Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism

Cell Host and Microbe

Volumn 17, Issue 5, 2015, Pages 681-689

  Leone, Vanessa ^a   Gibbons, Sean M ^a,b   Martinez, Kristina ^a   Hutchison, Alan L ^a   Huang, Edmond Y ^a   Cham, Candace M ^a   Pierre, Joseph F ^a   Heneghan, Aaron F ^c   Nadimpalli, Anuradha ^a   Hubert, Nathaniel ^a   Zale, Elizabeth ^a   Wang, Yunwei ^a   Huang, Yong ^a   Theriault, Betty ^a   Dinner, Aaron R ^a   Musch, Mark W ^a   Kudsk, Kenneth A ^c   Prendergast, Brian J ^d   Gilbert, Jack A ^a,b   Chang, Eugene B ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b Institute for Genomics and Systems Biology   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN SULFIDE;

ANIMAL EXPERIMENT; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; DYSBIOSIS; FAT INTAKE; GENE EXPRESSION; HOST; INTESTINE FLORA; LIVER CELL; MALE; MEDIOBASAL HYPOTHALAMUS; METABOLISM; METABOLITE; MICROBIAL COMMUNITY; MOUSE; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; TRANSCRIPTOMICS; ANIMAL; BODY WEIGHT; CHEMICALLY INDUCED; DISEASE MODEL; DNA SEQUENCE; GASTROINTESTINAL TRACT; GENE EXPRESSION PROFILING; LIPID DIET; LIPID METABOLISM; LIVER; MICROBIOLOGY; MOLECULAR GENETICS; OBESITY; PATHOLOGY;

MUS;

ANIMALS; BODY WEIGHT; CIRCADIAN CLOCKS; DIET, HIGH-FAT; DISEASE MODELS, ANIMAL; DYSBIOSIS; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; GENE EXPRESSION PROFILING; LIPID METABOLISM; LIVER; MICE; MOLECULAR SEQUENCE DATA; OBESITY; SEQUENCE ANALYSIS, DNA;

EID: 84929300092     PISSN: 19313128     EISSN: 19346069     Source Type: Journal    
DOI: 10.1016/j.chom.2015.03.006     Document Type: Article

References (38)

1. F. Bäckhed, H. Ding, T. Wang, L.V. Hooper, G.Y. Koh, A. Nagy, C.F. Semenkovich, and J.I. Gordon The gut microbiota as an environmental factor that regulates fat storage Proc. Natl. Acad. Sci. USA 101 2004 15718 15723
2. F. Bäckhed, J.K. Manchester, C.F. Semenkovich, and J.I. Gordon Mechanisms underlying the resistance to diet-induced obesity in germ-free mice Proc. Natl. Acad. Sci. USA 104 2007 979 984
3. A. Balsalobre, F. Damiola, and U. Schibler A serum shock induces circadian gene expression in mammalian tissue culture cells Cell 93 1998 929 937
4. J. Bass, and F.W. Turek Sleepless in America: a pathway to obesity and the metabolic syndrome? Arch. Intern. Med. 165 2005 15 16
5. B. Björkholm, C.M. Bok, A. Lundin, J. Rafter, M.L. Hibberd, and S. Pettersson Intestinal microbiota regulate xenobiotic metabolism in the liver PLoS ONE 4 2009 e6958
6. J.G. Caporaso, K. Bittinger, F.D. Bushman, T.Z. DeSantis, G.L. Andersen, and R. Knight PyNAST: a flexible tool for aligning sequences to a template alignment Bioinformatics 26 2010 266 267
7. J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Peña, J.K. Goodrich, and J.I. Gordon QIIME allows analysis of high-throughput community sequencing data Nat. Methods 7 2010 335 336
8. F.A. Carvalho, O. Koren, J.K. Goodrich, M.E. Johansson, I. Nalbantoglu, J.D. Aitken, Y. Su, B. Chassaing, W.A. Walters, and A. González Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice Cell Host Microbe 12 2012 139 152
9. L.A. David, A.C. Materna, J. Friedman, M.I. Campos-Baptista, M.C. Blackburn, A. Perrotta, S.E. Erdman, and E.J. Alm Host lifestyle affects human microbiota on daily timescales Genome Biol. 15 2014 R89
10. -/- mice Nature 487 2012 104 108
11. C. Dibner, U. Schibler, and U. Albrecht The mammalian circadian timing system: organization and coordination of central and peripheral clocks Annu. Rev. Physiol. 72 2010 517 549
12. K.L. Eckel-Mahan, V.R. Patel, S. de Mateo, R. Orozco-Solis, N.J. Ceglia, S. Sahar, S.A. Dilag-Penilla, K.A. Dyar, P. Baldi, and P. Sassone-Corsi Reprogramming of the circadian clock by nutritional challenge Cell 155 2013 1464 1478
13. J. Friedman, and E.J. Alm Inferring correlation networks from genomic survey data PLoS Comput. Biol. 8 2012 e1002687
14. W. Huang, K.M. Ramsey, B. Marcheva, and J. Bass Circadian rhythms, sleep, and metabolism J. Clin. Invest. 121 2011 2133 2141
15. E.Y. Huang, V.A. Leone, S. Devkota, Y. Wang, M.J. Brady, and E.B. Chang Composition of Dietary Fat Source Shapes Gut Microbiota Architecture and Alters Host Inflammatory Mediators in Mouse Adipose Tissue. J. Parenter. Enteral Nutr. 37 2013 746 754
16. M. Huch, C. Dorrell, S.F. Boj, J.H. van Es, V.S. Li, M. van de Wetering, T. Sato, K. Hamer, N. Sasaki, and M.J. Finegold In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration Nature 494 2013 247 250
17. A.L. Hutchison, M. Maienschein-Cline, A.H. Chiang, S.M.A. Tabei, H. Gudjonson, N. Bahroos, R. Allada, and A.R. Dinner Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data PLoS Comp. Biol. 11 2015 e1004094 10.1371/journal.pcbi.1004094
18. S.A. Joyce, J. MacSharry, P.G. Casey, M. Kinsella, E.F. Murphy, F. Shanahan, C. Hill, and C.G.M. Gahan Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut Proc. Natl. Acad. Sci. USA 111 2014 7421 7426
19. R.V. Kartha, J. Zhou, L.B. Hovde, B.W. Cheung, and H. Schröder Enhanced detection of hydrogen sulfide generated in cell culture using an agar trap method Anal. Biochem. 423 2012 102 108
20. A. Kohsaka, A.D. Laposky, K.M. Ramsey, C. Estrada, C. Joshu, Y. Kobayashi, F.W. Turek, and J. Bass High-fat diet disrupts behavioral and molecular circadian rhythms in mice Cell Metab. 6 2007 414 421
21. E. Larsson, V. Tremaroli, Y.S. Lee, O. Koren, I. Nookaew, A. Fricker, J. Nielsen, R.E. Ley, and F. Bäckhed Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88 Gut 61 2012 1124 1131
22. S. Liu, J.D. Brown, K.J. Stanya, E. Homan, M. Leidl, K. Inouye, P. Bhargava, M.R. Gangl, L. Dai, and B. Hatano A diurnal serum lipid integrates hepatic lipogenesis and peripheral fatty acid use Nature 502 2013 550 554
23. P. Louis, P. Young, G. Holtrop, and H.J. Flint Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene Environ. Microbiol. 12 2010 304 314
24. C. Lozupone, and R. Knight UniFrac: a new phylogenetic method for comparing microbial communities Appl. Environ. Microbiol. 71 2005 8228 8235
25. D. McDonald, M.N. Price, J. Goodrich, E.P. Nawrocki, T.Z. DeSantis, A. Probst, G.L. Andersen, R. Knight, and P. Hugenholtz An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea ISME J. 6 2012 610 618
26. A. Mukherji, A. Kobiita, T. Ye, and P. Chambon Homeostasis in intestinal epithelium is orchestrated by the circadian clock and microbiota cues transduced by TLRs Cell 153 2013 812 827
27. M.N. Price, P.S. Dehal, and A.P. Arkin FastTree 2 - approximately maximum-likelihood trees for large alignments PLoS ONE 5 2010 e9490
28. S. Rabot, M. Membrez, A. Bruneau, P. Gérard, T. Harach, M. Moser, F. Raymond, R. Mansourian, and C.J. Chou Germ-free C57BL/6J mice are resistant to high-fat-diet-induced insulin resistance and have altered cholesterol metabolism FASEB J. 24 2010 4948 4959
29. G. Renom, P. Bulois, S. Hafraoui, J.F. Colombel, and P.M. Degand Simple gas chromatography analysis of faecal butyrate: application to patients at risk of pouchitis Clin. Chem. Lab. Med. 39 2001 15 19
30. V.K. Ridaura, J.J. Faith, F.E. Rey, J. Cheng, A.E. Duncan, A.L. Kau, N.W. Griffin, V. Lombard, B. Henrissat, and J.R. Bain Gut microbiota from twins discordant for obesity modulate metabolism in mice Science 341 2013 1241214
31. C.A. Thaiss, D. Zeevi, M. Levy, G. Zilberman-Schapira, J. Suez, A.C. Tengeler, L. Abramson, M.N. Katz, T. Korem, and N. Zmora Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis Cell 159 2014 514 529
32. P.J. Turnbaugh, R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis, and J.I. Gordon An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 2006 1027 1031
33. E. Van Cauter, K.S. Polonsky, and A.J. Scheen Roles of circadian rhythmicity and sleep in human glucose regulation Endocr. Rev. 18 1997 716 738
34. M. Vital, C.R. Penton, Q. Wang, V.B. Young, D.A. Antonopoulos, M.L. Sogin, H.G. Morrison, L. Raffals, E.B. Chang, and G.B. Huffnagle A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community Microbiome 1 2013 8 21
35. M. Vital, J. Gao, M. Rizzo, T. Harrison, and J.M. Tiedje Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia ISME J. 9 2014 1 12
36. Q. Wang, G.M. Garrity, J.M. Tiedje, and J.R. Cole Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl. Environ. Microbiol. 73 2007 5261 5267
37. Y. Wang, J.D. Hoenig, K.J. Malin, S. Qamar, E.O. Petrof, J. Sun, D.A. Antonopoulos, E.B. Chang, and E.C. Claud 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis ISME J. 3 2009 944 954
38. A. Zarrinpar, A. Chaix, S. Yooseph, and S. Panda Diet and feeding pattern affect the diurnal dynamics of the gut microbiome Cell Metab. 20 2014 1006 1017