Considering the Lives of Microbes in Microbial Communities

Shank, Elizabeth A.

doi:10.1128/msystems.00155-17

Title: Considering the Lives of Microbes in Microbial Communities

Journal Article · Tue Apr 10 00:00:00 EDT 2018 · mSystems

DOI:https://doi.org/10.1128/msystems.00155-17· OSTI ID:1511022

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Univ. of North Carolina, Chapel Hill, NC (United States)

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.

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Research Organization:: University of North Carolina, Chapel Hill, NC (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0013887

OSTI ID:: 1511022

Journal Information:: mSystems, Vol. 3, Issue 2; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 17 works

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Cited By (5)

Microbe-driven chemical ecology: past, present and future Schmidt, Ruth; Ulanova, Dana; Wick, Lukas Y. The ISME Journal, Vol. 13, Issue 11 https://doi.org/10.1038/s41396-019-0469-x	journal	July 2019
Spatial metabolomics of in situ host–microbe interactions at the micrometre scale Geier, Benedikt; Sogin, Emilia M.; Michellod, Dolma Nature Microbiology, Vol. 5, Issue 3 https://doi.org/10.1038/s41564-019-0664-6	journal	February 2020
Unravelling interspecies interactions across heterogeneities in complex biofilm communities Røder, Henriette L.; Olsen, Nanna M. C.; Whiteley, Marvin Environmental Microbiology, Vol. 22, Issue 1 https://doi.org/10.1111/1462-2920.14834	journal	November 2019
The role of active movement in fungal ecology and community assembly Bielčik, Miloš; Aguilar-Trigueros, Carlos A.; Lakovic, Milica Movement Ecology, Vol. 7, Issue 1 https://doi.org/10.1186/s40462-019-0180-6	journal	November 2019
The role of active movement in fungal ecology and community assembly Bielčik, Miloš; Aguilar-Trigueros, Carlos A.; Lakovic, Milica Freie Universität Berlin https://doi.org/10.17169/refubium-26288	text	January 2019

Figures / Tables (1)

X" 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." data-ostiid="1511022">

FIG 1(p. 2) FIG 1

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Bacillus subtilis
bacterial heterogeneity
cell-cell communication
microbial communities
microcosm
secondary metabolism
specialized metabolites