Tools for the Microbiome: Nano and Beyond

Biteen, JS, Blainey PC, Cardon ZG, Chun MY, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD.  2016.  Tools for the Microbiome: Nano and Beyond. Acs Nano. 10:6-37.

Date Published:



airborne bacterial communities, atmospheric ice nuclei, biofilms, human gut microbiome, imaging mass-spectrometry, pseudomonas-aeruginosa, scanning-tunneling-microscopy, sea spray aerosol, self-assembled monolayers, single-cell genomics, squid-vibrio, symbiosis


The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.