16S rRNA gene sequencingStandardized protocolNext-generation sequencingPoultryMicrobiotaBacteria are the major component of poultry gastrointestinal tract (GIT) microbiota and play an important role in host hea
High-throughput sequencing of bacterial 16S rRNA gene (16S-seq) is a useful and common method for studying bacterial community structures. However, contamination of the 16S rRNA genes from the mitochondrion and plastid hinders the sensitive bacterial 16S-seq in plant microbiota profiling, especially f...
Normalized DNA was submitted to the Centre for Genomic Research of the University of Liverpool (UK) for PCR amplification, library preparation and 16S high-throughput sequencing. The V4 hypervariable region of the bacterial 16S rRNA genes present in each caecal DNA sample was amplified by PCR usin...
We performed amplicon-based 16S rRNA gene sequencing of DNA extracted from swab samples collected from dairy cows affected with IH, infected IH, IP, and complicated SU, TN, and WLD lesions. DNA was also collected from healthy skin control swabs and was also analysed for comparative purposes. O...
Amplicon sequencing can detect known and novel variants within the region of interest (Figs. 3.3 and 3.4). The most common applications are amplicon sequencing of16S rRNA(for bacteria),18S rRNA(for microeukaryotes and unicellular eukaryotes), orinternal transcribed spacers(ITS—for fungal communities...
Results: Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detec‑ tion of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. ...
Amplicon sequencing is a targeted sequencing method that uses polymerase chain reaction (PCR) to selectively amplify specific DNA fragments or genomic regions of interest.
One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit furt
The 16S rRNA and fungal 18S-ITS data are from traditional amplicon sequencing of a single genetic region (the “Methods” section). The LoopSeq genomic amplicon data is based on LoopSeq sequencing of randomly amplified regions of the genome of several bacteria (the “Methods” section). Lines...
16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1–V2 (V12) and the standard V3