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Amir Zarrinpar

Research

At the Zarrinpar Lab, we are pioneering the study of the gut microbiome and its impact on human health. We explore the intersection of circadian biology, gut physiology, and the gut microbiome to understand their collective influence on a number of diseases, such as obesity, type 2 diabetes, inflammatory bowel disease, cancer, infertility, and cognitive disorders.

The main area of our investigation is the relationship between the gut microbiome and the circadian rhythms of enterocytes and hepatic cells. We are particularly interested in understanding how dysfunctions at this interface contribute to metabolic and inflammatory disorders. Moreover, by studying the microbiome as a dynamic system, and by better understanding the role of specific bacterial functions, we can formulate hypotheses about the role of specific microbial functions affecting host health at specific times.

To test these hypotheses, the lab has pioneered a new technique to functionally manipulate the gut microbiome using engineered native bacteria. This allows for in-depth, mechanistic studies of host-microbe relationships. Our ground-breaking work facilitates the “knock-in” of specific functions to modulate physiology in conventionally-raised wild-type hosts in non-sterile facilities. Our ultimate objective is to translate these discoveries into effective therapies, hoping to significantly improve human health and reduce the impact of numerous diseases, thereby manifesting the true potential of microbiome manipulation. 

Select Publications

  • Russell BJ, Brown SD, Saran AR, Mai I, Lingaraju A, Siguenza N, Maissy E, Dantas Machado AC, Pinto AFM, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Saghatelian A, Knight R, Zarrinpar A. Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes. Cell. 2022 Aug 18;185(17):3263-3277.e15 PMCID: PMC9464905.
  • Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome. Cell Reports. 2022 Jul 5; 40(1):111008 PMCID: PMC9296000.
  • Allaband C, Lingaraju A, Flores Ramos S, Kumar T, Javaheri H, Tiu MD, Dantas Machado AC, Richter RA, Elijah E, Haddad GG, Leone VA, Dorrestein PC, Knight R, Zarrinpar A. Time of Sample Collection is Critical for Microbiome Analysis. Nature Metabolism. 2024 Jul;6(7):1282-1293. PMCID: PMC11309016.
  • Zarrinpar A, Chaix A, Yooseph S, Panda S. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metabolism. 2014; 20(6):1006-17. PMCID: PMC4255146.
  • Zarrinpar A*,†, Chaix A*, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S†. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nature Communications. 2018; 9(1):2872. PMCID: PMC6054678. (*Co-first; †co-corresponding)
  • Allaband C, Lingaraju A, Martino C, Russell B, Tripathi A, Dantas Machado AC, Poulsen O, Zhou D, Xue J, Elijah E, Malhotra A, Dorrestein PC, Knight R, Haddad GG, Zarrinpar A. Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome. mSystems (2021) Jun 29;6(3):e0011621. PMCID: PMC8269208.
  • Hatori M*, Vollmers C*, Zarrinpar A*, DiTacchio L*, Bushong EA, Gill S, Leblanc M, Chaix A, Joens M, Fitzpatrick JA, Ellisman MH, Panda S. Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metabolism. 2012; 15(6):848-60. PMCID: PMC3491655. (*Co-first authors).
  • Chaix A, Zarrinpar A, Miu P, Panda S. Time-restricted feeding is a preventative and therapeutic intervention against diverse nutritional challenges. Cell Metabolism. 2014; 20(6):991-1005. PMCID: PMC4255155.
  • Saran AR, Dave S, Zarrinpar A. Circadian Rhythms in the Pathogenesis and Treatment of Fatty Liver Disease. Gastroenterology. 2020. 158(7):1948-1966.e1. PMCID: PMC7279714.

Biography

Dr. Amir Zarrinpar is a Professor in the Division of Gastroenterology at UC San Diego. Dr. Zarrinpar is a renowned expert in the field of microbiome research and its applications to human health and disease. His work focuses on understanding the complex relationships between the gut microbiome, circadian rhythms, and host metabolism, with the goal of developing novel therapeutic strategies for diseases such as obesity, diabetes, and liver disease. Dr. Zarrinpar has published numerous papers in top-tier journals and has received several awards for his research, including the Litwin IBD Pioneer Award and the American Gastroenterological Association's Microbiome Junior Investigator Research Award. He is also a dedicated mentor and educator, having supervised numerous students, fellows, and junior faculty members in his laboratory.
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