臺灣博碩士論文加值系統

「冬蟲夏草」在中醫藥學使用上已經有多年的歷史了，在中草藥醫學記錄著具有免疫調控之功效。但冬蟲夏草在生物體內透過何種機制迄今尚未得知。近年來有文獻指出當腸道菌叢的菌相（組成及豐富性）改變時，容易伴隨著肥胖及第二型糖尿病的發生。在此篇研究中，我們探討冬蟲夏草菌絲體水萃液的多醣體是否能透過改善腸道菌相，進而預防小鼠在高脂飲食所造成的肥胖及第二型糖尿病。結果中我們發現分子量大於300 kDa的冬蟲夏草菌絲體水萃液多醣體(H1)明顯的降低了體重增加、腸道損傷滲漏以及肥胖衍生的代謝疾病症候群。其中發現肥胖鼠腸腔內的內毒素增加並透過腸道損傷滲漏而進入循環血流，造成全身性低程度發炎現象及併發的胰島素抗性、脂肪酸代謝走向三酸甘油脂合成，因口服餵食H1而明顯的改善。腸道菌叢定序分析結果中發現，高脂飲食造成了小鼠腸道菌相失去平衡，卻在H1條件下使得腸道菌相趨向正常老鼠的分佈，而腸道菌Parabacteroides goldsteinii隨著在H1處理後明顯的增加。進一步採取在小鼠飲用水中加入抗生素並搭配糞便菌叢轉移之策略，再次發現P. goldsteinii與所偵測的肥胖指標呈現負相關性，推測H1可透過恢復腸道中的P. goldsteinii豐富性，進而改善高脂飲食所造成的肥胖及第二型糖尿病。在厭氧的環境下培養腸道菌P. goldsteinii並每天口服餵食高脂飲食小鼠，不僅有效地改善了體重的增加、降低全身性發炎的現象、以及也避免了腸道損傷的滲漏。在結論中，冬蟲夏草多醣體(H1)與腸道菌P. goldsteinii分別扮演著功能性的益菌生與益生菌的角色，在臨床上能有效的預防應用在肥胖及第二型糖尿病。

The medicinal mushroom Ophiocordyceps sinensis and its anamorph Hirsutella sinensis have a long history of use in traditional Chinese medicine for their immuno-modulatory effects. Alterations of the gut microbiota have been described in obesity and type 2 diabetes. We examined the possibility that polysaccharides derived from H. sinensis mycelium (HSM) may prevent diet-induced obesity by modulating the composition of the gut microbiota. Fraction H1 containing high-molecular weight polysaccharides (>300 kDa) considerably reduced body weight gain, leaky gut and metabolic disorders in high-fat diet (HFD)-fed mice. These effects were associated with enhanced tight junction expression, reduced intestinal and systemic inflammation, and improved insulin sensitivity and lipid metabolism. Gut microbiota analysis revealed that H1 polysaccharides reversed gut dysbiosis and selectively promoted growth of Parabacteroides goldsteinii, a gut bacterium whose level was reduced in HFD-fed mice. Fecal microbiota transplantation (FMT) combined with antibiotic treatment showed that P. goldsteinii significant negatively correlate with obesity traits and were responsible for H1’s anti-obesogenic effects. HSM polysaccharides and the gut commensal bacterium P. goldsteinii represent novel prebiotics and probiotics, respectively, which may be used to combat the global epidemic of obesity and type 2 diabetes.

指導教授推薦書
口試委員會審定書
致謝 iii
中文摘要 iv
Abstract v
Content vi
Figures xi
Tables xiv
Abbreviation xv
Chapter 1. Introduction 1
1.1 Obesity: Epidemiology 1
1.1.1 Diet-induced obesity (DIO) model in mice 2
(i) Adipocyte dysfunction on obesity 4
(ii) Insulin signaling and insulin resistance 6
(iii) Non-alcoholic fatty liver disease (NAFLD) 8
1.1.2 The effects of obesity-induced metabolic inflammation: adipose tissue metabolic function 10
1.1.3 The effects of obesity-induced metabolic inflammation: liver metabolic dysfunction 13
1.1.4 Metabolic endotoxemia and gut permeability in obesity 16
1.2 The impact of microbiota 19
1.2.1 The biological functions of gut microbiota 22
1.2.2 The transmissible capacity 25
1.2.3 Gut microbiota and obesity-associated metabolic disorders 27
1.2.4 The impact of prebiotic, probiotic and antibiotic in obesity 29
1.3 Herbal medicine 33
1.3.1 Hirsutella Sinensis Mycelium (HSM) 35
1.4 Specific aim 36
Chapter 2. Results 37
2.1 Water extract Hirsutella Sinensis mycelium (HSM) ameliorated diet-induced obesity and metabolic disorders in mice 37
2.2 HSM polysaccharide ingredients improved diet-induced obesity and metabolic disorders in mice 38
2.3 The effects of HSM and polysaccharide ingredients on lipid metabolism in mice 39
2.4 The effects of HSM and polysaccharide ingredients on insulin sensitivity in mice 42
2.5 The anti-inflammatory effects of HSM and polysaccharide ingredients in mice 43
2.6 HSM and H1 reduced metabolic endotoxin-induced inflammation through lower gut permeability 45
2.7 Gut microbiota from HSM and H1 mice prevented obesity parameters in HFD feeding mice 47
2.8 Neomycin abolished H1 anti-obesity effects in HFD-fed mice 49
2.9 Characterizing changes in gut microbiota in response to H1 treatment 52
2.10. Characterizing key bacterial strains of gut microbiota modulated by H1 in response to anti-obesogenic effects 55
2.11 Neomycin-sensitive microbes reduced H1 anti-obesity effects 59
2.11 Characterization of P. goldsteinii was the major bacterial species on anti-obesogenic effects 61
2.12 Daily supplementation with P. goldsteinii reduced HFD-induced obesity traits 64
Chapter 3. Discussion 66
Chapter 4. Conclusion 73
Chapter 5. Material and method 74
5.1 Animals 74
5.2 Preparation of HSM polysaccharide ingredients 74
5.3 Fecal microbiota transplantation (FMT) 76
5.4 Antibiotic treatment 77
5.5 Antibiotic-treated fecal microbiota transplantation 77
5.6 Fungal strain 78
5.7 Preparation of water extracts HSM polysaccharide ingredients 79
5.8 Tissue sampling 81
5.9 Energy intake and fecal lipid content 81
5.10 ELISA detection for insulin, cytokines and endotoxin 81
5.11 Intestinal permeability assay 82
5.12 OGTT, ITT and HOMA-IR index 82
5.13 Histopathological staining, determination and scoring 83
5.14 Quantitative real-time PCR (QPCR) 84
5.15 Determination of bacteria by quantitative real-time PCR 84
5.16 Fecal microbiota transplantation (FMT) 85
5.17 Cecal microbiota DNA extraction 85
5.18 Illumina HiSeq sequencing and library construction 86
5.19 16S rRNA-based metagenomics analysis pipeline 87
5.20 Quantification of caecal microbiota by quantitative PCR 89
5.21 P. goldsteinii cultivation and treatment 89
5.22 Statistical analysis 90
Chapter 6. Reference 91
Chapter 7. Figures & Figure legends 122
Chapter 8. Tables 180
Chapter 9. Appendix 188


Figures
Figure 1. HSM reduces obesity in HFD-fed mice. ................................ 123
Figure 2. HSM and fraction H1 prevent HFD-induced obesity and
metabolic disorders. ................................................................. 124
Figure 3. Effects of HSM and H1 treatment in Chow-fed mice. ........... 126
Figure 4. HSM and polysaccharide fractions do not affect energy intake or
lipid absorption in HFD-fed mice. ........................................... 127
Figure 5. HSM and polysaccharide fractions do not affect intestinal
production of short chain fatty acids........................................ 128
Figure 6. Effects of HSM and polysaccharide fractions on serum
triglycerides and gene expression involved in lipid metabolism.
.................................................................................................. 129
Figure 7. HSM and H1 restore glucose and insulin sensitivity in HFDinduced
obese mice. ................................................................. 132
Figure 8. HSM and H1 prevent diet-induced metabolic inflammation. 133
Figure 9. HSM and H1 reduce adipocyte hypertrophy and crown-like
structures in HFD-fed mice...................................................... 134
Figure 10. HSM and H1 reduce pathological changes of NAFLD and
NASH in HFD-fed mice. ......................................................... 136
Figure. 11. HSM and H1 reduce metabolic endotoxemia, colonic inflammation and reverse intestinal tight junction expression. 138
Figure. 12. FMT from HSM- and H1-treated mice reduces obesity and
metabolic disorders in HFD recipients..................................... 141
Figure 13. FMT from HSM- and H1-treated mice reduces adipocyte
hypertrophy and CLS in HFD-fed mice................................... 144
Figure 14. FMT from HSM- and H1-treated mice reduces NAFLD and
NASH pathological changes. ................................................... 146
Figure 15. The effects of H1 combined with single antibiotic treatment on
HFD-induced obesity. .............................................................. 148
Figure 16. Neomycin treatment abrogates H1’s protective effects on
adipocyte hypertrophy and CLS in HFD-fed mice. ................. 149
Figure 17. Neomycin treatment abrogates H1’s protective effects on
NAFLD and NASH in HFD-fed mice. .................................... 151
Figure 18. H1 produces anti-obesogenic effects via neomycin-sensitive
gut bacteria............................................................................... 155
Figure 19. H1 treatment reverses HFD-induced gut dysbiosis.............. 159
Figure 20. H1 enriches a population of neomycin-sensitive gut bacteria
that negatively correlate with obesity traits. ............................ 162
Figure 21. Interplay between H1-modulated gut bacteria. .................... 163
Figure 22. Ex vivo neomycin treatment abolishes the anti-obesogenic effects of FMT from H1-treated mice...................................... 165
Figure 23. P. goldsteinii is significantly enriched in ex FMT H1 donor
and negatively correlates with obesity traits............................ 168
Figure 24. P. goldsteinii is significantly enriched in recipient mice and
negatively correlates with obesity traits................................... 170
Figure 25. P. goldsteinii reduces diet-induced obesity and metabolic
disorders................................................................................... 173
Figure 26. Effects of P. goldsteinii treatment in chow-fed mice. .......... 174
Figure 27. P. goldsteinii treatment prevents adipocyte hypertrophy and
CLS in HFD-fed mice.............................................................. 175
Figure 28. P. goldsteinii treatment prevents NAFLD and NASH in HFDfed
mice.................................................................................... 176
Figure 29. P. goldsteinii treatment normalizes gene expression involved
in lipid metabolism in HFD-fed mice. ..................................... 177
Figure 30. Heat-killed P. goldsteinii fails to prevent obesity in HFD-fed
mice.......................................................................................... 178
Figure 31. Proposed model to illustrate the anti-obesogenic effects of
HSM and H1 on diet-induced obesity...................................... 179

Tables
Table 1. The composition table of chow diet and high-fat diet.............. 180
Table 2. Molecular analysis of polysaccharide ingredients isolated from
Hirsutella Sinensis mycelium (HSM)........................................ 181
Table 3. Relative abundance of bacterial species showing differences
between H1-treated group and antibiotics groups during HFD
feeding for 12 weeks.................................................................. 182
Table 4. Relative abundance of bacterial species showing differences
between H1-treated donor group and antibiotics donor groups
during HFD feeding for 12 weeks ............................................. 183
Table 5. Relative abundance of bacterial species showing differences
between H1-treated recipient group and antibiotics recipient
groups during HFD feeding for 12 weeks ................................. 184
Table 6. Serum biochemistry analysis of mice treated with P. goldsteinii
for 8 weeks................................................................................. 185
Table 7. Monosaccharide composition of fraction H1........................... 186
Table 8. Primers used in this study ........................................................ 187

1. Ng M, Fleming T, Robinson M, Thomson B, Graetz N, Margono C, Mullany EC, et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 2014;384:766-781.
2. Heindel JJ, Newbold R, Schug TT. Endocrine disruptors and obesity. Nat Rev Endocrinol 2015;11:653-661.
3. Guilbert JJ. The world health report 2002 - reducing risks, promoting healthy life. Educ Health (Abingdon) 2003;16:230.
4. WHO. Global status report on noncommunicable diseases 2010. http://www.who.int/nmh/publications/ncd_report2010/en/.
5. Finkelstein EA, Trogdon JG, Cohen JW, Dietz W. Annual medical spending attributable to obesity: payer-and service-specific estimates. Health Aff (Millwood) 2009;28:w822-831.
6. Parks J AJ, Okrent AM. The External Health-Care cost of obesity in the United States. Available in http://vinecon.ucdavis.edu/publications/cwe1304.
7. Trogdon JG, Finkelstein EA, Hylands T, Dellea PS, Kamal-Bahl SJ. Indirect costs of obesity: a review of the current literature. Obes Rev 2008;9:489-500.
8. Gallou-Kabani C, Vige A, Gross MS, Rabes JP, Boileau C, Larue-Achagiotis C, Tome D, et al. C57BL/6J and A/J mice fed a high-fat diet delineate components of metabolic syndrome. Obesity (Silver Spring) 2007;15:1996-2005.
9. West DB, Boozer CN, Moody DL, Atkinson RL. Dietary obesity in nine inbred mouse strains. Am J Physiol 1992;262:R1025-1032.
10. Nilsson C, Raun K, Yan FF, Larsen MO, Tang-Christensen M. Laboratory animals as surrogate models of human obesity. Acta Pharmacol Sin 2012;33:173-181.
11. Wen SPL-E. Animal Model for Obesity-An Overview. Systematic Reviews in Pharmacy 2015;6:9-12.
12. Buettner R, Parhofer KG, Woenckhaus M, Wrede CE, Kunz-Schughart LA, Scholmerich J, Bollheimer LC. Defining high-fat-diet rat models: metabolic and molecular effects of different fat types. J Mol Endocrinol 2006;36:485-501.
13. Summers LK, Fielding BA, Bradshaw HA, Ilic V, Beysen C, Clark ML, Moore NR, et al. Substituting dietary saturated fat with polyunsaturated fat changes abdominal fat distribution and improves insulin sensitivity. Diabetologia 2002;45:369-377.
14. Vessby B, Uusitupa M, Hermansen K, Riccardi G, Rivellese AA, Tapsell LC, Nalsen C, et al. Substituting dietary saturated for monounsaturated fat impairs insulin sensitivity in healthy men and women: The KANWU Study. Diabetologia 2001;44:312-319.
15. Sato Mito N, Suzui M, Yoshino H, Kaburagi T, Sato K. Long term effects of high fat and sucrose diets on obesity and lymphocyte proliferation in mice. J Nutr Health Aging 2009;13:602-606.
16. Zaki ME, El-Bassyouni H, Kamal S, El-Gammal M, Youness E. Association of serum paraoxonase enzyme activity and oxidative stress markers with dyslipidemia in obese adolescents. Indian J Endocrinol Metab 2014;18:340-344.
17. Calligaris SD, Lecanda M, Solis F, Ezquer M, Gutierrez J, Brandan E, Leiva A, et al. Mice long-term high-fat diet feeding recapitulates human cardiovascular alterations: an animal model to study the early phases of diabetic cardiomyopathy. PLoS One 2013;8:e60931.
18. Sorisky A, Magun R, Gagnon AM. Adipose cell apoptosis: death in the energy depot. Int J Obes Relat Metab Disord 2000;24 Suppl 4:S3-7.
19. Cinti S, Mitchell G, Barbatelli G, Murano I, Ceresi E, Faloia E, Wang S, et al. Adipocyte death defines macrophage localization and function in adipose tissue of obese mice and humans. J Lipid Res 2005;46:2347-2355.
20. Morris DL, Cho KW, Delproposto JL, Oatmen KE, Geletka LM, Martinez-Santibanez G, Singer K, et al. Adipose tissue macrophages function as antigen-presenting cells and regulate adipose tissue CD4+ T cells in mice. Diabetes 2013;62:2762-2772.
21. Guilherme A, Virbasius JV, Puri V, Czech MP. Adipocyte dysfunctions linking obesity to insulin resistance and type 2 diabetes. Nat Rev Mol Cell Biol 2008;9:367-377.
22. Draznin B. Molecular mechanisms of insulin resistance: serine phosphorylation of insulin receptor substrate-1 and increased expression of p85alpha: the two sides of a coin. Diabetes 2006;55:2392-2397.
23. Ye J. Mechanisms of insulin resistance in obesity. Front Med 2013;7:14-24.
24. Gray SL, Donald C, Jetha A, Covey SD, Kieffer TJ. Hyperinsulinemia precedes insulin resistance in mice lacking pancreatic beta-cell leptin signaling. Endocrinology 2010;151:4178-4186.
25. Glass CK, Olefsky JM. Inflammation and lipid signaling in the etiology of insulin resistance. Cell Metab 2012;15:635-645.
26. Griffin ME, Marcucci MJ, Cline GW, Bell K, Barucci N, Lee D, Goodyear LJ, et al. Free fatty acid-induced insulin resistance is associated with activation of protein kinase C theta and alterations in the insulin signaling cascade. Diabetes 1999;48:1270-1274.
27. Ye J. Role of insulin in the pathogenesis of free fatty acid-induced insulin resistance in skeletal muscle. Endocr Metab Immune Disord Drug Targets 2007;7:65-74.
28. Samuel VT, Shulman GI. Mechanisms for insulin resistance: common threads and missing links. Cell 2012;148:852-871.
29. Wen H, Gris D, Lei Y, Jha S, Zhang L, Huang MT, Brickey WJ, et al. Fatty acid-induced NLRP3-ASC inflammasome activation interferes with insulin signaling. Nat Immunol 2011;12:408-415.
30. Ludwig J, Viggiano TR, McGill DB, Oh BJ. Nonalcoholic steatohepatitis: Mayo Clinic experiences with a hitherto unnamed disease. Mayo Clin Proc 1980;55:434-438.
31. Milic S, Stimac D. Nonalcoholic fatty liver disease/steatohepatitis: epidemiology, pathogenesis, clinical presentation and treatment. Dig Dis 2012;30:158-162.
32. Schuppan D, Schattenberg JM. Non-alcoholic steatohepatitis: pathogenesis and novel therapeutic approaches. J Gastroenterol Hepatol 2013;28 Suppl 1:68-76.
33. Willebrords J, Pereira IV, Maes M, Crespo Yanguas S, Colle I, Van Den Bossche B, Da Silva TC, et al. Strategies, models and biomarkers in experimental non-alcoholic fatty liver disease research. Prog Lipid Res 2015;59:106-125.
34. van den Berg SA, Guigas B, Bijland S, Ouwens M, Voshol PJ, Frants RR, Havekes LM, et al. High levels of dietary stearate promote adiposity and deteriorate hepatic insulin sensitivity. Nutr Metab (Lond) 2010;7:24.
35. Leclercq IA, Farrell GC, Field J, Bell DR, Gonzalez FJ, Robertson GR. CYP2E1 and CYP4A as microsomal catalysts of lipid peroxides in murine nonalcoholic steatohepatitis. J Clin Invest 2000;105:1067-1075.
36. Machado MV, Michelotti GA, Xie G, Almeida Pereira T, Boursier J, Bohnic B, Guy CD, et al. Mouse models of diet-induced nonalcoholic steatohepatitis reproduce the heterogeneity of the human disease. PLoS One 2015;10:e0127991.
37. Iyer S, Upadhyay PK, Majumdar SS, Nagarajan P. Animal Models Correlating Immune Cells for the Development of NAFLD/NASH. J Clin Exp Hepatol 2015;5:239-245.
38. Kennedy A, Martinez K, Chuang CC, LaPoint K, McIntosh M. Saturated fatty acid-mediated inflammation and insulin resistance in adipose tissue: mechanisms of action and implications. J Nutr 2009;139:1-4.
39. Hotamisligil GS. Inflammation and metabolic disorders. Nature 2006;444:860-867.
40. Weisberg SP, McCann D, Desai M, Rosenbaum M, Leibel RL, Ferrante AW, Jr. Obesity is associated with macrophage accumulation in adipose tissue. J Clin Invest 2003;112:1796-1808.
41. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, et al. Genetics of gene expression and its effect on disease. Nature 2008;452:423-428.
42. Kanda H, Tateya S, Tamori Y, Kotani K, Hiasa K, Kitazawa R, Kitazawa S, et al. MCP-1 contributes to macrophage infiltration into adipose tissue, insulin resistance, and hepatic steatosis in obesity. J Clin Invest 2006;116:1494-1505.
43. Lumeng CN, DelProposto JB, Westcott DJ, Saltiel AR. Phenotypic switching of adipose tissue macrophages with obesity is generated by spatiotemporal differences in macrophage subtypes. Diabetes 2008;57:3239-3246.
44. Alkhouri N, Gornicka A, Berk MP, Thapaliya S, Dixon LJ, Kashyap S, Schauer PR, et al. Adipocyte apoptosis, a link between obesity, insulin resistance, and hepatic steatosis. J Biol Chem 2010;285:3428-3438.
45. Ding S, Chi MM, Scull BP, Rigby R, Schwerbrock NM, Magness S, Jobin C, et al. High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse. PLoS One 2010;5:e12191.
46. Peraldi P, Hotamisligil GS, Buurman WA, White MF, Spiegelman BM. Tumor necrosis factor (TNF)-alpha inhibits insulin signaling through stimulation of the p55 TNF receptor and activation of sphingomyelinase. J Biol Chem 1996;271:13018-13022.
47. White MF. IRS proteins and the common path to diabetes. Am J Physiol Endocrinol Metab 2002;283:E413-422.
48. Ye J. Regulation of PPARgamma function by TNF-alpha. Biochem Biophys Res Commun 2008;374:405-408.
49. Weigert C, Brodbeck K, Staiger H, Kausch C, Machicao F, Haring HU, Schleicher ED. Palmitate, but not unsaturated fatty acids, induces the expression of interleukin-6 in human myotubes through proteasome-dependent activation of nuclear factor-kappaB. J Biol Chem 2004;279:23942-23952.
50. Gao Z, Zhang X, Zuberi A, Hwang D, Quon MJ, Lefevre M, Ye J. Inhibition of insulin sensitivity by free fatty acids requires activation of multiple serine kinases in 3T3-L1 adipocytes. Mol Endocrinol 2004;18:2024-2034.
51. Shoelson SE, Lee J, Goldfine AB. Inflammation and insulin resistance. J Clin Invest 2006;116:1793-1801.
52. Uysal KT, Wiesbrock SM, Marino MW, Hotamisligil GS. Protection from obesity-induced insulin resistance in mice lacking TNF-alpha function. Nature 1997;389:610-614.
53. Koenen TB, Stienstra R, van Tits LJ, Joosten LA, van Velzen JF, Hijmans A, Pol JA, et al. The inflammasome and caspase-1 activation: a new mechanism underlying increased inflammatory activity in human visceral adipose tissue. Endocrinology 2011;152:3769-3778.
54. Jager J, Gremeaux T, Cormont M, Le Marchand-Brustel Y, Tanti JF. Interleukin-1beta-induced insulin resistance in adipocytes through down-regulation of insulin receptor substrate-1 expression. Endocrinology 2007;148:241-251.
55. McGillicuddy FC, Harford KA, Reynolds CM, Oliver E, Claessens M, Mills KH, Roche HM. Lack of interleukin-1 receptor I (IL-1RI) protects mice from high-fat diet-induced adipose tissue inflammation coincident with improved glucose homeostasis. Diabetes 2011;60:1688-1698.
56. Nguyen-Lefebvre AT, Horuzsko A. Kupffer Cell Metabolism and Function. J Enzymol Metab 2015;1.
57. Fox ES, Thomas P, Broitman SA. Comparative studies of endotoxin uptake by isolated rat Kupffer and peritoneal cells. Infect Immun 1987;55:2962-2966.
58. Su GL. Lipopolysaccharides in liver injury: molecular mechanisms of Kupffer cell activation. Am J Physiol Gastrointest Liver Physiol 2002;283:G256-265.
59. Neyrinck AM, Cani PD, Dewulf EM, De Backer F, Bindels LB, Delzenne NM. Critical role of Kupffer cells in the management of diet-induced diabetes and obesity. Biochem Biophys Res Commun 2009;385:351-356.
60. Lanthier N, Molendi-Coste O, Cani PD, van Rooijen N, Horsmans Y, Leclercq IA. Kupffer cell depletion prevents but has no therapeutic effect on metabolic and inflammatory changes induced by a high-fat diet. FASEB J 2011;25:4301-4311.
61. Manco M, Marcellini M, Giannone G, Nobili V. Correlation of serum TNF-alpha levels and histologic liver injury scores in pediatric nonalcoholic fatty liver disease. Am J Clin Pathol 2007;127:954-960.
62. Crespo J, Cayon A, Fernandez-Gil P, Hernandez-Guerra M, Mayorga M, Dominguez-Diez A, Fernandez-Escalante JC, et al. Gene expression of tumor necrosis factor alpha and TNF-receptors, p55 and p75, in nonalcoholic steatohepatitis patients. Hepatology 2001;34:1158-1163.
63. Feldstein AE, Werneburg NW, Canbay A, Guicciardi ME, Bronk SF, Rydzewski R, Burgart LJ, et al. Free fatty acids promote hepatic lipotoxicity by stimulating TNF-alpha expression via a lysosomal pathway. Hepatology 2004;40:185-194.
64. Barbuio R, Milanski M, Bertolo MB, Saad MJ, Velloso LA. Infliximab reverses steatosis and improves insulin signal transduction in liver of rats fed a high-fat diet. J Endocrinol 2007;194:539-550.
65. Satapathy SK, Garg S, Chauhan R, Sakhuja P, Malhotra V, Sharma BC, Sarin SK. Beneficial effects of tumor necrosis factor-alpha inhibition by pentoxifylline on clinical, biochemical, and metabolic parameters of patients with nonalcoholic steatohepatitis. Am J Gastroenterol 2004;99:1946-1952.
66. Erridge C, Attina T, Spickett CM, Webb DJ. A high-fat meal induces low-grade endotoxemia: evidence of a novel mechanism of postprandial inflammation. Am J Clin Nutr 2007;86:1286-1292.
67. Deopurkar R, Ghanim H, Friedman J, Abuaysheh S, Sia CL, Mohanty P, Viswanathan P, et al. Differential effects of cream, glucose, and orange juice on inflammation, endotoxin, and the expression of Toll-like receptor-4 and suppressor of cytokine signaling-3. Diabetes Care 2010;33:991-997.
68. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, Neyrinck AM, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56:1761-1772.
69. Guo S, Al-Sadi R, Said HM, Ma TY. Lipopolysaccharide causes an increase in intestinal tight junction permeability in vitro and in vivo by inducing enterocyte membrane expression and localization of TLR-4 and CD14. Am J Pathol 2013;182:375-387.
70. Cani PD, Possemiers S, Van de Wiele T, Guiot Y, Everard A, Rottier O, Geurts L, et al. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut 2009;58:1091-1103.
71. Farquhar MG, Palade GE. Junctional complexes in various epithelia. J Cell Biol 1963;17:375-412.
72. Al-Sadi R, Ye D, Dokladny K, Ma TY. Mechanism of IL-1beta-induced increase in intestinal epithelial tight junction permeability. J Immunol 2008;180:5653-5661.
73. Graham WV, Wang F, Clayburgh DR, Cheng JX, Yoon B, Wang Y, Lin A, et al. Tumor necrosis factor-induced long myosin light chain kinase transcription is regulated by differentiation-dependent signaling events. Characterization of the human long myosin light chain kinase promoter. J Biol Chem 2006;281:26205-26215.
74. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, Burcelin R. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008;57:1470-1481.
75. Gulhane M, Murray L, Lourie R, Tong H, Sheng YH, Wang R, Kang A, et al. High Fat Diets Induce Colonic Epithelial Cell Stress and Inflammation that is Reversed by IL-22. Sci Rep 2016;6:28990.
76. Brun P, Castagliuolo I, Di Leo V, Buda A, Pinzani M, Palu G, Martines D. Increased intestinal permeability in obese mice: new evidence in the pathogenesis of nonalcoholic steatohepatitis. Am J Physiol Gastrointest Liver Physiol 2007;292:G518-525.
77. Verdam FJ, Rensen SS, Driessen A, Greve JW, Buurman WA. Novel evidence for chronic exposure to endotoxin in human nonalcoholic steatohepatitis. J Clin Gastroenterol 2011;45:149-152.
78. Cani PD, Delzenne NM. The gut microbiome as therapeutic target. Pharmacol Ther 2011;130:202-212.
79. Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell 2012;148:1258-1270.
80. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, et al. Diversity of the human intestinal microbial flora. Science 2005;308:1635-1638.
81. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070-11075.
82. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
83. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech 2015;8:1-16.
84. Aron-Wisnewsky J, Clement K. The gut microbiome, diet, and links to cardiometabolic and chronic disorders. Nat Rev Nephrol 2016;12:169-181.
85. Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, et al. Dietary intervention impact on gut microbial gene richness. Nature 2013;500:585-588.
86. Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013;500:541-546.
87. Cario E, Gerken G, Podolsky DK. Toll-like receptor 2 controls mucosal inflammation by regulating epithelial barrier function. Gastroenterology 2007;132:1359-1374.
88. Shanahan F. Physiological basis for novel drug therapies used to treat the inflammatory bowel diseases I. Pathophysiological basis and prospects for probiotic therapy in inflammatory bowel disease. Am J Physiol Gastrointest Liver Physiol 2005;288:G417-421.
89. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355-1359.
90. Donohoe DR, Garge N, Zhang X, Sun W, O'Connell TM, Bunger MK, Bultman SJ. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 2011;13:517-526.
91. Bellahcene M, O'Dowd JF, Wargent ET, Zaibi MS, Hislop DC, Ngala RA, Smith DM, et al. Male mice that lack the G-protein-coupled receptor GPR41 have low energy expenditure and increased body fat content. Br J Nutr 2013;109:1755-1764.
92. Zhou J, Hegsted M, McCutcheon KL, Keenan MJ, Xi X, Raggio AM, Martin RJ. Peptide YY and proglucagon mRNA expression patterns and regulation in the gut. Obesity (Silver Spring) 2006;14:683-689.
93. Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011;331:337-341.
94. Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013;500:232-236.
95. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008;453:620-625.
96. Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, Mazmanian SK. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011;332:974-977.
97. Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, Glickman JN, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013;341:569-573.
98. Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013;504:446-450.
99. Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 2004;101:15718-15723.
100. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027-1031.
101. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 2008;3:213-223.
102. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013;341:1241214.
103. Vrieze A, Van Nood E, Holleman F, Salojarvi J, Kootte RS, Bartelsman JF, Dallinga-Thie GM, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012;143:913-916 e917.
104. O'Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep 2006;7:688-693.
105. Packey CD, Sartor RB. Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 2009;22:292-301.
106. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 2010;107:14691-14696.
107. Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012;488:178-184.
108. Gangarapu V, Yildiz K, Ince AT, Baysal B. Role of gut microbiota: obesity and NAFLD. Turk J Gastroenterol 2014;25:133-140.
109. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014;11:506-514.
110. Rajkumar H, Mahmood N, Kumar M, Varikuti SR, Challa HR, Myakala SP. Effect of probiotic (VSL#3) and omega-3 on lipid profile, insulin sensitivity, inflammatory markers, and gut colonization in overweight adults: a randomized, controlled trial. Mediators Inflamm 2014;2014:348959.
111. Wang J, Tang H, Zhang C, Zhao Y, Derrien M, Rocher E, van-Hylckama Vlieg JE, et al. Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice. ISME J 2015;9:1-15.
112. Yoo SR, Kim YJ, Park DY, Jung UJ, Jeon SM, Ahn YT, Huh CS, et al. Probiotics L. plantarum and L. curvatus in combination alter hepatic lipid metabolism and suppress diet-induced obesity. Obesity (Silver Spring) 2013;21:2571-2578.
113. Delzenne NM, Kok N. Effects of fructans-type prebiotics on lipid metabolism. Am J Clin Nutr 2001;73:456S-458S.
114. Cani PD, Neyrinck AM, Fava F, Knauf C, Burcelin RG, Tuohy KM, Gibson GR, et al. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 2007;50:2374-2383.
115. Everard A, Lazarevic V, Derrien M, Girard M, Muccioli GG, Neyrinck AM, Possemiers S, et al. Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes 2011;60:2775-2786.
116. Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 2013;13:790-801.
117. Membrez M, Blancher F, Jaquet M, Bibiloni R, Cani PD, Burcelin RG, Corthesy I, et al. Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice. FASEB J 2008;22:2416-2426.
118. Yanovski SZ, Yanovski JA. Long-term drug treatment for obesity: a systematic and clinical review. JAMA 2014;311:74-86.
119. Filippatos TD, Derdemezis CS, Gazi IF, Nakou ES, Mikhailidis DP, Elisaf MS. Orlistat-associated adverse effects and drug interactions: a critical review. Drug Saf 2008;31:53-65.
120. Yin J, Zhang H, Ye J. Traditional chinese medicine in treatment of metabolic syndrome. Endocr Metab Immune Disord Drug Targets 2008;8:99-111.
121. Wasser SP. Medicinal mushroom science: Current perspectives, advances, evidences, and challenges. Biomed J 2014;37:345-356.
122. Lindequist U, Niedermeyer TH, Julich WD. The pharmacological potential of mushrooms. Evid Based Complement Alternat Med 2005;2:285-299.
123. Kong LY, Tan RX. Artemisinin, a miracle of traditional Chinese medicine. Nat Prod Rep 2015;32:1617-1621.
124. Chang CJ, Lin CS, Lu CC, Martel J, Ko YF, Ojcius DM, Tseng SF, et al. Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota. Nat Commun 2015;6:7489.
125. Huang TT, Lai HC, Ko YF, Ojcius DM, Lan YW, Martel J, Young JD, et al. Hirsutella sinensis mycelium attenuates bleomycin-induced pulmonary inflammation and fibrosis in vivo. Sci Rep 2015;5:15282.
126. Wu LY, Wu MF, Lu HF, Liu CH, Lee CH, Chen YL, Hsueh SC, et al. Evaluation of Hirsutella sinensis mycelium for antifatigue effect. In Vivo 2015;29:263-267.
127. Huang TT, Chong KY, Ojcius DM, Wu YH, Ko YF, Wu CY, Martel J, et al. Hirsutella sinensis mycelium suppresses interleukin-1beta and interleukin-18 secretion by inhibiting both canonical and non-canonical inflammasomes. Sci Rep 2013;3:1374.
128. Zhu ZY, Liu XC, Fang XN, Sun HQ, Yang XY, Zhang YM. Structural characterization and anti-tumor activity of polysaccharide produced by Hirsutella sinensis. Int J Biol Macromol 2016;82:959-966.
129. Lo HC, Hsieh C, Lin FY, Hsu TH. A systematic review of the mysterious caterpillar fungus Ophiocordyceps sinensis in Dong-ChongXiaCao ( Dong Chong Xia Cao) and related bioactive ingredients. J Tradit Complement Med 2013;3:16-32.
130. Winzell MS, Ahren B. The high-fat diet-fed mouse: a model for studying mechanisms and treatment of impaired glucose tolerance and type 2 diabetes. Diabetes 2004;53 Suppl 3:S215-219.
131. Xu H, Barnes GT, Yang Q, Tan G, Yang D, Chou CJ, Sole J, et al. Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance. J Clin Invest 2003;112:1821-1830.
132. Liang W, Menke AL, Driessen A, Koek GH, Lindeman JH, Stoop R, Havekes LM, et al. Establishment of a general NAFLD scoring system for rodent models and comparison to human liver pathology. PLoS One 2014;9:e115922.
133. Hawkesworth S, Moore SE, Fulford AJ, Barclay GR, Darboe AA, Mark H, Nyan OA, et al. Evidence for metabolic endotoxemia in obese and diabetic Gambian women. Nutr Diabetes 2013;3:e83.
134. Yang SQ, Lin HZ, Lane MD, Clemens M, Diehl AM. Obesity increases sensitivity to endotoxin liver injury: implications for the pathogenesis of steatohepatitis. Proc Natl Acad Sci U S A 1997;94:2557-2562.
135. Kim KA, Gu W, Lee IA, Joh EH, Kim DH. High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One 2012;7:e47713.
136. Al-Sadi RM, Ma TY. IL-1beta causes an increase in intestinal epithelial tight junction permeability. J Immunol 2007;178:4641-4649.
137. Guay D. Update on clindamycin in the management of bacterial, fungal and protozoal infections. Expert Opin Pharmacother 2007;8:2401-2444.
138. Lofmark S, Edlund C, Nord CE. Metronidazole is still the drug of choice for treatment of anaerobic infections. Clin Infect Dis 2010;50 Suppl 1:S16-23.
139. Kohanski MA, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol 2010;8:423-435.
140. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006;444:1022-1023.
141. Yang JY, Kweon MN. The gut microbiota: a key regulator of metabolic diseases. BMB Rep 2016;49:536-541.
142. Yang JY, Lee YS, Kim Y, Lee SH, Ryu S, Fukuda S, Hase K, et al. Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice. Mucosal Immunol 2017;10:104-116.
143. Loy A, Pfann C, Steinberger M, Hanson B, Herp S, Brugiroux S, Gomes Neto JC, et al. Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems 2017;2.
144. Ussar S, Griffin NW, Bezy O, Fujisaka S, Vienberg S, Softic S, Deng L, et al. Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome. Cell Metab 2015;22:516-530.
145. Johnson-Henry KC, Donato KA, Shen-Tu G, Gordanpour M, Sherman PM. Lactobacillus rhamnosus strain GG prevents enterohemorrhagic Escherichia coli O157:H7-induced changes in epithelial barrier function. Infect Immun 2008;76:1340-1348.
146. Chiu CM, Huang WC, Weng SL, Tseng HC, Liang C, Wang WC, Yang T, et al. Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches. Biomed Res Int 2014;2014:906168.
147. Lee H, Ko G. Effect of metformin on metabolic improvement and gut microbiota. Appl Environ Microbiol 2014;80:5935-5943.
148. Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, et al. Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing. BMC Gastroenterol 2015;15:100.
149. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, Guiot Y, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 2013;110:9066-9071.
150. Martel J, Ojcius DM, Chang CJ, Lin CS, Lu CC, Ko YF, Tseng SF, et al. Anti-obesogenic and antidiabetic effects of plants and mushrooms. Nat Rev Endocrinol 2017;13:149-160.
151. Zhang Z, Zhang H, Li B, Meng X, Wang J, Zhang Y, Yao S, et al. Berberine activates thermogenesis in white and brown adipose tissue. Nat Commun 2014;5:5493.
152. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012;3:289-306.
153. Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature 2016;535:75-84.
154. Klaring K, Hanske L, Bui N, Charrier C, Blaut M, Haller D, Plugge CM, et al. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol 2013;63:4606-4612.
155. Dunne JC, Kelly WJ, Leahy SC, Li D, Bond JJ, Peng L, Attwood GT, et al. The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus. Proteomes 2015;3:347-368.
156. Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, Kong Z, Pacheco DM, et al. The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS One 2010;5:e11942.
157. Abell GC, Cooke CM, Bennett CN, Conlon MA, McOrist AL. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol Ecol 2008;66:505-515.
158. Shen Y, Giardino Torchia ML, Lawson GW, Karp CL, Ashwell JD, Mazmanian SK. Outer membrane vesicles of a human commensal mediate immune regulation and disease protection. Cell Host Microbe 2012;12:509-520.
159. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013;155:1451-1463.
160. Schneeberger M, Everard A, Gomez-Valades AG, Matamoros S, Ramirez S, Delzenne NM, Gomis R, et al. Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice. Sci Rep 2015;5:16643.
161. Eeckhaut V, Ducatelle R, Sas B, Vermeire S, Van Immerseel F. Progress towards butyrate-producing pharmabiotics: Butyricicoccus pullicaecorum capsule and efficacy in TNBS models in comparison with therapeutics. Gut 2014;63:367.
162. Eeckhaut V, Machiels K, Perrier C, Romero C, Maes S, Flahou B, Steppe M, et al. Butyricicoccus pullicaecorum in inflammatory bowel disease. Gut 2013;62:1745-1752.
163. Ohkawara S, Furuya H, Nagashima K, Asanuma N, Hino T. Oral administration of butyrivibrio fibrisolvens, a butyrate-producing bacterium, decreases the formation of aberrant crypt foci in the colon and rectum of mice. J Nutr 2005;135:2878-2883.
164. Xin J, Zeng D, Wang H, Ni X, Yi D, Pan K, Jing B. Preventing non-alcoholic fatty liver disease through Lactobacillus johnsonii BS15 by attenuating inflammation and mitochondrial injury and improving gut environment in obese mice. Appl Microbiol Biotechnol 2014;98:6817-6829.
165. Xu D, Gao J, Gillilland M, 3rd, Wu X, Song I, Kao JY, Owyang C. Rifaximin alters intestinal bacteria and prevents stress-induced gut inflammation and visceral hyperalgesia in rats. Gastroenterology 2014;146:484-496 e484.
166. Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, Iwasaki A. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci U S A 2011;108:5354-5359.
167. Neff CP, Rhodes ME, Arnolds KL, Collins CB, Donnelly J, Nusbacher N, Jedlicka P, et al. Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties. Cell Host Microbe 2016;20:535-547.
168. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005;122:107-118.
169. Li M, Liang P, Li Z, Wang Y, Zhang G, Gao H, Wen S, et al. Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis. Front Microbiol 2015;6:692.
170. Kraus D, Yang Q, Kahn BB. Lipid extraction from mouse feces. Bio Protoc 2015;5.
171. Gupta J, del Barco Barrantes I, Igea A, Sakellariou S, Pateras IS, Gorgoulis VG, Nebreda AR. Dual function of p38alpha MAPK in colon cancer: suppression of colitis-associated tumor initiation but requirement for cancer cell survival. Cancer Cell 2014;25:484-500.
172. Wang CY, Liao JK. A mouse model of diet-induced obesity and insulin resistance. Methods Mol Biol 2012;821:421-433.
173. Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011;27:2957-2963.
174. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-336.
175. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 2013;10:57-U11.
176. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194-2200.
177. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011;21:494-504.
178. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26:2460-2461.
179. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10:996-998.
180. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006;72:5069-5072.
181. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012;6:610-618.
182. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73:5261-5267.
183. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010;26:266-267.
184. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005;71:8228-8235.
185. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011;5:169-172.
186. White JR, Nagarajan N, Pop M. Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. Plos Computational Biology 2009;5.
187. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 2009;5:e1000352.
188. Benjamini Y, Krieger AM, Yekutieli D. Adaptive linear step-up procedures that control the false discovery rate. Biometrika 2006;93:491-507.