scholarly journals Escherichia fergusonii identified in preputial swabs from healthy Aceh cattle by phylogenetic 16S rRNA analysis

2018 ◽  
Author(s):  
Balqis, U., ◽  
Hambal, M., ◽  
Admi, M., ◽  
Safika ◽  
Meutia, N., ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Analysis

scholarly journals Optimized Protocol for Cyanobacterial 16S rRNA Analysis in Danube Delta Lakes

2021 ◽  
Author(s):  
Maria Iasmina Moza ◽  
Carmen Postolache
Keyword(s):  
16S Rrna ◽  
Dna Extraction ◽  
Phytoplankton Biomass ◽  
Extraction Method ◽  
Seasonal Difference ◽  
Danube Delta ◽  
16S Rrna Analysis ◽  
Dna Extraction Method ◽  
Optimized Protocol ◽  
Cyanobacterial Biomass

AbstractMolecular biology protocols have been more and more accessible to researchers for ecological investigations, however, these protocols always require optimization steps for the analysis of specific types of samples. The purpose of this study was to optimize a molecular protocol for the analysis of cyanobacterial 16S rRNA in Danube Delta shallows lakes. In this regard, several commercial DNA extraction kits were tested in comparison with potassium ethyl xanthogenate extraction method on different matrices. The obtained DNA was further used for 16S rRNA PCR optimization. Finally, an optimized protocol is proposed for the molecular analysis of cyanobacteria group in freshwater samples. The best DNA extraction method was the potassium xanthogenate extraction from dried cyanobacterial biomass. A dynamic in total genomic eDNA was observed, reflecting the seasonal difference in phytoplankton biomass from the studied lakes. The PCR protocol optimized by us can be successfully applied for the identification of a broad range of cyanobacterial genetic markers.

Characterization of oral bacteria in the tongue coating of patients with halitosis using 16S rRNA analysis

2020 ◽  
Vol 78 (7) ◽  
pp. 541-546 ◽  
Author(s):  
Akiko Oshiro ◽  
Takashi Zaitsu ◽  
Masayuki Ueno ◽  
Yoko Kawaguchi
Keyword(s):  
16S Rrna ◽  
Oral Bacteria ◽  
Tongue Coating ◽  
16S Rrna Analysis

scholarly journals Changes in Host Cytokine Patterns of TB Patients with Different Bacterial Loads Detected Using 16S rRNA Analysis

PLoS ONE ◽  
2016 ◽  
Vol 11 (12) ◽  
pp. e0168272 ◽  
Author(s):  
Rhiannon Heslop ◽  
Adama L. Bojang ◽  
Sheikh Jarju ◽  
Joseph Mendy ◽  
Sarah Mulwa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Analysis

scholarly journals Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

1999 ◽  
Vol 65 (8) ◽  
pp. 3287-3292 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Chih-Ching Chien ◽  
Bruce J. Paster ◽  
Rebecca L. Ericson ◽  
Roger P. Orcutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
Single Species ◽  
Rapid Identification ◽  
Sequence Information ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified asLactobacillus acidophilus (strain ASF 360),Lactobacillus salivarius (strain ASF 361), andBacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus andLactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in theCytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipesphylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes,Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster,Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.

16S rRNA analysis of electrogenic bacterial communities in microbial fuel cells developed from temperate soils

BIOS ◽  
2020 ◽  
Vol 91 (1) ◽  
pp. 9
Author(s):  
Luis Jimenez ◽  
Margarita Kulko ◽  
Ryan Kim ◽  
Theranda Jashari ◽  
Tina Choe
Keyword(s):  
Fuel Cells ◽  
16S Rrna ◽  
Microbial Fuel Cells ◽  
Bacterial Communities ◽  
16S Rrna Analysis ◽  
Temperate Soils

scholarly journals Isolation and Identification of Pyrene MineralizingMycobacteriumspp. from Contaminated and Uncontaminated Sources

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Christopher W. M. Lease ◽  
Richard H. Bentham ◽  
Sharyn E. Gaskin ◽  
Albert L. Juhasz
Keyword(s):  
16S Rrna ◽  
Agricultural Soil ◽  
Prior Exposure ◽  
Environmental Matrices ◽  
Isolation And Identification ◽  
Diverse Range ◽  
16S Rrna Analysis ◽  
Catabolic Activity ◽  
Grey Kangaroo ◽  
Western Grey Kangaroo

Mycobacteriumisolates obtained from PAH-contaminated and uncontaminated matrices were evaluated for their ability to degrade three-, four- and five-ring PAHs. PAH enrichment studies were prepared using pyrene and inocula obtained from manufacturing gas plant (MGP) soil, uncontaminated agricultural soil, and faeces fromMacropus fuliginosus(Western Grey Kangaroo). Three pyrene-degrading microorganisms isolated from the corresponding enrichment cultures had broad substrate ranges, however, isolates could be differentiated based on surfactant, phenol, hydrocarbon and PAH utilisation. 16S rRNA analysis identified all three isolates asMycobacteriumsp. TheMycobacteriumspp. could rapidly degrade phenanthrene and pyrene, however, no strain had the capacity to utilise fluorene or benzo[a]pyrene. When pyrene mineralisation experiments were performed, 70–79% of added14C was evolved as14CO2after 10 days. The present study demonstrates that PAH degrading microorganisms may be isolated from a diverse range of environmental matrices. The present study demonstrates that prior exposure to PAHs was not a prerequisite for PAH catabolic activity for two of theseMycobacteriumisolates.

Comparison of 16S ribosomal RNA genes inClavibacter michiganensissubspecies with other coryneform bacteria

1995 ◽  
Vol 41 (10) ◽  
pp. 925-929 ◽  
Author(s):  
Xiang Li ◽  
Solke H. De Boer
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clavibacter Michiganensis ◽  
Arthrobacter Simplex ◽  
16S Rrna Analysis ◽  
Coryneform Bacteria ◽  
Clavibacter Michiganensis Subsp ◽  
Complete Sequences

Nearly complete sequences (97–99%) of the 16S rRNA genes were determined for type strains of Clavibacter michiganensis subsp. michiganensis, Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. sepedonicus, and Clavibacter michiganensis subsp. nebraskensis. The four subspecies had less than 1% dissimilarity in their 16S rRNA genes. Comparative studies indicated that the C. michiganensis subsp. shared relatively high homology with the 16S rRNA gene of Clavibacter xyli. Further comparison with representatives of other Gram-positive coryneform and related bacteria with high G + C% values showed that this group of bacteria was subdivided into three clusters. One cluster consisted of the Clavibacter michiganensis subsp., Clavibacter xyli, Arthrobacter globiformis, Arthrobacter simplex, and Frankia sp.; another cluster consisted of members of the corynebacteria–mycobacteria–nocardia (CMN) group of Mycobacteriaceae including Tsukamurella paurometabolum; and Propionibacterium freudenreichii alone formed a unique cluster, which was remote from other coryneform bacteria analyzed. The three clusters may reflect a systematic rank higher than the genus level among these bacteria.Key words: Clavibacter, coryneform bacteria, phylogeny, 16S rRNA analysis.

scholarly journals Effects of Industrial and Ruminant Trans-fatty Acids-Enriched Diet on Fecal Microbiome and Short Chain Fatty Acid Metabolites of C57BL/6 Mice

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 1171-1171
Author(s):  
Farzad Mohammadi ◽  
Emma Tolsdorf ◽  
Karine Greffard ◽  
Élodie Chotard ◽  
Jean-François Bilodeau ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Butyric Acid ◽  
Relative Abundance ◽  
Trans Fatty Acids ◽  
Valeric Acid ◽  
Short Chain ◽  
16S Rrna Analysis ◽  
Fecal Microbiome

Abstract Objectives We hypothesized that the intake of industrially originated trans-fatty acids (elaidic acid (EA trans 18: 1n-9)) and ruminant trans fatty acids (trans-palmitoleic acid (TPA t16:1 n-7)) will differentially modify gut microbiota and short-chain fatty acids (SCFA) profiles. The objective is to compare the long- and short-term effects of EA and TPA on the fecal microbiome and SCFAs profiles in mice. Methods Forty C57BL/6 mice were divided to 4 groups. Each group was given one of the following 4 formulations in the drinking water: lecithin nanovesicles, nanovesicles containing either lecithin with EA or TPA (86:14 (w/w)) or water alone (control) for 28 days with a normal fat diet. Fecal samples were collected at days 0, 7 and 28. Gut microbiota profiles were determined by 16S rRNA gene sequencing. SCFAs were measured by headspace gas chromatography coupled to a single quadrupole mass spectrometer. Baseline data (relative abundance of bacteria or levels of SCFAs) was pooled and then compared with data from day 7 or day 28 for each formulation. Results After 7 days of lecithin, 16S rRNA analysis revealed an increase in the relative abundance of Lactobacillus. After 28 days of lecithin, an increase in the relative abundance of Lactobacillus, Erysipelotrichaceae, and Enterobacteriaceae together with a decrease in Bacteroidaceae was observed. Further, a tendency to increase level of butyric acid (P = 0.053) was observed after 28 days of lecithin. After 7 days of EA, an increase in the relative abundance of Lactobacillus, whereas a decrease in the relative abundance of Parabacteroides, Bacteroides, Rumininococcaceae, Lachnospiraceae and Peptococcaceae was observed. After 7 days of TPA, results show a decreased level of isovaleric acid (P = 0.04) and valeric acid (P = 0.03). After 28 days of TPA, data demonstrates an increase in the level of butyric acid (P = 0.01) and propionic acid (P = 0.01). Water intake for 28 days decreased the level of valeric acid (P = 0.02). Conclusions Consumption of industrial and ruminant trans-fatty acids modify differentially bacterial taxa present in the gut microbiome and SCFA profiles. Funding Sources NSERC, CMDO.

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