REFERENCES

1. Tsao CW, Aday AW, Almarzooq ZI, et al. Heart disease and stroke statistics-2022 update: a report from the American Heart Association. Circulation 2022;145:e153-639.

2. Masana L, Zamora A, Plana N, et al. Incidence of cardiovascular disease in patients with familial hypercholesterolemia phenotype: analysis of 5 years follow-up of real-world data from more than 1.5 million patients. J Clin Med 2019;8:1080.

3. Parhofer KG. Interaction between glucose and lipid metabolism: more than diabetic dyslipidemia. Diabetes Metab J 2015;39:353-62.

4. Khan TJ, Ahmed YM, Zamzami MA, et al. Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Sci Rep 2018;8:662.

5. Scaldaferri F, Pizzoferrato M, Ponziani FR, Gasbarrini G, Gasbarrini A. Use and indications of cholestyramine and bile acid sequestrants. Intern Emerg Med 2013;8:205-10.

6. Chen L, McNulty J, Anderson D, et al. Cholestyramine reverses hyperglycemia and enhances glucose-stimulated glucagon-like peptide 1 release in Zucker diabetic fatty rats. J Pharmacol Exp Ther 2010;334:164-70.

7. Larsson E, Tremaroli V, Lee YS, et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut 2012;61:1124-31.

8. Rodrigues RR, Greer RL, Dong X, et al. Antibiotic-induced alterations in gut microbiota are associated with changes in glucose metabolism in healthy mice. Front Microbiol 2017;8:2306.

9. Williams RC, Showalter R, Kern F Jr. In vivo effect of bile salts and cholestyramine on intestinal anaerobic bacteria. Gastroenterology 1975;69:483-91.

10. Buffie CG, Bucci V, Stein RR, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 2015;517:205-8.

11. Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol 2014;30:332-8.

12. Jia W, Xie G, Jia W. Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat Rev Gastroenterol Hepatol 2018;15:111-28.

13. Newman NK, Macovsky MS, Rodrigues RR, et al. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nat Protoc 2024;19:1750-78.

14. Li Z, Gurung M, Rodrigues RR, et al. Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages. J Exp Med 2022;219:e20220017.

15. Newman NK, Zhang Y, Padiadpu J, et al. Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome. Microbiome 2023;11:208.

16. Morgun A, Dzutsev A, Dong X, et al. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 2015;64:1732-43.

17. Kong B, Wang L, Chiang JY, Zhang Y, Klaassen CD, Guo GL. Mechanism of tissue-specific farnesoid X receptor in suppressing the expression of genes in bile-acid synthesis in mice. Hepatology 2012;56:1034-43.

18. Nair AB, Jacob S. A simple practice guide for dose conversion between animals and human. J Basic Clin Pharm 2016;7:27-31.

19. Caporaso JG, Lauber CL, Walters WA, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 2011;108:4516-22.

20. Greer RL, Dong X, Moraes AC, et al. Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. Nat Commun 2016;7:13329.

21. Shulzhenko N, Yambartsev A, Goncalves-Primo A, Gerbase-DeLima M, Morgun A. Selection of control genes for quantitative RT-PCR based on microarray data. Biochem Biophys Res Commun 2005;337:306-12.

22. Øvstebø R, Haug KB, Lande K, Kierulf P. PCR-based calibration curves for studies of quantitative gene expression in human monocytes: development and evaluation. Clin Chem 2003;49:425-32.

23. Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019;37:852-7.

24. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 2016;13:581-3.

25. McDonald D, Price MN, Goodrich J, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012;6:610-8.

26. Boratyn GM, Camacho C, Cooper PS, et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res 2013;41:W29-33.

27. Chong J, Liu P, Zhou G, Xia J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat Protoc 2020;15:799-821.

28. Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J. MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res 2017;45:W180-8.

29. Yambartsev A, Perlin MA, Kovchegov Y, et al. Unexpected links reflect the noise in networks. Biol Direct 2016;11:52.

30. VanderWeele TJ, Robins JM. Signed directed acyclic graphs for causal inference. J R Stat Soc Series B Stat Methodol 2010;72:111-27.

31. Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504.

32. Hagberg A, Swart PJ, Schult DA. Exploring network structure, dynamics, and function using NetworkX. Available from: https://www.osti.gov/biblio/960616. [Last accessed on 1 Jul 2024].

33. Dong X, Yambartsev A, Ramsey SA, Thomas LD, Shulzhenko N, Morgun A. Reverse enGENEering of regulatory networks from big data: a roadmap for biologists. Bioinform Biol Insights 2015;9:61-74.

34. Thomas LD, Vyshenska D, Shulzhenko N, Yambartsev A, Morgun A. Differentially correlated genes in co-expression networks control phenotype transitions. F1000Res 2016;5:2740.

35. Kahalehili HM, Newman NK, Pennington JM, et al. Dietary indole-3-carbinol activates AhR in the gut, alters Th17-microbe interactions, and exacerbates insulitis in NOD mice. Front Immunol 2020;11:606441.

36. McCulloch JA, Davar D, Rodrigues RR, et al. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. Nat Med 2022;28:545-56.

37. Chiang JYL, Ferrell JM. Bile acid metabolism in liver pathobiology. Gene Expr 2018;18:71-87.

38. Kliewer SA, Mangelsdorf DJ. Bile acids as hormones: the FXR-FGF15/19 pathway. Dig Dis 2015;33:327-31.

39. Greer R, Dong X, Morgun A, Shulzhenko N. Investigating a holobiont: microbiota perturbations and transkingdom networks. Gut Microbes 2016;7:126-35.

40. Rodrigues RR, Shulzhenko N, Morgun A. Transkingdom networks: a systems biology approach to identify causal members of host-microbiota interactions. Methods Mol Biol 2018;1849:227-42.

41. Garg A, Grundy SM. Cholestyramine therapy for dyslipidemia in non-insulin-dependent diabetes mellitus. A short-term, double-blind, crossover trial. Ann Intern Med 1994;121:416-22.

42. Bays HE, Goldberg RB, Truitt KE, Jones MR. Colesevelam hydrochloride therapy in patients with type 2 diabetes mellitus treated with metformin: glucose and lipid effects. Arch Intern Med 2008;168:1975-83.

43. Fonseca VA, Rosenstock J, Wang AC, Truitt KE, Jones MR. Colesevelam HCl improves glycemic control and reduces LDL cholesterol in patients with inadequately controlled type 2 diabetes on sulfonylurea-based therapy. Diabetes Care 2008;31:1479-84.

44. Kondo K, Kadowaki T. Colestilan monotherapy significantly improves glycaemic control and LDL cholesterol levels in patients with type 2 diabetes: a randomized double-blind placebo-controlled study. Diabetes Obes Metab 2010;12:246-51.

45. Brønden A, Mikkelsen K, Sonne DP, et al. Glucose-lowering effects and mechanisms of the bile acid-sequestering resin sevelamer. Diabetes Obes Metab 2018;20:1623-31.

46. White JW, Saunders GF. Structure of the human glucagon gene. Nucleic Acids Res 1986;14:4719-30.

47. Park S, Zhang T, Yue Y, Wu X. Effects of bile acid modulation by dietary fat, cholecystectomy, and bile acid sequestrant on energy, glucose, and lipid metabolism and gut microbiota in mice. Int J Mol Sci 2022;23:5935.

48. Pfeiffer N, Desmarchelier C, Blaut M, Daniel H, Haller D, Clavel T. Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse. Arch Microbiol 2012;194:901-7.

49. Yamashita H, Fujisawa K, Ito E, et al. Improvement of obesity and glucose tolerance by acetate in Type 2 diabetic Otsuka Long-Evans Tokushima Fatty (OLETF) rats. Biosci Biotechnol Biochem 2007;71:1236-43.

50. Gao Z, Yin J, Zhang J, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 2009;58:1509-17.

51. Khan S, Jena G. Sodium butyrate reduces insulin-resistance, fat accumulation and dyslipidemia in type-2 diabetic rat: a comparative study with metformin. Chem Biol Interact 2016;254:124-34.

52. Alvaro A, Solà R, Rosales R, et al. Gene expression analysis of a human enterocyte cell line reveals downregulation of cholesterol biosynthesis in response to short-chain fatty acids. IUBMB Life 2008;60:757-64.

53. Pathak P, Xie C, Nichols RG, et al. Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism. Hepatology 2018;68:1574-88.

54. Chiang JYL, Ferrell JM. Targeting the gut microbiota for treating colitis: is FGF19 a magic bullet? EBioMedicine 2020;55:102754.

55. Pirozzi C, Coretti L, Opallo N, et al. Palmitoylethanolamide counteracts high-fat diet-induced gut dysfunction by reprogramming microbiota composition and affecting tryptophan metabolism. Front Nutr 2023;10:1143004.

56. Li B, Zhang J, Chen Y, et al. Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis. Gut Microbes 2021;13:1946366.

57. Li JY, Gillilland M 3rd, Lee AA, Wu X, Zhou SY, Owyang C. Secondary bile acids mediate high-fat diet-induced upregulation of R-spondin 3 and intestinal epithelial proliferation. JCI Insight 2022;7:e148309.

58. Neimark E, Chen F, Li X, Shneider BL. Bile acid-induced negative feedback regulation of the human ileal bile acid transporter. Hepatology 2004;40:149-56.

59. Keely SJ, Walters JR. The farnesoid X receptor: good for BAD. Cell Mol Gastroenterol Hepatol 2016;2:725-32.

60. Zhang Y, Klaassen CD. Effects of feeding bile acids and a bile acid sequestrant on hepatic bile acid composition in mice. J Lipid Res 2010;51:3230-42.

61. Chiang JYL. Bile acid metabolism and signaling in liver disease and therapy. Liver Res 2017;1:3-9.

62. Chiang JYL, Ferrell JM. Up to date on cholesterol 7 alpha-hydroxylase (CYP7A1) in bile acid synthesis. Liver Res 2020;4:47-63.

63. Sonne DP, Hansen M, Knop FK. Bile acid sequestrants in type 2 diabetes: potential effects on GLP1 secretion. Eur J Endocrinol 2014;171:R47-65.

64. Hirasawa A, Tsumaya K, Awaji T, et al. Free fatty acids regulate gut incretin glucagon-like peptide-1 secretion through GPR120. Nat Med 2005;11:90-4.

65. Trabelsi MS, Lestavel S, Staels B, Collet X. Intestinal bile acid receptors are key regulators of glucose homeostasis. Proc Nutr Soc 2017;76:192-202.

66. Caparrós-Martín JA, Lareu RR, Ramsay JP, et al. Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism. Microbiome 2017;5:95.

67. Fuchs CD, Paumgartner G, Mlitz V, et al. Colesevelam attenuates cholestatic liver and bile duct injury in Mdr2-/- mice by modulating composition, signalling and excretion of faecal bile acids. Gut 2018;67:1683-91.

68. Kriaa A, Bourgin M, Potiron A, et al. Microbial impact on cholesterol and bile acid metabolism: current status and future prospects. J Lipid Res 2019;60:323-32.

69. Ruiz L, Margolles A, Sánchez B. Bile resistance mechanisms in Lactobacillus and Bifidobacterium. Front Microbiol 2013;4:396.

70. Lagkouvardos I, Lesker TR, Hitch TCA, 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.

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