Assistant Professor
Biotechnology Building G53/Savage Hall 211
Ithaca, New York
Division of Nutritional Sciences

Our goal is to elucidate the interactions between host genetics, dietary intake, and gut microbes in order to benefit host health. Our current projects focus on  the amylase locus, a result of gene copy number variation, which encodes an enzyme involved in starch degradation. Amylase gene copy number has been associated with glucose homeostasis, but knowledge of the underlying mechanisms is incomplete. We seek to determine the association of this locus with host health status. Additionally, we are interested in microbial involvement in starch digestion. Our research is interdisciplinary; we combine knowledge from genetics, nutrition, physiology, microbiology, and computational biology. Our findings could help to develop a systems biology approach to personalized nutrition to assist in treating metabolic disorders or decreasing disease risk.

Poole AC, Goodrich JK, Youngblut ND, Ruaud A, Luque GG, Sutter JL, Waters JL, Shi Q, Mohamed E-H, Johnson LM, Bar HY, Huson DH, Booth JG, Ley RE. Human salivary amylase gene copy number modulates the diversity and function of the gut microbiome. Manuscript revised and resubmitted. Preprints available on bioRxiv.

Bibliography on PubMed:

Poole AC*, Pischel L*, Ley C, Suh G, Goodrich JK, Haggerty TD, Ley RE, Parsonnet J. Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome. mSphere, American Society for Microbiology. 2016 May 18; 1(3). PMID: 27303746.

Jackson MA, Goodrich JK, Maxan M-E, Freedberg DE, Abrams JA, Poole AC, Sutter JL, Welter D, Ley RE, Bell JT, Spector TD, Steves CJ. Proton pump inhibitors alter the composition of the gut microbiota. Gut.  2016 May; 65(5): 749-56. PMID: 26719299.

Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley RE, Walter MT, Angenent L. Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics. Front. Microbiol. 2016 Jan 11; 6: 1523. PMID: 26793170.

Sun S, Lourie R, Cohen SB, Ji Y, Goodrich JK, Poole AC, Ley RE, Denkers EY, McGuckin MA, Long Q, Duhamel GE, Simpson KW, Qi L. Epithelial Sel1L is required for the maintenance of intestinal homeostasis. Molecular Biology of the Cell. 2015 Dec 2; Epub. PMID: 26631554.

Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, Gewirtz AT. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. 2015 Mar 5; 519(7541): 92-6. PMID: 25731162.

Panke-Buisse K, Poole AC, Goodrich JK, Ley RE, Kao-Kniffin J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME Journal. 2015 Mar 17; 9(4): 980-89. PMID: 25350154.

Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE. Human genetics shape the gut microbiome. Cell. 2014 Nov 6; 159(4): 789-99. PMID: 25417156.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell. 2014 Jul 17; 158(2): 250-62. PMID: 25036628.

Ji Y, Sun S, Goodrich JK, Kim H, Poole AC, Duhamel GE, Ley RE, Qi L. Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Cell Reports. 2014 Jul 10; 8(1): 137-49. PMID: 24953658.

Dissected Drosophila brain stained with anti-tyrosine hydroxylase and imaged with confocal microscopy. Credit: A. Poole

Burman JL, Yu S, Poole AC, Decal RB, Pallanck LJ. Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26): 10438-43. PMID: 22691499.

Poole AC*, Thomas RE*, Yu S, Vincow ES, Pallanck LJ. The mitochondrial fusion-promoting factor Mitofusin is a substrate of the PINK1/Parkin pathway. PLoS One. 2010 Apr 7. PMID: 20383334.

Poole AC*, Thomas RE*, Andrews LA, McBride HM, Whitworth AJ, Pallanck LJ. The PINK1/Parkin pathway regulates mitochondrial morphology. Proc Natl Acad Sci U S A. 2008 Feb 5; 105(5): 1638-43. PMID: 18230723.

Kumar KG, Poole AC, York B, Volaufova J, Zuberi A, Richards BK. Quantitative trait loci for carbohydrate and total energy intake on mouse chromosome 17: congenic strain confirmation and candidate gene analyses (Glo1, Glp1r). Am J Physiol Regul Integr Comp Physiol. 2006 Jan; 292(1): R207-16. PMID: 16946080.

Smith Richards BK, Belton BN, Poole AC, Mancuso JJ, Churchill GA, Li R, Volaufova J, Zuberi A, York B. QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories. Physiol Genomics. 2002 Dec 3; 11(3): 205-17. PMID: 12388789.

* co-first author

NS 4200: Diet and the microbiome

Course description: In this course, students will acquire a present-day overview of the reported effects of diet on the microbiome with an emphasis on host physiology outcomes. The microbiome field is rapidly evolving, and this course has no textbook; we will mainly be assessing primary literature and scientific reviews. Students will learn to critically analyze the conclusions drawn from microbiome studies to empower them to make informed judgements as new research findings are reported. This course is independent of BIOMI 3210 Human microbes and health and BME 6130 Engineering the microbiome. Students could potentially take all three.

Examples of topics to be covered:

  • Carnivores versus herbivores
  • Bacteria-produced metabolites and heart disease
  • Soy metabolites and health
  • Dietary fiber and colon cancer risk
  • Prebiotics, probiotics, and synbiotics
  • Inflammation in the gut – artificial sweeteners, dietary emulsifiers, and cricket consumption
  • Study design
  • Reproducibility in science

Caltech (California Institute of Technology) 
Bachelor of Science, Engineering and Applied Sciences, 1999

University of Washington
Doctor of Philosophy, Genome Sciences, 2010
Research Advisor: Dr. Leo J. Pallanck

Cornell University
Post-Doctoral Research, Microbiology and Molecular Biology and Genetics, 2011 – 2017
Research Advisor: Dr. Ruth E. Ley