scholarly journals 16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens

2019 ◽  
Vol 98 (2) ◽  
pp. 842-854 ◽  
Author(s):  
Muhammad Saeed ◽  
Xu Yatao ◽  
Zhang Tiantian ◽  
Ren Qian ◽  
Sun Chao
Keyword(s):  
Immune Response ◽  
Rna Sequencing ◽  
Ribosomal Rna ◽  
Broiler Chickens ◽  
16S Ribosomal Rna ◽  
Intestinal Microbiome

A comparison of culture vs 16S ribosomal RNA sequencing of chronic granulation tissue microbiota in cats and dogs

2018 ◽  
pp. 540-540
Author(s):  
Phil Franklin ◽  
Jane Ladlow ◽  
Xiaopei Su ◽  
Cinzia Cantacessi ◽  
Andrew Grant ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Rna ◽  
Granulation Tissue ◽  
16S Ribosomal Rna

scholarly journals Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0216709 ◽  
Author(s):  
Andrew M. Smith ◽  
Miten Jain ◽  
Logan Mulroney ◽  
Daniel R. Garalde ◽  
Mark Akeson
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Modified Nucleobases

scholarly journals Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology

2016 ◽  
Vol 16 (2) ◽  
pp. 150-158 ◽  
Author(s):  
Mukesh Verma
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Rna ◽  
Human Microbiome ◽  
Cancer Epidemiology ◽  
16S Ribosomal Rna ◽  
Cancer Risk Assessment ◽  
Sample Collection ◽  
Primer Selection ◽  
Technical Challenges ◽  
Epidemiology Studies

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from “omics” studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

Postoperative pyoderma gangrenosum: diagnostic value of 16s ribosomal RNA sequencing and review of the literature

2009 ◽  
Vol 34 (5) ◽  
pp. 598-602 ◽  
Author(s):  
C. Ferrandiz-Pulido ◽  
R. Bartralot ◽  
M. J. Fuente ◽  
C. Heras ◽  
P. Bassas ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Pyoderma Gangrenosum ◽  
Ribosomal Rna ◽  
Diagnostic Value ◽  
16S Ribosomal Rna ◽  
Review Of The Literature

scholarly journals Phylogenic homogeneity ofCoxiella burnetiistrains as determinated by 16S ribosomal RNA sequencing

1993 ◽  
Vol 113 (3) ◽  
pp. 339-344 ◽  
Author(s):  
A. Stein ◽  
N.A. Saunders ◽  
A.G. Taylor ◽  
D. Raoult
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna

scholarly journals A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis

2021 ◽  
Author(s):  
Fangchao Song ◽  
Jennifer V. Kuehl ◽  
Arjun Chandran ◽  
Adam P. Arkin
Keyword(s):  
Microbial Communities ◽  
Rna Sequencing ◽  
Ribosomal Rna ◽  
Cost Effective ◽  
Community Analysis ◽  
Extraction Methods ◽  
16S Ribosomal Rna ◽  
Direct Pcr ◽  
Microbial Composition ◽  
Pcr Method

ABSTRACTBacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16s ribosomal RNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial amount of samples becomes necessary to analyses that parse the factors that determine microbial composition. A common bottleneck in performing these kinds of experiments is genomic DNA (gDNA) extraction, which can be biased on the types of species, time-consuming and expensive. Direct PCR methods are a potentially simpler and more accurate alternative to gDNA extraction methods that do not require the intervening purification step. In this study, we evaluated three variations of direct PCR methods using diverse heterogeneous bacterial cultures, ZymoBIOMICS Microbial Community Standards, and groundwater. By comparing direct PCR methods with DNeasy blood and tissue kits and DNeasy Powersoil kits, we found a specific variant of the direct PCR method exhibits a comparable overall accuracy to the conventional DNeasy Powersoil protocol. We also found the method showed higher efficiency for extracting gDNA from the gram negative strains compared to DNeasy blood and tissue protocol. This direct PCR method is 1600 times cheaper ($0.34 for 96 samples), 10 times simpler (15 min hands-on time for 96 samples) than DNeasy Powersoil protocol. The direct PCR method can also be fully automated, and is compatible with small volume samples, thereby permitting scaling of samples and replicates needed to support high-throughput large-scale bacterial community analysis.IMPORTANCEUnderstanding bacterial interaction and assembling in complex microbial communities using 16s ribosomal RNA sequencing normally requires a large experimental load. However, the current DNA extraction methods including cell disruption and genome DNA purification are normally biased, costly, time and labor consuming, and not amenable to miniaturization by droplets or 1536 well plates due to the significant DNA loss during purification step for tiny volume and low cell density samples. Direct PCR method could potentially solve these problems. In this study, we demonstrate a direct PCR method which exhibits similar accuracy as the widely used method – DNeasy Powersoil protocol, while 1600 times cheaper and 10 times faster to execute. This simple, cost-effective, and automation friendly direct PCR based 16s ribosomal RNA sequencing method allows us to study the dynamics, microbial interaction and assembly of varying microbial communities in a high throughput fashion.

scholarly journals Native Valve Infective Endocarditis due to Staphylococcus lugdunensis Confirmed by 16S Ribosomal RNA Sequencing

2011 ◽  
Vol 43 (4) ◽  
pp. 372 ◽  
Author(s):  
Young Eun Ha ◽  
Seong-Yeol Ryu ◽  
Kwan Soo Ko ◽  
Eun-Jeong Joo ◽  
So Yeon Park ◽  
...  
Keyword(s):  
Infective Endocarditis ◽  
Rna Sequencing ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Staphylococcus Lugdunensis ◽  
Native Valve
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