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With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of “unculturable” species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges. 

The need for assessment tools for microbial dynamics has necessitated the miniaturization of cell-culturing techniques, and the design of microsystems that facilitate the interrogation of microorganisms in-well-defined environments. The nanocultures, as described in this work, are such an assessment tool: nanoliter-sized microcapsules generated using a flow-focusing microfluidic device to sequester and cultivate microbes in a high-throughput manner. By manipulating the chemistry of their polymeric shell, the nanocultures can be designed to achieve functionalities, such as selective permeability, facilitating the transport of metabolites and other small molecules essential to control cell growth and to characterize community dynamics. In this work, the transport properties of a poly(dimethylsiloxane)-based membrane functionalized with N,N-dimethylallylamine (DMAA) have been examined by investigating the diffusion of selected molecules relevant to controlling cell dynamics, including antimicrobials, fluorescent staining probes, and sugars. Furthermore, the Flory–Huggins interaction parameter was evaluated as a predictive tool to elucidate the partitioning and transport of selected molecules into the nanocultures. Diffusion of molecules was confirmed experimentally by generating nanocultures containing Escherichia coli cells, whereby cell growth was used as a proxy for determination of successful molecule diffusion. In our study, we determined that the Flory–Huggins interaction parameters can accurately predict the diffusion of a subset of molecules across PDMS membrane, notably, those with an interaction parameter below a designated critical threshold. However, the prediction becomes less accurate as interaction parameters increased. Overall, these findings will pave the way in our understanding of effectively using the nanocultures to study complex synergistic and antagonistic microbial behaviors in both natural and synthetic communities, with the goal of better simulating natural microenvironments and increasing discoverability of unknown molecules that are relevant to complex microbial communities.