scholarly journals Characterization of Bacteria in Biopsies of Colon and Stools by High Throughput Sequencing of the V2 Region of Bacterial 16S rRNA Gene in Human

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16952 ◽  
Author(s):  
Yukihide Momozawa ◽  
Valérie Deffontaine ◽  
Edouard Louis ◽  
Juan F. Medrano
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Bacterial 16S Rrna Gene

scholarly journals Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

scholarly journals Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41484 ◽  
Author(s):  
Marcio C. Costa ◽  
Luis G. Arroyo ◽  
Emma Allen-Vercoe ◽  
Henry R. Stämpfli ◽  
Peter T. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Emilie Lefèvre ◽  
Courtney M Gardner ◽  
Claudia K Gunsch
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Rrna Gene ◽  
Plant Host ◽  
Plant Chloroplast

ABSTRACT Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

scholarly journals High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e38094 ◽  
Author(s):  
Martin J. Sergeant ◽  
Chrystala Constantinidou ◽  
Tristan Cogan ◽  
Charles W. Penn ◽  
Mark J. Pallen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Annealing Temperature ◽  
Extraction Procedure ◽  
Rrna Gene
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