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Title: Considering the Lives of Microbes in Microbial Communities

Abstract

ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Yet, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

Authors:
ORCiD logo [1]
  1. Univ. of North Carolina, Chapel Hill, NC (United States)
Publication Date:
Research Org.:
Univ. of North Carolina, Chapel Hill, NC (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1511022
Grant/Contract Number:  
SC0013887
Resource Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 3; Journal Issue: 2; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bacillus subtilis; bacterial heterogeneity; cell-cell communication; microbial communities; microcosm; secondary metabolism; specialized metabolites

Citation Formats

Shank, Elizabeth A. Considering the Lives of Microbes in Microbial Communities. United States: N. p., 2018. Web. doi:10.1128/msystems.00155-17.
Shank, Elizabeth A. Considering the Lives of Microbes in Microbial Communities. United States. doi:10.1128/msystems.00155-17.
Shank, Elizabeth A. Tue . "Considering the Lives of Microbes in Microbial Communities". United States. doi:10.1128/msystems.00155-17. https://www.osti.gov/servlets/purl/1511022.
@article{osti_1511022,
title = {Considering the Lives of Microbes in Microbial Communities},
author = {Shank, Elizabeth A.},
abstractNote = {ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Yet, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.},
doi = {10.1128/msystems.00155-17},
journal = {mSystems},
number = 2,
volume = 3,
place = {United States},
year = {2018},
month = {4}
}

Journal Article:
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