scholarly journals 16S rRNA gene profiling of planktonic and biofilm microbial populations in the Gulf of Guinea using Illumina NGS

2016 ◽  
Vol 122 ◽  
pp. 105-112 ◽  
Author(s):  
Sukriye Celikkol-Aydin ◽  
Christine C. Gaylarde ◽  
Tim Lee ◽  
Robert E. Melchers ◽  
Devin L. Witt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Profiling ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Gulf Of Guinea

scholarly journals Bacterial DNAemia is associated with serum zonulin levels in older subjects

2020 ◽  
Author(s):  
Giorgio Gargari ◽  
Valentina Taverniti ◽  
Cristian Del Bo’ ◽  
Stefano Bernardi ◽  
Cristina Andres-Lacueva ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Serum Levels ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Blood Samples ◽  
Gene Copies ◽  
Older Subjects ◽  
Pcr Targeting

AbstractThe increased presence of bacteria in blood is a plausible contributing factor in the development and progression of aging-associated diseases. In this context, we performed the quantification and the taxonomic profiling of the bacterial DNA in blood samples collected from a group of forty-three older subjects enrolled in a nursing home. Quantitative PCR targeting the 16S rRNA gene revealed that all the older volunteers contained detectable amounts of bacterial DNA in their blood. The total amount of 16S rRNA gene copies varied considerably between subjects. Correlation analyses revealed that the bacterial DNAemia (expressed as concentration of 16S rRNA gene copies in blood) significantly correlated with the serum levels of zonulin, an emerging marker of intestinal permeability. This result was confirmed by the analysis of a second set of blood samples collected after approximately four months from the same subjects. Analyses of 16S rRNA gene profiling revealed that most of the bacterial DNA detected in blood was ascribable to the phylum Proteobacteria with a predominance of Pseudomonadaceae and Enterobacteriaceae. Several control samples were also analyzed to assess the influence exerted by contaminant bacterial DNA potentially originating from reagents and materials. The date reported here suggest that para-cellular permeability of epithelial (and potentially also endothelial) cell layers may play an important role in bacterial migration into the bloodstream. Bacterial DNAemia is likely to impact on several aspects of host physiology and could underpin the development and prognosis of various diseases in older subjects.

scholarly journals Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0204600
Author(s):  
Renee M. Petri ◽  
Poulad Pourazad ◽  
Ratchaneewan Khiaosa-ard ◽  
Fenja Klevenhusen ◽  
Barbara U. Metzler-Zebeli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Temporal Dynamics ◽  
Gene Profiling ◽  
Rrna Gene

scholarly journals Benchmark taxonomic classification of chicken gut bacteria based on 16S rRNA gene profiling in correlation with various feeding strategies

2020 ◽  
Vol 32 (1) ◽  
pp. 1034-1041
Author(s):  
Zubia Rashid ◽  
Syed Muddassar Hussain Gilani ◽  
Asma Ashraf ◽  
Sitwat Zehra ◽  
Abid Azhar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Bacteria ◽  
Taxonomic Classification ◽  
Gene Profiling ◽  
Feeding Strategies ◽  
Rrna Gene

scholarly journals 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics

PLoS ONE ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. e0213869 ◽  
Author(s):  
Christine Tara Peterson ◽  
Vandana Sharma ◽  
Stanislav N. Iablokov ◽  
Levent Albayrak ◽  
Kamil Khanipov ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Neurodegenerative Disease ◽  
Medicinal Herbs ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Genome Reconstruction ◽  
Metabolic Interactions

scholarly journals Miniprimer PCR, a New Lens for Viewing the Microbial World

2007 ◽  
Vol 74 (3) ◽  
pp. 840-849 ◽  
Author(s):  
Thomas A. Isenbarger ◽  
Michael Finney ◽  
Carlos Ríos-Velázquez ◽  
Jo Handelsman ◽  
Gary Ruvkun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Microbial Populations ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Microbial World ◽  
Pcr Method ◽  
Environmental Sequences ◽  
The 16S Rrna Gene

ABSTRACT Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.

scholarly journals The Microbial Community Structure in Petroleum-Contaminated Sediments Corresponds to Geophysical Signatures

2007 ◽  
Vol 73 (9) ◽  
pp. 2860-2870 ◽  
Author(s):  
Jonathan P. Allen ◽  
Estella A. Atekwana ◽  
Eliot A. Atekwana ◽  
Joseph W. Duris ◽  
D. Dale Werkema ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Sediments ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Community Structures ◽  
Microbial Community Structures ◽  
Gene Libraries ◽  
Cost Efficient

ABSTRACT The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes.

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