scholarly journals Biomolecular characterization and efficacy evaluation of pathogen Erwinia tracheiphila against plant oils

2021 ◽  
Vol 42 (4) ◽  
pp. 988-994
Author(s):  
S. Pattanayak ◽  
◽  
G. Biswal ◽  
S. Das ◽  
◽  
...  
Keyword(s):  
16S Rrna ◽  
Disease Severity ◽  
Cucurbita Pepo ◽  
Molecular Detection ◽  
Biochemical Characterization ◽  
Mustard Oil ◽  
Plant Oils ◽  
Clove Oil ◽  
Erwinia Tracheiphila ◽  
Management Approaches

Aim: To investigate patho-dyanamics of Erwinia tracheiphila on Cucurbita pepo with biochemical, molecular characterization and eco-friendly management approaches. Methodology: Variability study of Erwinia tracheiphila was done by collecting the isolates from different places in Odisha. Disease severity was calculated and analyzed from 2016-18 to predict trend of emergence and disease progress. Molecular detection of pathogen was done through 16S rRNA sequencing. Biochemical characterization and identification of pathogenic nature of Erwinia tracheiphila was performed through Ortho-Nitrophenyl β-Galactoside, Esculin hydrolysis, Citrate and Malonate utilization in the presence of different carbohydrate molecules. Efficacy of eight different plant oils were tested by in-vitro inhibition zone (IVIZ) assay against Erwinia tracheiphila as eco-friendly management approaches. Results: Analysis of disease severity data from 2016-18 ranged between 29% to 33%. Molecular detection of causal pathogen was further confirmed by 16S rRNA region sequencing with 99% identity of NCBI-GenBank published Erwinia tracheiphila (MK356446 and MK356441) database and phylogenetic analysis. The results of IVIZT revealed that the clove oil treatment showed maximum inhibitory effect on the growth of Erwinia tracheiphila followed by mustard oil and neem oil. Sesamum oil showed the lowest efficacy against Erwinia tracheiphila. Optimum temperature range between 25-28°C, 80-85% relative humidity and 150-180 mm average rainfall triggered the disease progress and turned to be a severe one under experimental agro-climatic situation. Interpretation: Biochemical characterization and molecular detection of causal isolate confirmed the pathogen as Erwinia tracheiphila, causing wilt disease of Cucurbita pepo. This study also revealed the potential efficacy of clove oil and mustard oil against Erwinia tracheiphila as compared to other selected plant oils.

scholarly journals MOLECULAR IDENTIFICATION AND ANTIBIOGRAM PROFILES OF ESCHERICHIA COLI ISOLATED FROM APPARENTLY HEALTHY AND DIARRHEIC GOATS

2017 ◽  
Vol 14 (2) ◽  
pp. 203-208 ◽  
Author(s):  
F. Begum ◽  
M. M. Islam ◽  
M. Sohidullah ◽  
S. M. L. Kabir ◽  
M. Islam ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Teaching Hospital ◽  
Molecular Detection ◽  
Biochemical Characterization ◽  
Rrna Gene ◽  
E Coli ◽  
Goat Farm ◽  
Apparently Healthy

The present study was designed for the cultural, biochemical characterization and molecular detection of E. coli from apparently healthy and diarrheic goats in and around BAU campus including their antibiogram study. A total of 50 fecal samples were collected among which 13 originated from diarrheic goat and 37 from apparently healthy goats. Out of 50 samples, 35 were found positive for E. coli i.e., overall 70% occurrence. Occurrences of E. coli from diarrheic and apparently healthy goats were 92% and 62% respectively. Occurrences were 60%, 80% and 70% in case of BAU Goat Farm, Veterinary Teaching Hospital and Boyra respectively. On age basis 93%, 54%, 66% and 54% samples originated from 6 months, 7-12 months, 13-18 months and 19 months aged goats were found positive respectively. Occurrences of E. coli on the basis of sex were 78% for male and 62% for female. In case of breed, the occurrences were 69% in Black Bengal and 100% in for Jamunapari. Molecular detection was done by PCR and 13 out of 20 isolates tested gave the bands at the 585 bp specific for E. coli 16S rRNA gene. All the isolates (100%) were found sensitive to ciprofloxacin and norfloxacin; 100% and 35% were intermediately resistant to tetracycline and gentamicin respectively and 25% isolates were resistant to streptomycin. Ciprofloxacin and norfloxacin were found to be the best choice of antibiotics for the treatment of colibacillosis in goats in the study area.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Molecular characterisation of Leptospira strains in Pakistan

2016 ◽  
Vol 60 (4) ◽  
pp. 417-421
Author(s):  
Muhammad Luqman Sohail ◽  
Muhammad Sarwar Khan ◽  
Muhammad Avais ◽  
Muhammad Yasir Zahoor ◽  
Irfan Khattak ◽  
...  
Keyword(s):  
16S Rrna ◽  
Animal Species ◽  
Molecular Detection ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Intermediate Species ◽  
Specific Primers ◽  
Pathogenic Leptospira ◽  
Wide Range ◽  
Serological Studies

Abstract Introduction: Leptospirosis affects a wide range of mammals, humans, and even a few poikilothermic animal species. In Pakistan, serological studies of equine leptospirosis have reported a prevalence of over 40%, but no study has ever been conducted towards molecular detection of Leptospira in horses. Material and Methods: Blood samples from 128 horses were screened using ELISA and 41 positive samples were examined for the presence of leptospiral DNA using specific primers for 16S rRNA gene. Results: Out of 41 tested samples, 20 samples were found to be PCR-positive, revealing a fragment of 306 bp after gel electrophoresis. Sequencing and phylogenetic analysis of positive samples revealed circulation of pathogenic Leptospira spp. in Pakistani horses. No evidence of circulation of intermediate species was found in this study. Conclusion: This study reports the first molecular evidence of equine leptospirosis in Pakistan and lays ground for further research in this area. It also confirms the efficiency of 16S rRNA for the diagnosis of equine leptospirosis.

scholarly journals A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1003
Author(s):  
Jacky Flipse ◽  
Birgitta Duim ◽  
Janny A. Wallinga ◽  
Laetitia R. H. de Wijkerslooth ◽  
Linda van der Graaf-van Bloois ◽  
...  
Keyword(s):  
16S Rrna ◽  
Clinical Condition ◽  
Molecular Detection ◽  
Chronic Diarrhea ◽  
Immunocompromised Patient ◽  
Continuous Exposure ◽  
Persistent Diarrhea ◽  
Colon Biopsy ◽  
Stool Samples ◽  
Campylobacter Species

A man with a well-controlled HIV infection, previously diagnosed with lymphogranuloma venereum and treated for Hodgkin’s lymphoma, was suffering from chronic diarrhea. He travelled to Indonesia in the month prior to the start of complaints. Over a 15-month period, sequences related to Campylobactertroglodytis/upsaliensis, C. pinnepediorum/mucosalis/concisus and C. hominis were detected by 16S rRNA qPCR-based assays in various stool samples and in a colon biopsy. Culture revealed the first isolation of “candidatus Campylobacter infans”, a species identified recently by molecular methods only. The patient was treated with azithromycin, ciprofloxacin and tetracycline. To identify potential continuous exposure of the patient to Campylobacter, stool samples of the partner and the cat of the patient were analyzed and C. pinnepediorum/mucosalis/concisus and C. helveticus, respectively, were detected. The diversity in detected species in this immunocompromised patient with a lack of repeatedly consistent findings resulted in the conclusion that not any of the Campylobacter species was the primary cause of the clinical condition. This study shows the challenges in detection and interpretation of diagnostic results regarding Campylobacter.

Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2841-2847 ◽  
Author(s):  
S. P. Glaeser ◽  
H. Galatis ◽  
K. Martin ◽  
P. Kämpfer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Biochemical Characterization ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hirudo Verbana

A Gram-staining-negative, non-endospore-forming, yellow-pigmented strain (E89T) was isolated from the skin of the medical leech Hirudo verbana obtained from a leech farm located in Biebertal, Germany. 16S rRNA gene sequencing analysis showed that the isolate was grouped in the genus Flavobacterium . Strain E89T was most closely related to Flavobacterium chilense LM-09-FpT (98.2 %), Flavobacterium chungangense CJ7T (98.1 %), and Flavobacterium oncorhynchi 631-08T (98.1 %). 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were ≤97.4 %. A menaquinone of the type MK-6 was found to be the predominant respiratory quinone and the polar lipid profile consisted of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids, one unknown phospholipid and two unknown lipids. The fatty acid profile was composed of iso-C15 : 0, C15 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) found in major amounts and several hydroxylated fatty acids in smaller amounts, among them iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. All these data support the allocation of the isolate in the genus Flavobacterium . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. Based on these data, strain E89T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium cutihirudinis sp. nov. is proposed. The type strain is E89T ( = DSM 25795T = LMG 26922T = CIP 110374T).

scholarly journals Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia

2020 ◽  
Vol 8 (12) ◽  
pp. 1967
Author(s):  
Tamara N. Nazina ◽  
Salimat K. Bidzhieva ◽  
Denis S. Grouzdev ◽  
Diyana S. Sokolova ◽  
Tatyana P. Tourova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Petroleum Reservoir ◽  
Ph Range ◽  
The 16S Rrna Gene

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.

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