Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome
Ana Carolina Dantas Machado,
Steven D. Brown,
Amulya Lingaraju,
Vignesh Sivaganesh,
Cameron Martino,
Amandine Chaix,
Peng Zhao,
Antonio F.M. Pinto,
Max W. Chang,
R. Alexander Richter,
Alan Saghatelian,
Alan R. Saltiel,
Rob Knight,
Satchidananda Panda,
Amir Zarrinpar
Affiliations
Ana Carolina Dantas Machado
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Steven D. Brown
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Amulya Lingaraju
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Vignesh Sivaganesh
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Cameron Martino
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Amandine Chaix
Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
Peng Zhao
Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
Antonio F.M. Pinto
Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA
Max W. Chang
Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
R. Alexander Richter
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Alan Saghatelian
Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA
Alan R. Saltiel
Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
Rob Knight
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Satchidananda Panda
Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, USA
Amir Zarrinpar
Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; VA Health Sciences, San Diego, La Jolla, CA, USA; Corresponding author
Summary: Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity (DIO). Although time-restricted feeding (TRF) maintains circadian synchrony and protects against DIO, its impact on the dynamics of the cecal gut microbiome is modest. Thus, other regions of the gut, particularly the ileum, the nexus for incretin and bile acid signaling, may play an important role in entraining peripheral circadian rhythms. We demonstrate the effect of diet and feeding rhythms on the ileal microbiome composition and transcriptome in mice. The dynamic rhythms of ileal microbiome composition and transcriptome are dampened in DIO. TRF partially restores diurnal rhythms of the ileal microbiome and transcriptome, increases GLP-1 release, and alters the ileal bile acid pool and farnesoid X receptor (FXR) signaling, which could explain how TRF exerts its metabolic benefits. Finally, we provide a web resource for exploration of ileal microbiome and transcriptome circadian data.
