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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]
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  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)
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.
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Shank, Elizabeth A. Considering the Lives of Microbes in Microbial Communities. United States. https://doi.org/10.1128/msystems.00155-17
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Shank, Elizabeth A. Tue . "Considering the Lives of Microbes in Microbial Communities". United States. https://doi.org/10.1128/msystems.00155-17. https://www.osti.gov/servlets/purl/1511022.
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@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}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1128/msystems.00155-17
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Cited by: 8 works
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Figures / Tables:

FIG 1 FIG 1: Schematic representations of methods that are revealing the “lives of microbes.” (A) Example of a strain containing modular fluorescent reporter constructs integrated into its genome at two different neutral loci. This combinatorial approach creates multiply fluorescent strains for use in investigating the relationships between different cells types usingmore » multispectrum imaging. "PX" indicates the promoter of gene x (e.g., a gene upregulated during bacterial differentiation or metabolite production); colored arrows represent genes encoding fluorescent proteins with distinct spectral properties. The right side of the panel illustrates four possible multiply fluorescent cells that could arise from this single genotype. (B) When grown in coculture, bacteria alter their phenotypes (as visualized by colony morphology; top panel) and metabolite production (as visualized by a false-color representation of a metabolite detected using imaging mass spectrometry; bottom panel). The center panel is an overlay image. (C) Synthetic study systems that capture some of the physical and chemical heterogeneity of natural soils will allow us to iteratively study microbial interactions in the laboratory and in their native environments. (D) We have developed microcosms containing a transparent soil-like substrate (green) that allows us to visualize individual microbes (magenta) and their cell-cell interactions in three dimensions over time.« less
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Works referenced in this record:

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Pirated Siderophores Promote Sporulation in Bacillus subtilis
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text, January 2015

  • Rachel, Bleich,; D., Watrous, Jeramie; A., Shank, Elizabeth
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/4r9h-ea25

Pirated Siderophores Promote Sporulation in Bacillus subtilis
text, January 2017

  • Lews, Caro,; M., Grandchamp, Gabrielle; A., Shank, Elizabeth
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/z4t6-s572
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    journal, February 2020

    Unravelling interspecies interactions across heterogeneities in complex biofilm communities
    journal, November 2019

    • Røder, Henriette L.; Olsen, Nanna M. C.; Whiteley, Marvin
    • Environmental Microbiology, Vol. 22, Issue 1
    • DOI: 10.1111/1462-2920.14834

    The role of active movement in fungal ecology and community assembly
    journal, November 2019

    • Bielčik, Miloš; Aguilar-Trigueros, Carlos A.; Lakovic, Milica
    • Movement Ecology, Vol. 7, Issue 1
    • DOI: 10.1186/s40462-019-0180-6

    The role of active movement in fungal ecology and community assembly
    text, January 2019

    • Bielčik, Miloš; Aguilar-Trigueros, Carlos A.; Lakovic, Milica
    • Freie Universität Berlin
    • DOI: 10.17169/refubium-26288
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