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@ARTICLE{NguyenLe:274563,
      author       = {T. A. Nguyen-Le and X. Zhao and M. Bachmann$^*$ and P.
                      Ruelens and J. A. G. M. d. Visser and L. Baraban},
      title        = {{H}igh-{T}hroughput {G}el {M}icrobeads as {I}ncubators for
                      {B}acterial {C}ompetition {S}tudy.},
      journal      = {Micromachines},
      volume       = {14},
      number       = {3},
      issn         = {2072-666X},
      address      = {Basel},
      publisher    = {MDPI},
      reportid     = {DKFZ-2023-00640},
      pages        = {645},
      year         = {2023},
      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.},
      keywords     = {agarose microbeads (Other) / bacterial co-existence (Other)
                      / co-culture (Other) / fluorescence-tagged E. coli (Other) /
                      high-throughput (Other) / millifluidic (Other)},
      cin          = {DD01},
      ddc          = {620},
      cid          = {I:(DE-He78)DD01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36985052},
      doi          = {10.3390/mi14030645},
      url          = {https://inrepo02.dkfz.de/record/274563},
}