Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.

Autor: Calderón-Franco D; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands., van Loosdrecht MCM; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands., Abeel T; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Weissbrodt DG; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands. david.weissbrodt@ntnu.no.; Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway. david.weissbrodt@ntnu.no.
Jazyk: angličtina
Zdroj: Antonie van Leeuwenhoek [Antonie Van Leeuwenhoek] 2023 Jul; Vol. 116 (7), pp. 667-685. Date of Electronic Publication: 2023 May 08.
DOI: 10.1007/s10482-023-01834-z
Abstrakt: The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L -1 ). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L -1 ). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
(© 2023. The Author(s).)
Databáze: MEDLINE
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