16S rRNA amplicon sequencing

In the present study, we collected mucus samples from bleached and healthy Fungia sp. colonies in Nha Trang bay to investigate biodiversity and bacterial community composition using 16S rRNA gene amplicon next-generation sequencing.

12p vimulcahy 18-09-2023 10 3   Download

African populations provide a unique opportunity to interrogate hostmicrobe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon.

32p viarchimedes 26-01-2022 8 0   Download

The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case.

11p spiritedaway36 25-11-2021 8 1   Download

Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2.

11p vilichoo2711 25-06-2021 14 1   Download

This study reports the analyses of the rhizospheric microbiome of the groundnut (Arachis hypogaea L.) from Gujarat, India. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere.

9p cothumenhmong11 11-05-2021 9 2   Download

Taxonomic classification is a corner stone for the characterisation and comparison of microbial communities. Currently, most existing methods are either slow, restricted to specific communities, highly sensitive to taxonomic inconsistencies, or limited to genus level classification.

8p vikentucky2711 24-11-2020 12 1   Download

The popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencing technologies suffers from sequencing errors originating from different factors

10p vikentucky2711 24-11-2020 10 1   Download

Reducing the effects of sequencing errors and PCR artifacts has emerged as an essential component in amplicon-based metagenomic studies. Denoising algorithms have been designed that can reduce error rates in mock community data, but they change the sequence data in a manner that can be inconsistent with the process of removing errors in studies of real communities.

9p vikentucky2711 24-11-2020 11 2   Download

Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities.

6p vioklahoma2711 19-11-2020 6 0   Download

Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data.

12p viflorida2711 30-10-2020 15 2   Download

Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample.

10p viconnecticut2711 28-10-2020 11 0   Download

The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene amplicons are often preprocessed into composition or relative abundance.

15p vijisoo2711 27-10-2020 9 0   Download

A plant’s microbiota has various implications for the plant’s health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.).

10p caygaocaolon1 13-11-2019 10 0   Download