scholarly journals A framework for IS200, 16S rRNA gene and plasmid-profile analysis in Salmonella serogroup D1

1994 ◽  
Vol 41 (2) ◽  
pp. 112-119 ◽  
Author(s):  
J. Stanley ◽  
N. Powell ◽  
C. Jones ◽  
A. P. Burnens
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Plasmid Profile ◽  
Rrna Gene

scholarly journals Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol-contaminated soil

2011 ◽  
Vol 61 (9) ◽  
pp. 2231-2237 ◽  
Author(s):  
Margarita Gomila ◽  
Ludmila Tvrzová ◽  
Andrea Teshim ◽  
Ivo Sedláček ◽  
Narjol González-Escalona ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Profile Analysis ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Selective Enrichment

A polyphasic taxonomic approach was applied to the study of a Gram-negative bacterium (B2T) isolated from soil by selective enrichment with pentachlorophenol. 16S rRNA gene sequence analysis of strain B2T showed that the strain belongs to the genus Achromobacter within the Betaproteobacteria. The 16S rRNA gene sequence displayed more than 99 % similarity to the sequences of the type strains of all species of Achromobacter, with the highest sequence similarity to those of Achromobacter spanius CCM 7183T and A. piechaudii CCM 2986T (99.8 %). On the basis of phylogenetic analysis, genomic DNA–DNA relatedness and phenotypic characteristics, including chemotaxonomic (cellular fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2T ( = CCM 7608T  = CCUG 56371T  = CECT 7342T).

Diversity ofcrygenes and genetic characterization ofBacillus thuringiensisisolated from Brazil

2004 ◽  
Vol 50 (8) ◽  
pp. 605-613 ◽  
Author(s):  
Gislayne Trindade Vilas-Bôas ◽  
Manoel Victor Franco Lemos
Keyword(s):  
Genetic Diversity ◽  
Bacillus Thuringiensis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genetic Characterization ◽  
Geographic Origin ◽  
Spatial Separation ◽  
Plasmid Profile ◽  
Rrna Gene ◽  
The 16S Rrna Gene

Two hundred and eighteen Bacillus thuringiensis isolates from Brazil were characterized by the presence of crystal protein genes by PCR with primers specific to different cry and cyt genes. Among these isolates, 95 were selected according to their geographic origin for genetic characterization with the 16S rRNA gene, RAPD, and plasmid profile. Isolates containing cry1 genes were the most abundant (48%) followed by the cry11 and cyt (7%) and cry8 genes (2%). Finally, 40.3% of the isolates did not produce any PCR product. The plasmid profile and RAPD analysis showed a remarkable diversity among the isolates of B. thuringiensis not observed in the 16S rRNA gene. These results suggest that the genetic diversity of B. thuringiensis species results from the influence of different ecological factors and spatial separation between strains generated by the conquest of different habitats.Key words: Bacillus thuringiensis, cry genes, 16S rRNA gene, RAPD, plasmid profile, genetic diversity, ecology.

scholarly journals Characterization of The Microbiome In Bile From Normal Human Gallbladders

2021 ◽  
Author(s):  
Shin Watanabe ◽  
Tadashi Shinoda ◽  
Masaaki Minagawa ◽  
Mari Toya ◽  
Daisuke Motooka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Bacterial Flora ◽  
Normal Liver ◽  
Ribosomal Gene ◽  
Gallbladder Bile ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Gene Profile

Abstract Background: Scientists previously believed that bacteria could not grow in bile, which is rich in bacteriostatic compounds such as bile acids. Therefore, the biliary tract was considered to be a sterile environment. However, high-throughput (i.e., amplicon) sequencing analysis methods have recently been used to discover the bacterial flora in gallbladder bile in brain-dead patients with normal gallbladders. In a bacterial flora analysis targeting the 16S ribosomal gene, a specific flora was present in the bile of normal gallbladders. However, these results were not obtained from truly healthy individuals. Therefore, the aim of this study was to analyze the microbial flora of bile collected from pathologically normal gallbladders that were surgically removed from patients with hepatobiliary pancreatic diseases who had normal liver function.Results: All 12 bile samples obtained from the gallbladders had negative culture results, although a bacterial flora was detected in all samples via 16S ribosome gene analysis. The composition of the bacterial flora was very simple, and the Firmicutes, Proteobacteria, and Actinobacteria phyla were identified in all samples. Based on 16S rRNA gene profile analysis, the composition ratio accounted for more than 80% of the total number of reads. The Anaerobacillus, Delftia, Bacillus, Ralstonia, Ochrobactrum, Acidovorax, and Curvibacter genera were detected in all 12 samples. Based on 16S rRNA gene profile analysis, at the genus level, Anaerobacillus and Delftia accounted for 58.62%–87.63% of the identified bacteria in each sample. Conclusions: In this study, the bacterial flora in the gallbladder bile was not diverse. Contrary to previous reports, few bacteria belonging to the Bacteroidetes phylum were detected. The functional significance of the gallbladder bacterial flora requires further investigation.

scholarly journals Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shantelle Claassen-Weitz ◽  
Sugnet Gardner-Lubbe ◽  
Kilaza S. Mwaikono ◽  
Elloise du Toit ◽  
Heather J. Zar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Induced Sputum ◽  
Rrna Gene ◽  
Gene Profile

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

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