Metagenomics: a path to understanding the gut microbiome

The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral compon...

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Bibliographic Details
Published in:Mammalian genome Vol. 32; no. 4; pp. 282 - 296
Main Authors: Yen, Sandi, Johnson, Jethro S.
Format: Journal Article
Language:English
Published: New York Springer US 01.08.2021
Springer Nature B.V
Subjects:
Animal Genetics and Genomics
bioinformatics
Biomedical and Life Sciences
Cell Biology
Computational Biology - standards
Computer applications
data collection
Digestive system
Gastrointestinal Microbiome - genetics
Gene expression
genome
Genomes
Genomics
Gut microbiota
High-Throughput Nucleotide Sequencing - standards
Human Genetics
Humans
Intestinal microflora
intestinal microorganisms
Life Sciences
mammals
Metagenome - genetics
Metagenomics
microbiome
Microbiomes
Microbiota
Microbiota - genetics
Microorganisms
Next-generation sequencing
Pathogens
RNA, Ribosomal, 16S - genetics
Software
Taxonomy
ISSN:0938-8990, 1432-1777, 1432-1777
Online Access:Get full text
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Summary:The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.
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ISSN:0938-8990
1432-1777
1432-1777
DOI:10.1007/s00335-021-09889-x