Microbiome Publications

Selected publications supported by Phases 1-3:

  1.  Muegge BDKuczynski JKnights DClemente JCGonzález AFontana LHenrissat BKnight RGordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, May 20: 904-7, 2011.
  2.  Kuczynski JCostello EKNemergut DRZaneveld JLauber CLKnights DKoren OFierer NKelley STLey REGordon JIKnight R. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol.,11(5):210, 2010
  3.  Caporaso JGKuczynski JStombaugh JBittinger KBushman FDCostello EKFierer NPeña AGGoodrich JKGordon JIHuttley GAKelley STKnights D,Koenig JELey RELozupone CAMcDonald DMuegge BDPirrung MReeder JSevinsky JRTurnbaugh PJWalters WAWidmann JYatsunenko T,Zaneveld JKnight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods,.May;7(5):335-6, 2010
  4. Turnbaugh PJRidaura VKFaith JJRey FEKnight RGordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. Nov 11;1(6):6ra14, 2009

Phase 3b is an ongoing study led by Dr. Balfour Sartor, MD, and comprehensively compares the fecal microbiome of 30 patients with Crohn’s disease with that of their non-affected sibling and parents daily to coincide the occurrence of flare with any change in the patient’s microbial composition. This study is designed to identify microbial markers that are linked to disease onset or remission.


Publications supported by phase 4 studies:

  1. Presley LLYe JLi XLeblanc JZhang ZRuegger PMAllard JMcGovern DIppoliti ARoth BCui XJeske DRElashoff DGoodglick LBraun JBorneman J. Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface. Inflammatory Bowel Diseases, 18:409-17, 2012
  2. Li E, Hamm CM, Gulati A, Sartor RB, Chen H, Wu X, Zhang T, Rohlf FJ, Zhu W, Gu C, Robertson CE, Pace NR, Boedeker EC, Harpaz N, Yuan J, Weinstock GM, Sodergren E, Frank DN.  Inflammatory bowel diseases phenotype, C. difficile and NOD 2 genotype are associated with shifts in human ileal-associated microbial composition.  PLoS-ONE, accepted for publication.
  3. Frank DN, Robertson CE, Hamm C, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, Pace NR, Li E.  Disease phenotype and genotype are associated with shifts in intestinal associated microbiota in inflammatory bowel diseases.  Inflammatory Bowel Diseases, 17:179-184, 2011
  4. Frank DN, Zhu W, Sartor, RB, Li E.  Investigating the biological and clinical significance of human dysbioses.  Trends in Microbiology, 19:427-34, 2011
  5. Buhlmann P and Horthorn T. Boosting Algorithms: Regularization, Prediction and Model Fitting. Statistical Science 2007;22(4):477-505.
  6.  Dobson AJ. An Introduction to Generalized Linear Models. London: Chapman and Hall, 1990.
  7. Lê S, Josse J and Husson, F. FactoMineR: An R Package for Multivariate Analysis. Journal of Statistical Software. 2008;25(1):1-18.
  8. Bevins, C. L. and N. H. Salzman, 2011. The potter’s wheel: The host’s role in sculpting its microbiota. Cellular and Molecular Life Sciences, in press.
  9. Bevins, C. L. and N. H. Salzman. 2011.  Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nature Reviews Microbiology, 9:356-368, Epub 2011 Mar 22. PMID: 21423246