1. Tilg H, Moschen AR. Microbiota and diabetes: an evolving relationship. Gut. 2014; 63:1513–1521.
2. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010; 5:e9085.

3. Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, et al. Human gut microbiota changes reveal the progression of glucose intolerance. PLoS One. 2013; 8:e71108.

4. Horton F, Wright J, Smith L, Hinton PJ, Robertson MD. Increased intestinal permeability to oral chromium (51 Cr): EDTA in human type 2 diabetes. Diabet Med. 2014; 31:559–563.
5. Cani PD, Geurts L, Matamoros S, Plovier H, Duparc T. Glucose metabolism: focus on gut microbiota, the endocannabinoid system and beyond. Diabetes Metab. 2014; 40:246–257.
6. Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab. 2014; 20:731–741.

9. Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. mBio. 2014; 5:e00889.

10. Levy R, Borenstein E. Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules. Gut Microbes. 2014; 5:265–270.
11. Pimentel M, Mathur R, Chang C. Gas and the microbiome. Curr Gastroenterol Rep. 2013; 15:356.
12. Gundberg CM, Markowitz ME, Mizruchi M, Rosen JF. Osteocalcin in human serum: a circadian rhythm. J Clin Endocrinol Metab. 1985; 60:736–739.
13. Knapen MH, Braam LA, Drummen NE, Bekers O, Hoeks AP, Vermeer C. Menaquinone-7 supplementation improves arterial stiffness in healthy postmenopausal women: a double-blind randomised clinical trial. Thromb Haemost. 2015; 113:1135–1144.
15. Choi HJ, Yu J, Choi H, An JH, Kim SW, Park KS, et al. Vitamin K2 supplementation improves insulin sensitivity via osteocalcin metabolism: a placebo-controlled trial. Diabetes Care. 2011; 34:e147.

16. Healey G, Brough L, Murphy R, Hedderley D, Butts C, Coad J. Validity and reproducibility of a habitual dietary fibre intake short food frequency questionnaire. Nutrients. 2016; 8:E558.

18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30:2114–2120.

19. Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016; 44:D471–D480.

20. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015; 12:902–903.
21. Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012; 488:178–184.

23. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012; 490:55–60.
24. Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol. 2016; 14:508–522.
25. Abul-Hajj YJ. Isolation of vitamin K2(35) from Nocardia restrictus and Corynebacterium simplex: a natural electron acceptor in microbial steroid ring A dehydrogenations. J Biol Chem. 1978; 253:2356–2360.
26. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012; 486:222–227.

27. Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012; 489:242–249.

28. An R, Wilms E, Masclee AAM, Smidt H, Zoetendal EG, Jonkers D. Age-dependent changes in GI physiology and microbiota: time to reconsider. Gut. 2018; 67:2213–2222.
30. Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, et al. MetaHIT consortium. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 2015; 528:262–266.

32. Chassaing B, Gewirtz AT. Gut microbiota, low-grade inflammation, and metabolic syndrome. Toxicol Pathol. 2014; 42:49–53.
33. Conly JM, Stein K. The production of menaquinones (vitamin K2) by intestinal bacteria and their role in maintaining coagulation homeostasis. Prog Food Nutr Sci. 1992; 16:307–343.
34. Suttie JW. The importance of menaquinones in human nutrition. Annu Rev Nutr. 1995; 15:399–417.
36. Yamaguchi M, Weitzmann MN. Vitamin K2 stimulates osteoblastogenesis and suppresses osteoclastogenesis by suppressing NF-κB activation. Int J Mol Med. 2011; 27:3–14.
37. Thakore AH, Guo CY, Larson MG, Corey D, Wang TJ, Vasan RS, et al. Association of multiple inflammatory markers with carotid intimal medial thickness and stenosis (from the Framingham Heart Study). Am J Cardiol. 2007; 99:1598–1602.
38. Sakamoto N, Nishiike T, Iguchi H, Sakamoto K. Possible effects of one week vitamin K (menaquinone-4) tablets intake on glucose tolerance in healthy young male volunteers with different descarboxy prothrombin levels. Clin Nutr. 2000; 19:259–263.
40. Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J Infect Dis. 2015; 211:19–27.
41. Schaubeck M, Clavel T, Calasan J, Lagkouvardos I, Haange SB, Jehmlich N, et al. Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence. Gut. 2016; 65:225–237.
43. Kosanam H, Thai K, Zhang Y, Advani A, Connelly KA, Diamandis EP, et al. Diabetes induces lysine acetylation of intermediary metabolism enzymes in the kidney. Diabetes. 2014; 63:2432–2439.
44. Jones JD, Burnett PC. Creatinine metabolism in humans with decreased renal function: creatinine deficit. Clin Chem. 1974; 20:1204–1212.