title: Microbial Nanoculture as an Artificial Microniche.
abstract: Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Tagbo H R
authors.initials: TH
authors.lastname: Niepa
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.|School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Likai
authors.initials: L
authors.lastname: Hou
authors.affiliation: School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Hongyuan
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Goulian
authors.affiliation: Department of Orthodontics, Pediatric Dentistry and Community Oral Health Divisions, University of Pennsylvania, PA19104, USA.
authors.forename: Hyun
authors.initials: H
authors.lastname: Koo
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Kathleen J
authors.initials: KJ
authors.lastname: Stebe
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Daeyeon
authors.initials: D
authors.lastname: Lee
mesh_terms: D001419:Bacteria / Q000254:growth & development*; D018441:Biofilms; D004129:Dimethylpolysiloxanes; D005658:Fungi / Q000254:growth & development*; D044085:Microfluidics / Q000379:methods*; D018613:Microscopy, Confocal; D036103:Nanotechnology
chemical_list: D004129:Dimethylpolysiloxanes; C013830:baysilon