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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Cytometric fingerprinting for analyzing microbial intracommunity structure variation and identifying subcommunity function
Nature Protocols, Volume 8, No. 1, Year 2013
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Description
Functions of complex natural microbial communities are realized by single cells that contribute differently to the overall performance of a community. Usually, molecular and, more recently, deep-sequencing techniques are used for detailed but resource-consuming phylogenetic or functional analyses of microbial communities. Here we present a method for analyzing dynamic community structures that rapidly detects functional (rather than phylogenetic) coherent subcommunities by monitoring changes in cell-specific and abiotic microenvironmental parameters. The protocol involves the use of flow cytometry to analyze elastic light scattering and fluorescent cell labeling, with subsequent determination of cell gate abundance and finally the creation of a cytometric community fingerprint. Abiotic parameter analysis data are correlated with the dynamic cytometric fingerprint to obtain a time-bound functional heat map. The map facilitates the identification of activity hot spots in communities, which can be further resolved by subsequent cell sorting of key subcommunities and concurrent phylogenetic analysis (terminal restriction fragment length polymorphism, tRFLP). The cytometric fingerprint information is based on gate template settings and the functional heat maps are created using an R script. Cytometric fingerprinting and evaluation can be accomplished in 1 d, and additional subcommunity composition information can be obtained in a further 6 d. © 2013 Nature America, Inc. All rights reserved.
Authors & Co-Authors
Koch, Christin
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Günther, Susanne
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Desta, Adey Feleke
Ethiopia, Addis Ababa
Addis Ababa University
Hübschmann, Thomas
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Müller, Susann
Germany, Leipzig
Helmholtz Zentrum Für Umweltforschung
Statistics
Citations: 5
Authors: 5
Affiliations: 2
Identifiers
Doi:
10.1038/nprot.2012.149
ISSN:
17542189
e-ISSN:
17502799