Welcoming Remarks

The diversity and abundance of species in the human microbiome have significant implications in the disease process. For instance, microbial communities in healthy mouth and gastrointestinal (GI) habitats can be affected by microenvironmental changes (e.g. temperature, humidity, pH, and chemical composition) that lead to unbalanced interactions promoting the growth of pathogens with consequences including periodontal diseases, C difficile infection, cancer, sepsis, and death. However, tools to characterize and model the signatures of healthy or diseased human microbiomes are lacking, in part due to the inability to culture some species implicated in such dynamics or define the exact cell interactions. Here, we propose to develop synthetic communities modeling human microbiome. Using a high-throughput microfluidic-based technique, we generate microbial communities in artificial microniches (nanocultures) to grow microbes with challenging culturability. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membranes. The PDMS shell provides long-lasting mechanical support, and transport properties enabling long term study of microbial dynamics in controlled microenvironments. The resulting system is used to investigate the physicochemical interactions involved in microbial pathophysiology, microbial persistence, and antibiotic resistance.