1. Husse J, Eichele G, Oster, H. Synchronization of the mammalian circadian timing system: light can control peripheral clocks independently of the SCN clock: alternate routes of entrainment optimize the alignment of the body's circadian clock network with external time. BioEssays 2015; 37: 1119-1128.
2. Yan RN, Ho C-T, Zhang X. Interaction between tea polyphenols and intestinal microbiota in host metabolic diseases from the perspective of the gut‐brain axis. Mol Nutr Food Res. 2020; 64: 2000187.
3. Musiek ES, Holtzman DM. Mechanisms linking circadian clocks, sleep, and neurodegeneration. Science. 2016; 354: 1004-1008.
4. Goel N, Basner M, Rao H, Dinges DF. Circadian rhythms, sleep deprivation, and human performance. Prog Mol Biol Transl Sci. 2013; 119: 155-190.
5. Dallmann R, Viola AU, Tarokh L, Cajochen C, Brown SA. The human circadian metabolome. Proc Natl Acad Sci USA. 2012; 109: 2625-2629.
6. Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Suez J, Tengeler AC, Abramson L, Katz MN, Korem T, Zmora N, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014; 159: 514-529.
7. Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, et al. Microbiota diurnal rhythmicity programs host transcriptome oscillations. Cell. 2016; 167: 1495-1510.
8. Gentile CL, Weir TL. The gut microbiota at the intersection of diet and human health. Science. 2018; 362: 776-780.
9. Wu JY, Wang K, Wang XM, Pang YL, Jiang CT. The role of the gut microbiome and its metabolites in metabolic diseases. Protein Cell. 2021; 12: 360-373.
10. Vuong HE, Yano JM, Fung TC, Hsiao EY. The microbiome and host behavior. Annu Rev Neurosci. 2017; 40: 21-49.
11. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015; 21: 8787-8803.
12. Qi GY, Mi YS, Liu ZG, Fan R, Qiao QL, Sun YL, Ren B, Liu XB. Dietary tea polyphenols ameliorate metabolic syndrome and memory impairment via circadian clock related mechanisms. J Funct Foods. 2017; 34: 168-180.
13. Zhang M, Zhang X, Ho C-T, Huang QR. Chemistry and health effect of tea polyphenol (-)-epigallocatechin 3-O-(3-O-Methyl) gallate. J Agric Food Chem. 2019; 67: 5374-5378.
14. Guo TT, Ho C-T, Zhang X, Cao JX, Wang HF, Shao XF, Pan DD, Wu ZF. Oolong tea polyphenols ameliorate circadian rhythm of intestinal microbiome and liver clock genes in mouse model. J Agric Food Chem.2019; 67: 11969-11976.
15. Zhang, X. Chen YH, Zhu JY, Zhang M, Ho C-T, Huang QR, Cao JX. Metagenomics analysis of gut microbiota in a high fat diet-induced obesity mouse model fed with (-)-epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3″Me). Mol Nutr Food Res. 2018; 62: e1800274.
16. Hou QQ, Zhang SM, Li Y, Wang HJ, Zhang D, Qi DM, Li YL, Jiang HQ. New insights on association between circadian rhythm and lipid metabolism in spontaneously hypertensive rats. Life Sci. 2021; 271: 119145.
17. Hwang B, Lee JH. Bang D. Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med. 2018; 50: 1-14.
18. Lagkouvardos I, Lesker TR, Hitch TCA, Gálvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, et al. Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. Microbiome. 2019; 7: 28.
19. Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015; 33: 496-503.
20. Brancaccio M, Edwards MD, Patton AP, Smyllie NJ, Chesham JE, Maywood ES, Hastings MH. Cell-autonomous clock of astrocytes drives circadian behavior in mammals. Science. 2019; 363(6423):187-192.
21. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28: 27-30.
22. Dunlap JC, Loros JJ. Yes, circadian rhythms actually do affect almost everything. Cell Res. 2016; 26: 759-760.
23. Yamazaki S, Numano R, Hida MAA, Takahashi R, Ueda M, Block GD, Sakaki Y, Menaker M, Tei H. Resetting central and peripheral circadian oscillators in transgenic rats. Science. 2020; 288: 682-685.
24. Parkar SG, Kalsbeek A, Cheeseman JF. Potential role for the gut microbiota in modulating host circadian rhythms and metabolic health. Microorganisms. 2019; 7: 41.
25. Duclos C, Dumont M, Jean P, Blais H, der Maren SV, Menon DK, Bernard F, Gosselin N.Sleep-wake disturbances in hospitalized patients with traumatic brain injury: association with brain trauma but not with an abnormal melatonin circadian rhythm. Sleep. 2020; 43: zsz191.
26. Wang LMC, Dragich JM, Kudo T, Odom IH, Welsh DK, O'Dell TJ, Colwell CS. Expression of the circadian clock gene Period2 in the hippocampus: possible implications for synaptic plasticity and learned behaviour. ASN Neuro.2009; 1: e00012.
27. Cho K. Chronic 'jet lag' produces temporal lobe atrophy and spatial cognitive deficits. Nat Neurosci. 2001; 4: 567-568.
28. Biasibetti R, Tramontina AC, Costa AP, Dutra MF, Quincozes-Santos A, Nardin P, Bernardi CL, Wartchow KM, Lunardi PS, Gonçalves CA. Green tea (-) epigallocatechin-3-gallate reverses oxidative stress and reduces acetylcholinesterase activity in a streptozotocin-induced model of dementia. Behav. Brain Res. 2013; 236: 186-193.
29. Voigt RM, Forsyth CB, Green SJ, Mutlu E, Engen P, Vitaterna MH, Turek FW, Keshavarzian A. Circadian disorganization alters intestinal microbiota. PLoS One. 2014; 9: e97500.
30. Piao SH, Zhu ZQ, Tan SY, Zhan HX, Rong XL, Guo J. An integrated fecal microbiome and metabolome in the aged mice reveal anti-aging effects from the intestines and biochemical mechanism of FuFang zhenshu TiaoZhi (FTZ). Biomed. Pharmacother. 2020; 121: 109421.
31. Smith BJ, Miller RA, Ericsson AC, Harrison DC, Strong R, Schmidt TM. Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice. BMC Microbiol. 2019; 19: 130.
32. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013; 54: 2325-2340.
33. Arnoldussen IAC, Wiesmann M, Pelgrim CE, Wielemaker EM, van Duyvenvoorde W, Amaral-Santos PL, Verschuren L, Keijser BJF, Heerschap A, Kleemann R, et al. Butyrate restores HFD-induced adaptations in brain function and metabolism in mid-adult obese mice. Int J Obes. 2017; 41: 935-944.
34. van de Wouw M, Boehme M, Lyte JM, Wiley N, Strain C, O'Sullivan O, Clarke G, Stanton C, Dinan TG, Cryan JF. Short-chain fatty acids: microbial metabolites that alleviate stress-induced brain-gut axis alterations. J Physiol. 2018; 596: 4923-4944.
35. Eckel-Mahan KL, Patel VR, Mohney RP, Vignola KS, Baldi P, Sassone-Corsi P. Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci USA. 2012; 109: 5541-5546.
36. Tahara Y, Yamazaki MY, Sukigara H, Motohashi H, Sasaki H, Miyakawa H, Haraguchi A, Ikeda Y, Fukuda S, Shibata S. Gut microbiota-derived short chain fatty acids induce circadian clock entrainment in mouse peripheral tissue. Sci Rep. 2018; 8: 1395.
37. Agus A, Planchais J, Sokol H. Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe. 2018; 23: 716-724.
38. Tsukahara T, Matsuda Y, Haniu H. Lysophospholipid-related diseases and PPARγ signaling pathway. Int J Mol Sci. 2017; 18: 2730.
39. Wiedeman AM. Dietary choline intake: current state of knowledge across the life cycle. Nutrients. 2018; 10: 1513.
40. Guo TT, Song D, Cheng L, Zhang X. Interactions of tea catechins with intestinal microbiota and their implication for human health. Food Sci Biotechnol. 2019; 28(6): 1617-1625.
41. Ide K, Matsuoka N, Yamada H, Furushima D, Kawakami K. Effects of tea catechins on Alzheimer's disease: recent updates and perspectives. Molecules. 2018; 23: 2357.
42. Zhang XJ, Choi FFK, Zhou Y, Leung FP, Tan S, Lin SH, Xu HX, Jia W, Sung JJY, Cai ZW, et al. Metabolite profiling of plasma and urine from rats with TNBS-induced acute colitis using UPLC-ESI-QTOF-MS-based metabonomics--a pilot study. FEBS J. 2012; 279: 2322-2338.
43. Deters BJ, Saleem M. The role of glutamine in supporting gut health and neuropsychiatric factors. Food Sci Hum Well, 2021; 10: 149-154.
44. de Souza AZZ, Zambom AZ, Abboud KY, Reis SK, Tannihão F, Guadagnini D, Saad MJA, Prada PO. Oral supplementation with L-glutamine alters gut microbiota of obese and overweight adults: a pilot study. Nutrition. 2015;31: 884-889.
45. Zhu YH, Huan F, Wang JF, Xie XX, Yu GQ, Wang X, Jiang L, Gao R, Xiao H, Ding HX, et al. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine induced Parkinson's disease in mouse: potential association between neurotransmitter disturbance and gut microbiota dysbiosis. ACS Chem Neurosci. 2020; 11: 3366-3376.
46. Gray LR, Tompkins SC, Taylor EB. Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci. 2014; 71: 2577-604.
47. Mukherji A, Bailey SM, Staels B, Baumert TF. The circadian clock and liver function in health and disease. J Hepatol. 2019; 71: 200-211.
48. Matenchuk BA, Mandhane PJ, Kozyrskyj AL. Sleep, circadian rhythm, and gut microbiota. Sleep Med Rev. 2020; 53: 101340.
49. Videnovic A, Lazar AS, Barker RA, Overeem S. 'The clocks that time us'--circadian rhythms in neurodegenerative disorders. Nat Rev Neurol. 2014; 10: 683-693.
50. Musiek ES, Lim MM, Yang GR, Bauer AQ, Qi L, Lee Y, Roh JH, Ortiz-Gonzalez X, Dearborn JT, Culver JP, et al. Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration. J Clin Invest. 2013; 123: 5389-5400.
51. Agus A, Planchais J, Sokol H. Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe. 2018; 23(6): 716-724.
52. Han XN, Chen M, Wang FS, Windrem M, Wang S, Shanz S, Xu QW, Oberheim NA, Bekar L, Betstadt S,et al. Forebrain engraftment by human glial progenitor cells enhances synaptic plasticity and learning in adult mice. Cell Stem Cell. 2013; 12: 342-53.
53. Wasling P, Daborg J, Riebe I, Andersson M, Portelius E, Blennow K, Hanse E, Zetterberg H. Synaptic retrogenesis and amyloid-beta in Alzheimer's disease. J Alzheimers Dis. 2009; 16: 1-14.
54. Guo TT, Song D, Ho C-T, Zhang X, Zhang CD, Cao JX, Wu ZF. Omics analyses of gut microbiota in a circadian rhythm disorder mouse model fed with oolong tea polyphenols. J Agric Food Chem. 2019; 67: 8847-8854.
55. Barbieri R, Coppo E, Marchese A, Daglia M, Sobarzo-Sánchez E, Nabavi SF, Nabavi SM. Phytochemicals for human disease: an update on plant-derived compounds antibacterial activity. Microbiol Res. 2017; 196: 44-68.
56. Cheng M, Zhang X, Zhu JY, Cheng L, Cao JX, Wu ZF, Weng PF, Zheng XJ. Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model. J Func Foods. 2018; 46: 268-277.
57. Choi BSY, Daniel N, Houde VP, Ouellette A, Marcotte B, Varin TV, Vors C, Feutry P, Ilkayeva O, Ståhlman M, et al. Feeding diversified protein sources exacerbates hepatic insulin resistance via increased gut microbial branched-chain fatty acids and mTORC1 signaling in obese mice. Nat Commun. 2021; 12: 3377.
58. Hamood HM, Al-Zubaidy AA. Neuroprotective effects of vitex agnus castus extract in rats' model of Alzheimer's disease. Eurasia. J Biosci. 2020; 14: 4165-4169.
59. Ren B, Wang LF, Shi L, Jin X, Liu Y, Liu RH, Yin F, Cadenas E, Dai XS, Liu ZG, et al. Methionine restriction alleviates age-associated cognitive decline via fibroblast growth factor 21. Redox Biol. 2021; 41: 101940.
60. Bolyen E. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol, 2019; 37: 852-857.
61. Koohi-Moghadam M, Borad MJ, Tran NL, Swanson KR, Boardman LA, Sun HZ, Wang JW. MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers. Bioinformatics. 2019; 35: 3812-3814.
62. Qiu YX, Yu HH, Hu Yi, Guo SY, Lei XN, Qin Y, Jian YQ, Li B, Liu LP, Peng CY. Transcriptomic and metabonomic profiling reveal the anti-obesity effects of Chikusetsusaponin V, a compound extracted from Panax japonicus. J Pharm. Pharmacol.2021; 73: 60-69.
63. Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J, Holmes E, Nicholson JK. Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc. 2010; 5: 1005-1018.
64. Yuan M, Breitkopf SB, Yang X, Asara JM. A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc. 2012; 7: 872-881.
65. Zhu XS, Li HD, Guo LL, Wu FX, Wang JX. Analysis of single-cell RNA-seq data by clustering approaches. Curr Bioinform. 2019; 14: 314-322.
66. Kramer A, Green J, Pollard J, Tugendreich S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014; 30: 523-530.
67. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pagès F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25: 1091-1093.