Current challenges and best-practice protocols for microbiome analysis

Abstract Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by expe...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Briefings in bioinformatics Jg. 22; H. 1; S. 178 - 193
Hauptverfasser: Bharti, Richa, Grimm, Dominik G
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 18.01.2021
Oxford Publishing Limited (England)
Schlagworte:
Animals
Annotations
Assembly
Computer applications
Design of experiments
DNA Barcoding, Taxonomic - methods
DNA Barcoding, Taxonomic - standards
Experimental design
Humans
Metagenomics
Metagenomics - methods
Metagenomics - standards
Microbiomes
Microbiota - genetics
Microorganisms
Next-generation sequencing
Practice Guidelines as Topic
Quality control
Review
RNA, Ribosomal, 16S - genetics
rRNA 16S
Sequence Analysis, DNA - methods
Sequence Analysis, DNA - standards
Species diversity
Statistical analysis
assembly
amplicon sequencing
microbiome
16S rRNA sequencing
metagenomics
functional and taxonomic classification
ISSN:1477-4054, 1467-5463, 1477-4054
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Abstract Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
ObjectType-Review-3
content type line 23
ISSN:1477-4054
1467-5463
1477-4054
DOI:10.1093/bib/bbz155