High throughput sequencing methods and analysis for microbiome research

doi:10.1016/J.MIMET.2013.08.011

Journal ArticleDOI

High throughput sequencing methods and analysis for microbiome research

Julia M. Di Bella, +7 more

- 01 Dec 2013 -

Journal of Microbiological Methods

- Vol. 95, Iss: 3, pp 401-414

TLDR

This review discusses techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms, that are becoming more widely used to study whole communities of prokaryotes in many niches.

About:

This article is published in Journal of Microbiological Methods.The article was published on 2013-12-01. It has received 240 citations till now. The article focuses on the topics: Metagenomics & Microbiome.

Citations

PDF

Open Access

More filters

Journal ArticleDOI

Waste not, want not: why rarefying microbiome data is inadmissible.

Paul J. McMurdie, +1 more

- 03 Apr 2014 -

PLOS Computational Biology

TL;DR: It is advocated that investigators avoid rarefying altogether and supported statistical theory is provided that simultaneously accounts for library size differences and biological variability using an appropriate mixture model.

...read moreread less

Journal ArticleDOI

The gut microbiome in health and in disease

Andrew B. Shreiner, +2 more

- 01 Jan 2015 -

Current Opinion in Gastroenterology

TL;DR: There is a fast growing collection of data describing the structure and functional capacity of the microbiome in a variety of conditions available to the research community for consideration and further exploration.

...read moreread less

Journal ArticleDOI

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Andrew D. Fernandes, +5 more

- 05 May 2014 -

Microbiome

TL;DR: Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach.

...read moreread less

Journal ArticleDOI

The microbiome of the urinary tract—a role beyond infection

Samantha A. Whiteside, +4 more

- 01 Feb 2015 -

Nature Reviews Urology

TL;DR: Urologists will need to consider possible influences of the microbiome in diagnosis and treatment of certain urological conditions, and new insights might provide an opportunity to predict the risk of developing certain urologogical diseases and could enable the development of innovative therapeutic strategies.

...read moreread less

Journal ArticleDOI

A new view of the fish gut microbiome: Advances from next-generation sequencing

Mahdi Ghanbari, +2 more

- 01 Nov 2015 -

Aquaculture

TL;DR: The potential of next-generation sequencing platforms for analysing fish gut microbiota is highlighted and promising results in this field are presented along with a focus on new perspectives and future research directions of fish gut microbial ecology.

...read moreread less

Collapse

References

PDF

Open Access

More filters

Journal ArticleDOI

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Stephen F. Altschul, +6 more

- 01 Sep 1997 -

Nucleic Acids Research

TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.

...read moreread less

Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, +1 more

- 01 Jul 2009 -

Bioinformatics

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.

...read moreread less

Journal ArticleDOI

Fast gapped-read alignment with Bowtie 2

Ben Langmead, +3 more

- 01 Apr 2012 -

Nature Methods

TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

...read moreread less

Journal ArticleDOI

QIIME allows analysis of high-throughput community sequencing data.

J. Gregory Caporaso, +27 more

- 11 Apr 2010 -

Nature Methods

TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.

...read moreread less

Journal ArticleDOI

KEGG: Kyoto Encyclopedia of Genes and Genomes

Minoru Kanehisa, +1 more

- 01 Jan 1999 -

Nucleic Acids Research

TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.

...read moreread less