scholarly journals Enterobacterial Repetitive Intergenic Consensus (ERIC) as a tool for genetic characterisation of bacterial isolates in Nigeria

2020 ◽  
Vol 37 (1) ◽  
pp. 122-128
Author(s):  
K. Otokunefor ◽  
C.J. Ogugbue ◽  
B.U. Fajoyomi
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Pcr Analysis ◽  
Bacterial Identification ◽  
Bacterial Isolates ◽  
Enterobacterial Repetitive Intergenic Consensus ◽  
16S Rrna Sequence ◽  
Genetic Characterisation ◽  
Polymerase Chain ◽  
Identification Tool

Genetic characterisation as a tool for identification of bacterial isolates in Nigeria has been on the increase in recent years, and the 16s rRNA typing has been a preferred method. Due to cost limitations, there is a need to explore other genetic options. Enterobacterial Repetitive Intergenic Consensus (ERIC) polymerase chain reaction (PCR) analysis is a PCR- only based system which offers the advantage of reduced cost. This study set out to explore the use of ERIC-PCR in genetic characterisation of some selected bacterial isolates from Nigeria and compare it with genetic characterisation using 16s rRNA sequence typing. ERIC-PCR and 16s rRNA typing were carried out on 15 isolates following previously described protocols. Using 16s rRNA typing, thirteen different bacterial species were identified of which majority (85.7%) were Gram negative, with 57.1% belonging to the Enterobacteriaceae family. Using ERIC-PCR, only 13 of the 15 isolates (86.7%) could be typed, resulting in the identification of the 13 different types. ERIC-PCR was able to accurately differentiate between two members of the Proteus species, as well as identify the organisms as similar based on the banding pattern. The results show that ERIC-PCR may play a role as a bacterial identification tool but this role might be more suited to differentiating closely related members of a genus or typing within species rather than general bacterial identification. Keywords: Genetic characterisation, 16s rRNA, ERIC-PCR, Nigeria

scholarly journals Detection of novel strains genetically related to Anaplasma platys in Tunisian one-humped camels (Camelus dromedarius)

2015 ◽  
Vol 9 (10) ◽  
pp. 1117-1125 ◽  
Author(s):  
Hanène Belkahia ◽  
Mourad Ben Said ◽  
Lotfi Sayahi ◽  
Alberto Alberti ◽  
Lilia Messadi
Keyword(s):  
Polymerase Chain Reaction ◽  
16S Rrna ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Chain Reaction ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Nested Polymerase Chain Reaction ◽  
16S Rrna Sequence Analysis ◽  
Polymerase Chain

Introduction: Little information is currently available regarding the presence of Anaplasma species in North African dromedaries. To fill this gap in knowledge, the prevalence, risk factors, and genetic diversity of Anaplasma species were investigated in Tunisian dromedary camels. Methodology: A total of 226 camels from three different bioclimatic areas were sampled and tested for the presence of Anaplasma species by quantitative polymerase chain reaction (qPCR) and nested polymerase chain reaction (nPCR) assays. Detected Anaplasma strains were characterized by 16S rRNA sequence analysis. Results: Overall infection rate of Anaplasma spp. was 17.7%, and was significantly higher in females. Notably, A. marginale, A. centrale, A. bovis, and A. phagocytophilum were not detected. Animals were severely infested by three tick species belonging to the genus Hyalomma (H. dromedarii, H. impeltatum, and H. excavatum). Alignment, similarity comparison, and phylogenetic analysis of the 16S rRNA sequence variants obtained in this study suggest that Tunisian dromedaries are infected by more than one novel Anaplasma strain genetically related to A. platys. Conclusions: This study reports the presence of novel Anaplasma sp. strains genetically related to A. platys in dromedaries from various bioclimatic areas of Tunisia. Findings raise new concerns about the specificity of the direct and indirect diagnostic tests routinely used to detect different Anaplasma species in ruminants and provide useful molecular information to elucidate the evolutionary history of bacterial species related to A. platys.

scholarly journals ISOLATION, IDENTIFICATION AND SENSITIVITY OF AMILOLITIC BACTERIA FROM MANGROVE ECOSYSTEM SEDIMENT IN PURNAMA MARINE STATION DUMAI ON THE PATHOGENIC BACTERIA

2020 ◽  
Vol 2 (3) ◽  
pp. 257-266
Author(s):  
Lamtiur Rotua Silitonga ◽  
Nursyirwani Nursyirwani ◽  
Irwan Effendi
Keyword(s):  
16S Rrna ◽  
Pathogenic Bacteria ◽  
Dna Analysis ◽  
Bacterial Species ◽  
Inhibition Zone ◽  
Bacterial Isolates ◽  
16S Rrna Sequence ◽  
Inhibition Zone Diameter ◽  
Zone Diameter ◽  
Marine Station

Litter from the weathering of dead mangrove stems and leaves contains a lot of starch which has potential to be degraded by amylolytic bacteria into simple compounds with the help of the amylase enzyme. Amylolytic bacteria are bacteria that hydrolyze starch into simpler compounds namely glucose with the help of the amylase enzyme. This study aims to 1) isolate, identify and test sensitivity of amylolytic bacterial isolates found at the Purnama Dumai Marine Station, 2) the ability of amylolytic bacterial isolates to inhibit the growth of pathogenic bacteria (Escherichia coli, Pseudomonas aeruginosa and Vibrio alginolyticus) and 3) to determine the of amylolytic bacterial species by 16S rRNA sequence analysis. The results showed 10 bacterial isolates (TR 2, TR 6, TR 7, TR 9, TR 11, TR 13, TR 15, TR 16, TR 18 and TR 20) were able to inhibit the growth of pathogenic bacteria (E.coli, P.aeruginosa and V.alginolyticus). The sensitivity test of isolate TR 20 against E.coli was categorized into weak with inhibition zone diameter of 4.65 mm. Sensitivity of isolate TR 6 against P.aeruginosa was categorized into medium with inhibition zone diameter of 5.22 mm. Then sensitivity of isolate TR 11 against V.algynolyticus was categorized into medium with inhibition zone diameter of 5.55 mm. DNA analysis using 16S rRNA method and BLAST analysis showed similarity of each isolate. Isolate TR 6 was similar to Bacillus paramycoides strain MCCC 1A04098, isolate TR 11 was in a group of Enterobacter cloacae strain ATCC 13047 and TR 20 was in a group of Vibrio harveyi strains of NBRC 15634.

Streptomyces rhizophilus Causes Potato Common Scab Disease

Plant Disease ◽  
2021 ◽  
Author(s):  
Qi Wei ◽  
Jie Li ◽  
Shuai Yang ◽  
Wenzhong Wang ◽  
Fanxiang Min ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Common Scab ◽  
Bacterial Species ◽  
Economic Losses ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Heilongjiang Province ◽  
Epidemic Disease ◽  
Genus Streptomyces

Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.

Group-specific differentiation of Rhizobium from clover species by PCR amplification of 23S rDNA sequences

1998 ◽  
Vol 44 (11) ◽  
pp. 1102-1105
Author(s):  
Mesfin Tesfaye ◽  
F Brian Holl
Keyword(s):  
Root Nodule ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Dna Amplification ◽  
Specific Detection ◽  
Rdna Sequences ◽  
Rhizobium Spp ◽  
Polymerase Chain ◽  
Inoculation Group ◽  
Identification Tool

Two 20-bp primers that provide group-specific detection of Rhizobium spp. by polymerase chain reaction (PCR) have been used to differentiate strains that belong to different effectiveness groups within the Rhizobium-Trifolium cross-inoculation group. The target for DNA amplification was a 370-bp fragment of the 23S rDNA region. Analysis of additional root-nodule forming, as well as root-associated bacterial species by PCR-primer assay revealed that variability within this 20-bp segment of the 23S rDNA region may be widespread and provide an effective identification tool. Our data suggest that strains of Rhizobium isolated from the perennial clover Trifolium semipilosum may be phylogenetically more closely related to Rhizobium etli.Key words: Rhizobium, Trifolium, detection, PCR, rDNA.

scholarly journals Polymerase Chain Reaction Multiplication for the Detection of Bacterial Isolates Causing Neonatal Sepsis

2020 ◽  
Vol 8 (A) ◽  
pp. 623-628
Author(s):  
Utari Hartati Suryani ◽  
Andri Rezano ◽  
Yunia Sribudiani
Keyword(s):  
Polymerase Chain Reaction ◽  
Neonatal Sepsis ◽  
Pcr Analysis ◽  
Local Alignment ◽  
Bacterial Isolates ◽  
Chain Reaction ◽  
E Coli ◽  
Initial Design ◽  
Pcr Multiplex ◽  
Polymerase Chain

BACKGROUND: Neonatal sepsis is a clinical syndrome caused by the presence of bacteria in the blood accompanied by symptoms and systemic signs of infection that occurs in the first 4 weeks of life after birth. The process of identifying pathogenic microorganisms is essential in determining the clinical condition in neonatal sepsis. AIM: The study was aimed to develop a multiplex polymerase chain reaction (PCR) method to identify bacterial isolates that cause neonatal sepsis in Indonesia with the main target of optimization of an initial design and PCR optimization. METHODS: This research is an explorative in vitro study for the optimization of an initial design and PCR methods for the detection of the main bacteria that cause sepsis neonatorum in Indonesia, namely, bacteria Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Pseudomonas aeruginosa. The study was conducted at the Biomolecular Laboratory of the Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia. RESULTS: Sequencing carried out and continued with Basic Local Alignment Search Tool (BLAST) sequencing results, it appears that the PCR product that has been produced conforms with the optimization targets that were previously set when doing the primer design. The level of homology found in all four species based on the results of BLAST in a sequence is as follows: K. pneumoniae 94%, P. aeruginosa 99%, E. cloacae 100%, and E. coli 100%. CONCLUSION: PCR multiplex method using design primers and conventional PCR analysis methods (using agarose gel) can be used to detect four species of bacteria that cause neonatal sepsis, namely, K. pneumoniae, P. aeruginosa, E. cloacae, and E. coli.

Genome-based reclassification of Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii as later heterotypic synonyms of Caldicellulosiruptor acetigenus

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Neeli Habib ◽  
Manik Prabhu Narsing Rao ◽  
Min Xiao ◽  
Sohail Ahmad Jan ◽  
Wen-Jun Li
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Relationship Of

The present study was carried out to re-clarify the taxonomic relationship of Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii . The 16S rRNA sequence similarities between these species of the genus Caldicellulosiruptor were above the threshold values (98.65%) for bacterial species delineation. Similarly, the digital DNA–DNA hybridization and average nucleotide and amino acid identity values were greater than the thresholds for bacterial species delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii clade together. The results of our analysis indicated that these three taxa are conspecific. Therefore, Caldicellulosiruptor lactoaceticus Mladenovska et al. 1997 and Caldicellulosiruptor kristjanssonii Bredholt et al. 1999 should be reclassified as later heterotypic synonyms of Caldicellulosiruptor acetigenus (Nielsen et al. 1994) Onyenwoke et al. 2006.

scholarly journals Isolation and Identification of Protease Enzyme Producing Bacteria from Fermentation of Gonad Sea Urchin (Echinothrix calamaris)

2019 ◽  
Vol 23 (4) ◽  
pp. 187
Author(s):  
Siani La Jamaludin ◽  
Johanis Fritzgal Rehena ◽  
Cecilia Anna Seumahu ◽  
Dominggus Rumahlatu
Keyword(s):  
16S Rrna ◽  
Sea Urchin ◽  
Enzyme Characterization ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Isolation And Identification ◽  
16S Rrna Sequence ◽  
Spontaneous Fermentation ◽  
Fermentation Products ◽  
Protease Enzyme

Bekasang of gonad sea urchin is one of the traditional fermentation products which generally involves microorganism spontaneous fermentation. Fermented paste products have a long shelf life and are processed quite easily using protease enzymes. Good exploration of producing protease from bakasang is needed to obtain the protease enzyme-producing microorganism with different characters. The method used in this research is screening with clear zone, measuring the activity of crude extract of protease enzyme characterization of bacteria through gram staining. Identification of potential microorganisms through 16S rRNA sequence. The results showed that there were eight isolates of protease enzyme-producing bacteria (G1, G2, G3, G4, G5, G6, G7, and G8) indicated by clear zones around single-colonic bacterial streaks. Only five bacterial isolates (G1, G4, G6, G7, and G8) were tested for the enzyme activity. These isolates have characteristics of positive gram bacteria. The interpretation of the results of molecular analysis using PCR and BLASTN sequences of 16S rRNA gene from five bacterial isolates, showed the identity of bacteria as: G1 was Staphylococcus piscifermentans strain CIP103958 with 99% similarity; Isolate G4 was Staphylococcus saprophyticus strain ATCC 15305 with 99% similarity; Isolate G6 was Staphylococcus condimenti F-2 strain with 99% similarity; Isolate G7 was Bacillus amyloliquefaciens subsp. plantarum strain FZB42 with 99% similarity; And G8 isolates was Lactobacillus plantarum strain JCM 1149 with 99% similarity.

scholarly journals Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India

2006 ◽  
Vol 56 (7) ◽  
pp. 1677-1680 ◽  
Author(s):  
Anil K. Tripathi ◽  
Subhash C. Verma ◽  
Soumitra Paul Chowdhury ◽  
Michael Lebuhn ◽  
Andreas Gattinger ◽  
...  
Keyword(s):  
16S Rrna ◽  
Deep Water ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Northern India ◽  
Gene Sequence Analysis ◽  
Genotypic Characteristics

A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195T was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96.8 %) to strain MTCC 4195T was shown by Ochrobactrum gallinifaecis DSM 15295T. Strain MTCC 4195T utilized γ-hydroxybutyric acid, adonitol, d-glucosaminic acid and arabinose as carbon sources, but failed to use gentiobiose or citrate. The cell-wall fatty acids of strain MTCC 4195T were characterized by the presence of a relatively large proportion of C18 : 1 ω7c and a relative small proportion of C16 : 0 in comparison with Ochrobactrum species. DNA–DNA relatedness studies showed less than 52 % binding with the DNAs of type strains of other species of the genus Ochrobactrum. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, the novel species Ochrobactrum oryzae sp. nov. is proposed, with MTCC 4195T (=DSM 17471T) as the type strain.

scholarly journals Study of an arsenic metabolizing bacteria from arsenic contaminated soil of Chandpur district, Bangladesh

2019 ◽  
Vol 8 (1) ◽  
pp. 57-65
Author(s):  
Roksana Khanam ◽  
Ripa Moni ◽  
Md Zahidul Islam ◽  
Md Morsaline Billah ◽  
Umme Salma Zohora ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Bacterial Species ◽  
Toxic Metal ◽  
Extracellular Enzyme ◽  
Bacterial Isolates ◽  
Toxic Heavy Metals ◽  
16S Rrna Sequence ◽  
Yeast Extract Mannitol ◽  
16S Rrna Sequence Analysis

Arsenic is a toxic metal found as inorganic oxyanion arsenate As(V) and arsenite As (III) species. The disposal of toxic heavy metals such as arsenic poses high risk to environment. The present study was undertaken to isolate arsenic-metabolizing bacteria from arsenic contaminated soil of Chandpur district, which is one of the most arsenic contaminated area in Bangladesh and later these bacteria were screened for their ability to metabolize arsenate. Out of ninety eight isolates, ten were found to be capable of metabolizing arsenic in Yeast Extract Mannitol (YEM) medium containing 2 mM arsenate at 37ºC. One of the bacterial isolates designated as I-25 was found to produce an extracellular enzyme which can reduce As(V) into As(III) and able to grow in presence of up to 500 mM arsenate. Subsequent molecular identification of this enzyme producing bacterial isolate using 16s rRNA sequence analysis was correlated with previously identified isolate as Bacillus aryabhatti. Further characterization of the enzyme showed that optimum pH of the extracellular enzyme by the bacterial species was 7 and optimum temperature for the enzyme activity was 60ºC. The bacterial isolates can be exploited for the study of possible bioremediation of arsenic contamination. Jahangirnagar University J. Biol. Sci. 8(1): 57-65, 2019 (June)

Sign in / Sign up

Export Citation Format

Share Document