title: Tools for the Microbiome: Nano and Beyond.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Julie S
authors.initials: JS
authors.lastname: Biteen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Blainey
authors.affiliation: The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States.
authors.forename: Zoe G
authors.initials: ZG
authors.lastname: Cardon
authors.affiliation: The Kavli Foundation , Oxnard, California 93030, United States.
authors.forename: Miyoung
authors.initials: M
authors.lastname: Chun
authors.affiliation: Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Pieter C
authors.initials: PC
authors.lastname: Dorrestein
authors.affiliation: Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Fraser
authors.affiliation: Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States.|Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.affiliation: Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: Jeff F
authors.initials: JF
authors.lastname: Miller
authors.forename: Aydogan
authors.initials: A
authors.lastname: Ozcan
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Prather
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.affiliation: Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States.
authors.forename: Edward G
authors.initials: EG
authors.lastname: Ruby
authors.affiliation: Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States.
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Silver
authors.affiliation: The Kavli Foundation , Oxnard, California 93030, United States.
authors.forename: Sharif
authors.initials: S
authors.lastname: Taha
authors.affiliation: Center for Marine Cytometry , Concrete, Washington 98237, United States.|Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile.
authors.forename: Ger
authors.initials: G
authors.lastname: van den Engh
authors.forename: Paul S
authors.initials: PS
authors.lastname: Weiss
authors.forename: Gerard C L
authors.initials: GC
authors.lastname: Wong
authors.affiliation: Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Aaron T
authors.initials: AT
authors.lastname: Wright
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Young
mesh_terms: D000391:Air Microbiology; D018441:Biofilms / Q000254:growth & development*; D035843:Biomedical Research / Q000295:instrumentation* / Q000379:methods; D004784:Environmental Monitoring / Q000379:methods; D005554:Forensic Medicine / Q000379:methods; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D064349:Genome, Microbial; D023281:Genomics / Q000295:instrumentation / Q000379:methods; D006801:Humans; D059013:Microbial Consortia / Q000235:genetics*; D056265:Microbial Interactions; D036103:Nanotechnology / Q000295:instrumentation* / Q000379:methods; D012988:Soil Microbiology; D014871:Water Microbiology