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Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics

Dam, H. T. 1; Vollmers, J. 1; Sobol, M. S. 1; Cabezas, A.; Kaster, A.-K. 1
1 Institut für Biologische Grenzflächen (IBG), Karlsruher Institut für Technologie (KIT)


Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.

Verlagsausgabe §
DOI: 10.5445/IR/1000123293
Veröffentlicht am 04.09.2020
DOI: 10.3389/fmicb.2020.01377
Zitationen: 12
Web of Science
Zitationen: 9
Zitationen: 13
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Biologische Grenzflächen (IBG)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2020
Sprache Englisch
Identifikator ISSN: 1664-302X
KITopen-ID: 1000123293
HGF-Programm 47.02.05 (POF III, LK 01) Zellpopul.auf Biofunk.Oberflächen IBG-5
Erschienen in Frontiers in microbiology
Verlag Frontiers Media
Band 11
Seiten Art.-Nr.: 1377
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
Vorab online veröffentlicht am 22.07.2020
Nachgewiesen in Web of Science
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