scholarly journals Characterization of Novel Bovine Gastrointestinal TractTreponemaIsolates and Comparison with Bovine Digital Dermatitis Treponemes

2010 ◽  
Vol 77 (1) ◽  
pp. 138-147 ◽  
Author(s):  
Nicholas J. Evans ◽  
Jennifer M. Brown ◽  
Richard D. Murray ◽  
Brian Getty ◽  
Richard J. Birtles ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phenotypic Diversity ◽  
Rrna Gene ◽  
Putative Virulence Factor ◽  
Gi Tract ◽  
Digital Dermatitis ◽  
Degenerate Pcr ◽  
Gene Encoding ◽  
Rrna Sequences

ABSTRACTThis study aimed to isolate and characterize treponemes present in the bovine gastrointestinal (GI) tract and compare them with bovine digital dermatitis (BDD) treponemes. Seven spirochete isolates were obtained from the bovine GI tract, which, on the basis of 16S rRNA gene comparisons, clustered within the genusTreponemaas four novel phylotypes. One phylotype was isolated from several different GI tract regions, including the omasum, colon, rumen, and rectum. These four phylotypes could be divided into two phylotype pairs that clustered closest with each other and then with different, previously reported rumen treponemes. The treponemes displayed great genotypic and phenotypic diversity between phylotypes and differed considerably from named treponeme species and those recently reported by metagenomic studies of the bovine GI tract. Phylogenetic inference, based on comparisons of 16S rRNA sequences from only bovine treponemes, suggested a marked divergence between two important groups. The dendrogram formed two major clusters, with one cluster containing GI tract treponemes and the other containing BDD treponemes. This division among the bovine treponemes is likely the result of adaptation to different niches. To further differentiate the bovine GI and BDD strains, we designed a degenerate PCR for a gene encoding a putative virulence factor,tlyC, which gave a positive reaction only for treponemes from the BDD cluster.

scholarly journals Characterization Physiology and Molecular Bacteria Symbiont- Entomopathogenic Nematodes based of Gene Sequences Encoding the 16S rRNA District of Bromo Probolinggo

2017 ◽  
Vol 18 (1) ◽  
pp. 39
Author(s):  
Bagus Setiawan ◽  
Didik Sulistyanto ◽  
Kartika Senjarini
Keyword(s):  
16S Rrna ◽  
Entomopathogenic Nematodes ◽  
Phenotypic Characterization ◽  
Bacterial Symbionts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Gene Encoding ◽  
Bacillus Strain ◽  
Rrna Sequences

This study aims to identify entomopathogenic nematodes symbiotic bacteria phenotypically and based on the gene encoding 16S rRNA sequences. Bacterial symbionts of entomopathogenic nematodes, obtained from isolates from the area Wonokerto (WN01) and isolates Sukapura (SP01), Bromo, Probolinggo, two symbiont bacteria was found in entomopathogenic nematodes Steinernema sp. The method used in this study are: the isolation of entomopathogenic nematodes Steinernema sp. and bacterial symbionts conventionally for the identification of phenotypically, after the characterization of bacterial isolates, the isolation of genomic DNA, 16S rRNA PCR, DNA purification and DNA sequence analysis. The results based on phenotypic characterization showed that isolates WN01 and SP01, yellowish white, gram positive, negative bioluminenscene, catalase positive, can not hydrolyze urea, and also can not produce H2S. The results of the gene encoding 16S rRNA sequence can be deduced WN01 isolates have in common with the bacteria Bacillus strain toyonensis BCT 7112, while the SP01 isolates have in common with the bacteria Bacillus strain cereus ATCC 14 579.

scholarly journals Molecular characterization of gene encoding halo tolerant amylase of Bacillus paralicheniformis isolated from Jazan region

2020 ◽  
Vol 2 ◽  
pp. 1
Author(s):  
Abdullah Ghazouani ◽  
Khaled El-Gayar ◽  
Emad Abada
Keyword(s):  
16S Rrna ◽  
Full Length ◽  
Rrna Gene ◽  
Scale Production ◽  
Amylase Gene ◽  
Specific Primers ◽  
Gene Encoding ◽  
Bacillus Paralicheniformis ◽  
Starch Agar

Objectives: This study aims to characterize the gene encoding halo tolerant amylase of bacteria isolated from Jazan region. Materials and Methods: Soil samples were collected from several area of Jazan region, KSA. The samples were serially diluted and plateted on starch agar plates. The amylase producing bacteria were detected by iodine test. To determine the halophilic amylase producing bacteria, several colonies were tested for their ability to grow at higher concentrations of NaCl ranging from 7 to 16%. The bacteria was identified by 16S rRNA and the full length amylase gene was fully identified by sequencing using specific primers. Results: One bacterial halophilic isolate was able to grow on starch agar medium up to 14% NaCl. The Gram stain of the isolate indicated that it is Gram-positive, bacilli. The 16S rRNA gene homology study showed that the bacterial isolate was identified as Bacillus paralicheniformis. Two specific primers were designed named S1F, S1R, to amplify the amylase gene (AMY) region using PCR and the PCR product was sequenced. The sequencing results showed that the full-length amy gene of B. paralicheniformis was of 1452 encoding 483 amino acids. The expected M.Wt. of the protein expressed is of 55 KDa. Conclusion: We report the isolation, identification, and characterization of an isolate of halophilic bacterium isolated from Jazan region. Based on molecular identification, this isolate was identified as Bacillus paralicheniformis. This bacterial strain has an α-amylase gene in its genome and is able to produce extracellular α-amylase. Based on the findings of this work we propose that Bacillus paralicheniformis amy gene could be cloned into expression vector for large scale production.

scholarly journals Characterization of an rRNA Operon (rrnB) of Mycobacterium fortuitum and Other Mycobacterial Species: Implications for the Classification of Mycobacteria

2002 ◽  
Vol 184 (4) ◽  
pp. 1078-1088 ◽  
Author(s):  
M. C. Menendez ◽  
M. J. Garcia ◽  
M. C. Navarro ◽  
J. A. Gonzalez-y-Merchand ◽  
S. Rivera-Gutierrez ◽  
...  
Keyword(s):  
16S Rrna ◽  
Rrna Synthesis ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Mycobacterial Species ◽  
A Cell ◽  
Rrna Sequences ◽  
Similar Organization

ABSTRACT Mycobacteria are thought to have either one or two rRNA operons per genome. All mycobacteria investigated to date have an operon, designated rrnA, located downstream from the murA gene. We report that Mycobacteriun fortuitum has a second rrn operon, designated rrnB, which is located downstream from the tyrS gene; tyrS is very close to the 3" end of a gene (3-mag) coding for 3-methylpurine-DNA-glycosylase. The second rrn operon of Mycobacterium smegmatis was shown to have a similar organization, namely, 5" 3-mag-tyrS-rrnB 3". The rrnB operon of M. fortuitum was found to have a single dedicated promoter. During exponential growth in a rich medium, the rrnB and rrnA operons were the major and minor contributors, respectively, to pre-rRNA synthesis. Genomic DNA was isolated from eight other fast-growing mycobacterial species. Samples were investigated by Southern blot analysis using probes for murA, tyrS, and 16S rRNA sequences. The results revealed that both rrnA and rrnB operons were present in each species. The results form the basis for a proposed new scheme for the classification of mycobacteria. The approach, which is phylogenetic in concept, is based on particular properties of the rrn operons of a cell, namely, the number per genome and a feature of 16S rRNA gene sequences.

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

scholarly journals Identification of Streptococci to Species Level by Sequencing the Gene Encoding the Manganese-Dependent Superoxide Dismutase

1998 ◽  
Vol 36 (1) ◽  
pp. 41-47 ◽  
Author(s):  
Claire Poyart ◽  
Gilles Quesne ◽  
Stephane Coulon ◽  
Patrick Berche ◽  
Patrick Trieu-Cuot
Keyword(s):  
Superoxide Dismutase ◽  
Pcr Assay ◽  
Degenerate Primers ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Type Strains ◽  
Internal Fragment ◽  
Rrna Sequences ◽  
16S Rrna Sequences

We have used a PCR assay based on the use of degenerate primers in order to characterize an internal fragment (sodAint ) representing approximately 85% of the genes encoding the manganese-dependent superoxide dismutase in various streptococcal type strains (S. acidominimus,S. agalactiae, S. alactolyticus, S. anginosus, S. bovis, S. constellatus,S. canis, S. cricetus, S. downei,S. dysgalactiae, S. equi subsp.equi, S. equi subsp. zooepidemicus,S. equinus, S. gordonii, S. iniae,S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis,S. pneumoniae, S. porcinus, S. pyogenes, S. salivarius, S. sanguis,S. sobrinus, S. suis, S. thermophilus, and S. vestibularis). Phylogenetic analysis of these sodAint fragments yields an evolutionary tree having a topology similar to that of the tree constructed with the 16S rRNA sequences. We have shown that clinical isolates could be identified by determining the positions of theirsodAint fragments on the phylogenetic tree of the sodAint fragments of the type species. We propose this method for the characterization of strains that cannot be assigned to a species on the basis of their conventional phenotypic reactions.

Characterization of the depth-related changes in the microbial communities in Lake Hovsgol sediment by 16S rRNA gene-based approaches

2008 ◽  
Vol 46 (2) ◽  
pp. 125-136 ◽  
Author(s):  
Young-Do Nam ◽  
Youlboong Sung ◽  
Ho-Won Chang ◽  
Seong Woon Roh ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Lake Hovsgol

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

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