine, blood, pus, and sputum. Identification using 16s rRNA-based showed that these isolates were closely related to Klebsiella pneumoniae (1/9), A. baumannii (5/9), Escherichia coli (2/9), and Lysinibacillus fusiformis (1/9). According to minimum inhibitory concentration using Vitek Automated Machine, four isolates of multi-drug resistant (MDR) bacteria were found. In contrast, five of them were categorized as extensively-drug resistant (XDR). Interestingly, all of the XDR isolates belonged to A. baumannii. These isolates were resistant to at least seven different antimicrobial classes. A comparison of partial 16s rRNA showed two E. coli had similar variance. While in A. baumannii isolates, we found one of five isolates had a different variance sequence, which suggests different clonality among this species. This study gives an insight into the prevalence of carbapenem-resistant bacteria with XDR criteria in Indonesia.

scholarly journals Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Lucas Blattner ◽  
Reinhard Gerecke ◽  
Stefanie von Fumetti
Keyword(s):  
Species Identification ◽  
Molecular Species ◽  
Species Delimitation ◽  
Mite Species ◽  
Water Mites ◽  
Water Mite ◽  
Barcoding Gap ◽  
Molecular Species Identification ◽  
True Diversity ◽  
Genetic Species

Abstract Background Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library. Methods We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels. Results A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6–6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels. Conclusions Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.

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