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An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases

by Wanping Aw 1,† and Shinji Fukuda 1,2,*,†
1
Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
2
RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Liang Zhao
Diseases 2015, 3(4), 341-359; https://doi.org/10.3390/diseases3040341
Received: 1 September 2015 / Revised: 30 October 2015 / Accepted: 2 November 2015 / Published: 6 November 2015
(This article belongs to the Special Issue Advances and Applications of Metabolomics in Human Diseases)
Recently, metagenomics and metabolomics are the two most rapidly advancing “omics” technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level. Our gut microbiota, which consists of prokaryotic cells together with its metabolites, creates a unique gut ecosystem together with the host eukaryotic cells. In this review, we will highlight the detailed relationships between gut microbiota and its metabolites on host health and the pathogenesis of various intestinal diseases such as inflammatory bowel disease and colorectal cancer. Therapeutic interventions such as probiotic and prebiotic administrations and fecal microbiota transplantations will also be discussed. We would like to promote this unique biology-wide approach of incorporating metagenome and metabolome information as we believe that this can help us understand the intricate interplay between gut microbiota and host metabolism to a greater extent. This novel integration of microbiome, metatranscriptome, and metabolome information will help us have an improved holistic understanding of the complex mammalian superorganism, thereby allowing us to gain new and unprecedented insights to providing exciting novel therapeutic approaches for optimal intestinal health. View Full-Text
Keywords: gut microbiota; luminal metabolites; colorectal cancer; inflammatory bowel disease; metabolomics; metagenomics gut microbiota; luminal metabolites; colorectal cancer; inflammatory bowel disease; metabolomics; metagenomics
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Aw, W.; Fukuda, S. An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases. Diseases 2015, 3, 341-359.

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