Week 8: Engineering the Gut Microbiome & Mircofluidics

What about this week on Engineering the Gut Microbiome & Microfluidics?

David Kong (MIT), Mariana Matus(Biobots.io).

Gut Microbiome and Microfluidic system

Part I: Design a milli-fluidic device for microbial cell-culture

Part II: Design experimental conditions for a microbial cross-feeding interaction?

Reference

    Requirement Background & Homework-Related Papers
  • Genetics of IBD
      Jostins et al Host Microbiome have shaped the genetic architecture of Inflammatory Bowel Disease. Nature 491:119-24 2012
  • Healthy microbiome - Human Microbiome Project (HMP)
      Jostins et al Host Microbiome have shaped the genetic architecture of Inflammatory Bowel Disease. Nature 491:119-24 2012
      Human Microbiome Consortium: A Framework for Human Microbiome Research Nature 486:215-12
      Glibert et al, Current Understanding of the human microbiome. Nature Medicine 24:392-400, 2018
  • Dysbiosis and diseases
      • Frank et al Molecular-Phylogenetic characterization of Microbial Community imbalances in human inflammatory Bowel Diseases Proc Natl Acad Sci USA 104:13780-5, 2007
      Yilmaz et al. Microbial Network Disturbances in relapsing refractory Crohn’s Disease. Nature Medicine March 7, 2019 Epub ahead of print
  • Host Microbe interactions
      • Dorrestein et al Finding the missing links among Metabolites, Microbes and the Host. Immunity 40:824-832, 2014
      Yilmaz et al. Microbial Network Disturbances in relapsing refractory Crohn’s Disease. Nature Medicine March 7, 2019 Epub ahead of print
      Blander et al Regulation of Inflammation by Microbiota interactions with the Host. Nature Immunology 18:851-860, 2017
  • Microbial Co-culture
      • Goers L, Freemont P, Polizzi KM. Co-culture systems and technologies: taking synthetic biology to the next level. J R Soc Interface. 2014 Jul 6;11(96):20140065. doi: 10.1098/rsif.2014.0065. PMID: 24829281; PMCID: PMC4032528.
      Massively parallel screening of synthetic microbial communities,Jared Kehe, Anthony Kulesa, Anthony Ortiz, Cheri M. Ackerman, Sri Gowtham Thakku, Daniel Sellers, Seppe Kuehn, Jeff Gore, Jonathan Friedman, Paul C. Blainey,Proceedings of the National Academy of Sciences Jun 2019, 116 (26) 12804-12809; DOI: 10.1073/pnas.1900102116
      The lost origin of chemical ecology in the late 19th century,Thomas Hartmann,Proceedings of the National Academy of Sciences Mar 2008, 105 (12) 4541-4546; DOI: 10.1073/pnas.0709231105