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Title: Microbiome-wide association studies link dynamic microbial consortia to disease

Abstract

Rapid advances in DNA sequencing, metabolomics, proteomics and computation dramatically increase accessibility of microbiome studies and identify links between the microbiome and disease. Microbial time-series and multiple molecular perspectives enable Microbiome-Wide Association Studies (MWAS), analogous to Genome-Wide Association Studies (GWAS). Rapid research advances point towards actionable results, although approved clinical tests based on MWAS are still in the future. Appreciating the complexity of interactions between diet, chemistry, health and the microbiome, and determining the frequency of observations needed to capture and integrate this dynamic interface, is paramount for addressing the need for personalized and precision microbiome-based diagnostics and therapies.

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1342303
Report Number(s):
PNNL-SA-118611
Journal ID: ISSN 0028-0836
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature (London); Journal Volume: 535; Journal Issue: 7610
Country of Publication:
United States
Language:
English
Subject:
MWAS; Microbiome

Citation Formats

Gilbert, Jack A., Quinn, Robert A., Debelius, Justine, Xu, Zhenjiang Z., Morton, James, Garg, Neha, Jansson, Janet K., Dorrestein, Pieter C., and Knight, Rob. Microbiome-wide association studies link dynamic microbial consortia to disease. United States: N. p., 2016. Web. doi:10.1038/nature18850.
Gilbert, Jack A., Quinn, Robert A., Debelius, Justine, Xu, Zhenjiang Z., Morton, James, Garg, Neha, Jansson, Janet K., Dorrestein, Pieter C., & Knight, Rob. Microbiome-wide association studies link dynamic microbial consortia to disease. United States. doi:10.1038/nature18850.
Gilbert, Jack A., Quinn, Robert A., Debelius, Justine, Xu, Zhenjiang Z., Morton, James, Garg, Neha, Jansson, Janet K., Dorrestein, Pieter C., and Knight, Rob. 2016. "Microbiome-wide association studies link dynamic microbial consortia to disease". United States. doi:10.1038/nature18850.
@article{osti_1342303,
title = {Microbiome-wide association studies link dynamic microbial consortia to disease},
author = {Gilbert, Jack A. and Quinn, Robert A. and Debelius, Justine and Xu, Zhenjiang Z. and Morton, James and Garg, Neha and Jansson, Janet K. and Dorrestein, Pieter C. and Knight, Rob},
abstractNote = {Rapid advances in DNA sequencing, metabolomics, proteomics and computation dramatically increase accessibility of microbiome studies and identify links between the microbiome and disease. Microbial time-series and multiple molecular perspectives enable Microbiome-Wide Association Studies (MWAS), analogous to Genome-Wide Association Studies (GWAS). Rapid research advances point towards actionable results, although approved clinical tests based on MWAS are still in the future. Appreciating the complexity of interactions between diet, chemistry, health and the microbiome, and determining the frequency of observations needed to capture and integrate this dynamic interface, is paramount for addressing the need for personalized and precision microbiome-based diagnostics and therapies.},
doi = {10.1038/nature18850},
journal = {Nature (London)},
number = 7610,
volume = 535,
place = {United States},
year = 2016,
month = 7
}
  • Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of its links with disease. In particular, time-series studies and multiple molecular perspectives are facilitating microbiome-wide association studies, which are analogous to genome-wide association studies. Early findings point to actionable outcomes of microbiome-wide association studies, although their clinical application has yet to be approved. An appreciation of the complexity of interactions among the microbiome and the host's diet, chemistry and health, as well as determining the frequency of observations that are needed to capture and integrate this dynamic interface, is paramountmore » for developing precision diagnostics and therapies that are based on the microbiome.« less
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  • It is widely accepted that microbial communities, not individual microorganisms, are the relevant ecological units, yet what we know about metabolic functioning of microbial communities could be written on a postage stamp. The recent developments in comprehensive molecular methods promise to gain a better understanding of how organisms within communities interact and how communities and their populations evolve. Here we highlight recent advances and insights gathered by the application of proteogenomics to microbial communities. We explore the history of how unrelated fields of microbial ecology, genomics, biological mass spectrometry and informatics converge to the development of a new field ofmore » metaproteomics.« less
  • Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8more » nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.« less