High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study

Author:

Nguyen-Le Trang Anh1,Zhao Xinne1,Bachmann Michael12345ORCID,Ruelens Philip6,Visser J. Arjan G. M. de6ORCID,Baraban Larysa17ORCID

Affiliation:

1. Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany

2. Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany

3. National Center for Tumor Diseases (NCT), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany

4. German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

5. German Cancer Consortium (DKTK), 01309 Dresden, Germany

6. Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands

7. Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01069 Dresden, Germany

Abstract

Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1–100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.

Funder

Else Kröner Fresenius Center and DFG

European Research Council

Helmholtz Initiative and Networking Fund

Publisher

MDPI AG

Subject

Electrical and Electronic Engineering,Mechanical Engineering,Control and Systems Engineering

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