Microbiome Publications

Selected publications supported by Phases 1-3:

  1.  Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, May 20: 904-7, 2011.
  2.  Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol.,11(5):210, 2010
  3.  Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D,Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T,Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods,.May;7(5):335-6, 2010
  4. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon 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 LL, Ye J, Li X, Leblanc J, Zhang Z, Ruegger PM, Allard J, McGovern D, Ippoliti A, Roth B, Cui X, Jeske DR, Elashoff D, Goodglick L, Braun J, Borneman 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