Open AccessCombination of high‐throughput microfluidics and FACS technologies to leverage the numbers game in natural product discovery
Author(s) -
Oberpaul Markus,
Brinkmann Stephan,
Marner Michael,
Mihajlovic Sanja,
Leis Benedikt,
Patras Maria A.,
Hartwig Christoph,
Vilcinskas Andreas,
Hammann Peter E.,
Schäberle Till F.,
Spohn Marius,
Glaeser Jens
Publication year - 2022
Publication title -
microbial biotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.287
H-Index - 74
ISSN - 1751-7915
DOI - 10.1111/1751-7915.13872
Subject(s) - bioprospecting , microbiology and biotechnology , metagenomics , computational biology , natural product , biology , drug discovery , bioinformatics , genetics , ecology , biochemistry , gene
Summary High‐throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence‐activated cell sorting (FACS)‐based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter ). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC‐QTOF‐MS/MS‐guided fractionation and microplate‐based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.