The candidate, Dr. Amir Zarrinpar, presents a 5-year career development plan that seeks to characterize the relationship of the gut microbiome and metabolism while establishing an academic career as a physician scientist in the field of gastroenterology. Obesity and its associated metabolic disease afflict more than one third of the population of the United States and are a source of considerable morbidity and mortality. Dr. Zarrinpar and his colleagues co-discovered time restricted feeding (TRF), a paradigm that preserves normal feeding/fasting cycles and prevents obesity and other metabolic disorders associated with a high fat diet. By maintaining the natural feeding rhythms without altering nutritional intake, mice on a TRF protocol do not become obese or have hallmarks of dysmetabolism. However, the mechanism for TRF still remains elusive, though it likely alters gut luminal signaling and the gut microbiome. Our primary hypothesis for the proposed studies is that TRF imparts its beneficial effects by altering the gut microbiome and the genes that the microflora express (i.e. the metatranscriptome). This hypothesis will be pursued with three specific aims that investigate the relationship between the gut microbiome, metabolism, and gut gene expression in context of the TRF paradigm.
Specific aim 1 tests the hypothesis that specific TRF-induced changes protect against obesity by altering host-microbiome homeostasis and luminal signaling. TRF will help identify a small set of candidate bacterial species/genes that play a protective role and another set that play a detrimental role in metabolism.
Specific aim 2 tests the hypothesis that TRF's beneficial effects result from changes in the gut microbiome. The microbiome will be changed by either using antibiotics, shared bedding in wild-type mice, or transplantation into germ-free mice. Lastly, specific aim 3 tests the hypothesis that the gut microbiome and TRF mediate their beneficial effects through bile acid signaling pathways. By pharmacologically manipulating this signaling pathway, its necessity in mediating the beneficial effects of TRF and gut microbiome changes can be observed.
These specific aims will help us understand the role of gut microbiome to intestinal homeostasis, gut gene expression, and luminal signaling. The anticipated results of these experiments are that the gut microbiome is a dynamic environment with cyclical changes in microflora populations and their gene expressions. Diet induced obesity disrupts this dynamic environment and selects for obesogenic bacteria. TRF on the other hand, maintains the cyclical changes in the gut microbiome and selects for obesity-protective species in the microflora. Any changes in the microbiome will be correlated to changes in the gut gene expression to find physiological consequences of these shifts. Alteration of the gut microbiome in antibiotic induced microbiome depletion and germ-free mice would confirm that microbiome changes are necessary for the metabolic phenotype observed in these mice. Furthermore, the bile acid signaling pathway is the main way that the gut microbiome mediates its protection against obesity. The three specific aims proposed will substantially advance our understanding of the physiological role that the gut microbiome plays in metabolism. By better understanding the gut microbiome's relationship to intestinal homeostasis, gut gene expression, and luminal signaling, these pathways can then be physiologically manipulated to treat and prevent obesity and its associated metabolic diseases. Dr. Zarrinpar is well qualified to carry out the research outlined in this proposal. He has successfully completed projects of comparable complexity as part of his PhD thesis. He will further his training by acquiring expertise in performing high quality gut microbiome experiments as well as further establish expertise in circadian biology, metabolic regulation, and intestinal homeostasis. Dr. Zarrinpar has recruited a team of outstanding mentors from three different local institutions. His mentor, Dr. Satchidananda Panda, has experience in studying circadian circuitry and using genetic, genomic, and biochemical approaches to identify numerous genes that are under circadian regulation. Dr. Mark Adams, Professor and Scientific Director of J. Craig Venter Institute (JCVI) will provide expertise in studying the gut microbiome. Dr. Christopher Glass, who has extensive experience training physician scientists, will advise him on major career related issues and help navigate the academic promotion process. In addition, Dr. Sheila Crowe, a nationally recognized educator and mentor, will serve on the advisory committee. She will mentor Dr. Zarrinpar as he finds translational and clinical applications of the studies proposed in his application. The advisory committee will meet, at minimum, every 6 months to ensure a successful scientific program. Successful completion of the specific aims and career development plan outlined in this proposal will allow Dr. Zarrinpar to learn how to perform high quality gut microbiome projects and to develop into an independent investigator in the field of gastroenterology and metabolism.

Public Health Relevance

Obesity and its associated metabolic diseases affects more than one-third of adults in the United States of America, with an estimated medical cost of $147 billion. The studies in this proposal investigate the relationship between circadian gene expression and the gut microbiome and how the two together contribute to, and protect from, obesity. By deciphering the ways in which the gut microbiome affects metabolism, novel therapies can be discovered to treat obesity and metabolic diseases.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Clinical Investigator Award (CIA) (K08)
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Kidney, Urologic and Hematologic Diseases D Subcommittee (DDK)
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Saslowsky, David E
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University of California, San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
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Zarrinpar, Amir; Chaix, Amandine; Xu, Zhenjiang Z et al. (2018) Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun 9:2872
Kurnool, S; Nguyen, N H; Proudfoot, J et al. (2018) High body mass index is associated with increased risk of treatment failure and surgery in biologic-treated patients with ulcerative colitis. Aliment Pharmacol Ther 47:1472-1479
Singh, Siddharth; Dulai, Parambir S; Zarrinpar, Amir et al. (2017) Obesity in IBD: epidemiology, pathogenesis, disease course and treatment outcomes. Nat Rev Gastroenterol Hepatol 14:110-121
Chaix, Amandine; Zarrinpar, Amir; Panda, Satchidananda (2016) The circadian coordination of cell biology. J Cell Biol 215:15-25
Anand, Gobind; Zarrinpar, Amir; Loomba, Rohit (2016) Targeting Dysbiosis for the Treatment of Liver Disease. Semin Liver Dis 36:37-47
Zarrinpar, Amir; Chaix, Amandine; Panda, Satchidananda (2016) Daily Eating Patterns and Their Impact on Health and Disease. Trends Endocrinol Metab 27:69-83
Marotz, Clarisse A; Zarrinpar, Amir (2016) Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation. Yale J Biol Med 89:383-388
Zarrinpar, Amir; Gupta, Shakti; Maurya, Mano R et al. (2016) Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study. Gut 65:1546-54
Chaix, Amandine; Zarrinpar, Amir (2015) The effects of time-restricted feeding on lipid metabolism and adiposity. Adipocyte 4:319-24