An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome

Metabolites
Rohan M ShahDavid J Beale

Abstract

Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated pers...Continue Reading

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Citations

Nov 10, 2020·Metabolomics : Official Journal of the Metabolomic Society·Rupasri MandalDavid S Wishart
Apr 3, 2021·The Science of the Total Environment·Rohan M ShahDavid J Beale
May 16, 2021·Biotechnology and Bioengineering·Lorenzo SardelliCarmen Giordano
Apr 20, 2021·Annual Review of Chemical and Biomolecular Engineering·Nick FacklerMichael Köpke
Jun 29, 2021·Journal of Autoimmunity·Mia Øgaard MønstedMartin Haupt-Jorgensen

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Methods Mentioned

BETA
biopsies
amplicon sequencing
nuclear magnetic resonance
NMR

Software Mentioned

Roary
MetAlign
XCMS
Tax4Fun
OrtholugeDB
PAIRUP
EzBioCloud
Piphillin
MicrobesOnline
PICRUST

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