Biotechnology Building G53
The goal of my research is to elucidate the interactions between host genetics, dietary intake, and gut microbes in order to benefit host health. My lab's 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.
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.
Bibliography on PubMed:
Poole AC. In the grand scheme of things: identifying reproducible microbial signatures in dietary intervention studies. Cell Host & Microbe. 2019 August 14 ; 26(2).
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 impacts oral and gut microbiomes. Cell Host & Microbe. 2019 April 10; 25(4).
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.
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
Professional Appointments and Memberships
• USDA NIFA grant review panel, study section on Food and Human Health,
• Associate Editor on the Editorial Board of Microbiome in Health and Disease, a
specialty section within Frontiers in Cellular and Infection Microbiology
• Member, Cornell University Center for Vertebrate Genomics
• Faculty Fellow, Cornell University Atkinson Center for a Sustainable Future
• Cornell Institute of Host-Microbe Interactions and Disease
• American Diabetes Association
Cornell University Graduate Field Memberships
• Nutritional Sciences
NS 4200: Diet and the microbiome
Offered Spring semester
All colleges and majors welcome.
Required prerequisites: Junior, senior, graduate enrollment status. One semester introductory biology lecture (e.g. BIOMG 1350) and one semester introductory chemistry (e.g. CHEM 2070).
Recommended prerequisites: Microbiology (e.g. BIOMI 2900) and introductory statistics (e.g. STSCI 2150, PAM 2100, AEM 2100, or equivalent).
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.
Learning objectives and outcomes:
- Engage in conversation using terms and techniques in the microbiome field
- Identify strengths, limits, and confounding factors in studies addressing diet:microbiome associations
- Assess the relevance of correlations between dietary intake, gut microbes, and physiological status
- Design a study to address a question
- Generate good arguments for both sides of an issue
- Present technical information clearly and in a convincing manner
Class format: You will get out of this class what you put into it. At least half of this course is flipped; there are not many formal lectures. If you hate active learning, NS 4200 may not be the best course for you. Prior to class, you will have been given a reading or written assignment. There will almost always be in-class discussion and/or activities counting toward your grade.
Assessment and evaluation:
Assessment and Percent of Grade:
- In-class assignments/activities/quizzes = 15%
- Thought questions and homework = 15%
- Shark Tank proposal = 20%
- Preliminary examination = 20%
- Group presentations = 20%
- Final Exam = 10%
Course evaluation feedback
In Spring 2019, the students gave this course an overall score of 4.5 / 5
When asked whether this course advanced their understanding of the subject matter, the average student rating was 4.7 / 5
When asked whether the instructor created and encouraged an inclusive classroom climate, the average student rating was 4.91 / 5
In the anonymous online course evaluation survey, I also asked the students, “What advice would you give someone trying to decide whether to take the class?” All of the responses seemed positive to me. Here are some examples:
Take it if you’re interested in the topic, otherwise the readings will be overwhelming
Understand that it is very group work focused, and involves a lot of learning through primary literature. A very hands-on course.
If you’re curious about the subject and want to gain more familiarity with analyzing scientific papers, this course is a great opportunity to learn more. It involves more in class question activities than lectures, so consider that with your learning style.
Please take this class,even if you have no interest in microbiome at least you will learn how to read scientific papers and critically think about them. Especially if you have yet to take the MCAT take this class
Take the course if you want a good introduction to the field of microbiome research and want to expand upon your analytical and evaluative skills when reading primary scientific literature
Don’t miss the first lecture
California Institute of Technology (Caltech)
Bachelor of Science, Engineering and Applied Sciences, 1999
University of Washington
Doctor of Philosophy, Genome Sciences, 2010
Research Advisor: Dr. Leo J. Pallanck
Post-Doctoral Research, Microbiology and Molecular Biology and Genetics
Research Advisor: Dr. Ruth E. Ley
- Division of Nutritional Sciences, Pre-Health Bridge Program PostBacc committee, October 2018 - April 2019
- Graduate Field of Nutrition Academic Affairs Committee, November 2019 - present