Highly parallelized droplet cultivation and prioritization on antibiotic producers from natural microbial communities
- Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Germany
Abstract
Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale-cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.
Data availability
- Amplicon sequence data were deposited to NCBI under the BioProject accession numbers PRJNA623865. For isolated axenic strains, 16S rRNA gene sequences were deposited to GenBank under the accession numbers MT320111 - MT320533.- Source data, encompassing numerical and or taxonomical data and R-analysis files, are provided as RData objects and R scripts for graphs: Fig 2ab, Fig 3abc, Fig 5, Fig 6.Figures 1ab, 4 and 7 do not contain analyzed experimental data but depict workflows and overview information.
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Isolated axenic strains 16S rRNA gene sequencesGenBank; MT320111 - MT320533.
Article and author information
Author details
Miriam A Rosenbaum
Funding
Thuringian Ministry of Eduction, Scienc and Culture (13008-715)
- Lisa Mahler
- Karin Martin
- Martin Roth
Thuringian Ministry of Economy, Labor and Technology (2014FE9037)
- Lisa Mahler
- Thomas Weber
- Martin Roth
German Center for Infection Research DZIF (TTU 09.811)
- Lisa Mahler
- Karin Martin
Deutsche Forschungsgemeinschaft (GSC 214)
- Lisa Mahler
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Bavesh D Kana, University of the Witwatersrand, South Africa
Version history
- Received: November 10, 2020
- Accepted: March 19, 2021
- Accepted Manuscript published: March 25, 2021 (version 1)
- Version of Record published: April 28, 2021 (version 2)
Copyright
© 2021, Mahler et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Highly parallelized droplet cultivation and prioritization on antibiotic producers from natural microbial communities
eLife 10:e64774.
https://doi.org/10.7554/eLife.64774
Further reading
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- Biochemistry and Chemical Biology
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Diverse chemical modifications fine-tune the function and metabolism of tRNA. Although tRNA modification is universal in all kingdoms of life, profiles of modifications, their functions, and physiological roles have not been elucidated in most organisms including the human pathogen, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To identify physiologically important modifications, we surveyed the tRNA of Mtb, using tRNA sequencing (tRNA-seq) and genome-mining. Homology searches identified 23 candidate tRNA modifying enzymes that are predicted to create 16 tRNA modifications across all tRNA species. Reverse transcription-derived error signatures in tRNA-seq predicted the sites and presence of nine modifications. Several chemical treatments prior to tRNA-seq expanded the number of predictable modifications. Deletion of Mtb genes encoding two modifying enzymes, TruB and MnmA, eliminated their respective tRNA modifications, validating the presence of modified sites in tRNA species. Furthermore, the absence of mnmA attenuated Mtb growth in macrophages, suggesting that MnmA-dependent tRNA uridine sulfation contributes to Mtb intracellular growth. Our results lay the foundation for unveiling the roles of tRNA modifications in Mtb pathogenesis and developing new therapeutics against tuberculosis.
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- Cell Biology
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