Gut Microbiota as Signatures in Non-communicable Diseases and Mucosal Immunity

  • Santosh Kumar Behera
  • Ardhendu Bhusan Praharaj
  • Gayathri Chalikonda
  • Gowru Srivani
  • Namita Mahapatra
Part of the Diagnostics and Therapeutic Advances in GI Malignancies book series (DTAGIM)


The human gut microbiota encompasses a complex and dynamic ecosystem that provides crucial signals for host development and physiology. The altering composition of the human microbiota is associated with modifications in human behavior and the rising prevalence of pathogenesis of late onset diseases such as life style non-communicable diseases, metabolic and neurological disorders etc. The factors that trigger modifications in the composition and function of the gut microbiota will aid in understanding and designing of therapies that target it, which may be quite formidable. Though several studies have been reported on altered gut microbial composition and its association with diseases, but information on mucin layer degradation, production and immune cell interactions is scanty. The alignment of the gut microbiota can be an emerging indicator or marker of health, as it could be a sensitive tool for identifying various risks. This review unzips the role and type of gut microbiota associated with different non-communicable diseases and their impact on intestinal mucosal immunity which could be the signatures required to promote the human health by the clinicians.


Gastrointestinal microbiome Late onset disorders Intestinal mucosa Mucosal immunity Mucins 



Alzheimer’s disease


Auto immune disease


Antibiotic associated diarrhoea


Amyotrophic lateral sclerosis


Autism spectrum disorder


Bio breeding diabetes prone


Body mass index


Chron’s disease


Chronic heart failure


Chronic kidney disease


Central nervous system


Colorectal Cancer


Cardio vascular disease


Endotoxin Unit


Gluten free diet


Glycoside hydrolases


Gastro intestinal tract


Germ free


G protein coupled receptor


Genome wide association studies


Hepatitis B Virus


Hepatocellular carcinoma


Hepatitis C Virus


Helicobacter pylori


Human Papilloma Virus


Inhibitor of apoptosis protein


Inflammatory bowel diseases


Irritable bowel syndrome




Low density lipoprotein




Nonalcoholic fatty liver diseases


Nonalcoholic steatohepatitis


Non communicable disease


Neuro fibrillary tangles


Non obese diabetic


Pathogen associated molecular patterns


Parkinson’s diseases


Pervasive developmental disorder


Peroxisome proliferator activated receptor


Pattern recognition receptor


Plant sterol esters


Rheumatoid arthritis


Short chain fatty acid


Systemic lupus erythematosus


Single nucleotide polymorphism


Type 1 diabetes


Type 2 diabetes


Toll like receptor




Triglyceride rich lipoprotein


Ulcerative colitis


World health organization



The work was supported by the financial assistance from the extramural research grant of Indian Council of Medical Research (ICMR), Second Phase of Biomedical Informatics Centres of ICMR Grant Number: BIC/12(19)/2013. The Authors acknowledge Department of Science and Technology, Government of India, New Delhi, for granting inspire fellowship to Mr. Ardhendu Bhusan Praharaj. The authors also acknowledge ICMR-Regional Medical Research Centre, Bhubaneswar for providing infrastructure facilities to carry out this work.

Conflict of Interest Disclosure

The authors declare no conflict of interest exists.

Declaration of Funding Sources

The work was supported by the financial assistance from the extramural research grant of Indian Council of Medical Research (ICMR), Second Phase of Biomedical Informatics Centres of ICMR Grant Number: BIC/12(19)/2013 and DST, Govt. of India.


  1. Aguirre M, Venema K (2015) Does the gut microbiota contribute to obesity? Going beyond the gut feeling. Microorganisms 3(2):213–235CrossRefPubMedPubMedCentralGoogle Scholar
  2. Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L (2013) Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst 105(24):1907–1911CrossRefPubMedPubMedCentralGoogle Scholar
  3. Ahrne S, Johansson Hagslatt M-L (2011) Effect of lactobacilli on paracellular permeability in the gut. Nutrients 3(1):104–117CrossRefPubMedPubMedCentralGoogle Scholar
  4. Álvarez-Arellano L, Maldonado-Bernal C (2014) Helicobacter pylori and neurological diseases: married by the laws of inflammation. World J Gastrointest Pathophysiol 5(4):400CrossRefPubMedPubMedCentralGoogle Scholar
  5. Amar J, Burcelin R, Ruidavets JB, Cani PD, Fauvel J, Alessi MC, Chamontin B, Ferriéres J (2008) Energy intake is associated with endotoxemia in apparently healthy men. Am J Clin Nutr 87(5):1219–1223CrossRefGoogle Scholar
  6. Andoh A, Kuzuoka H, Tsujikawa T, Nakamura S, Hirai F, Suzuki Y, Matsui T, Fujiyama Y, Matsumoto T (2012) Multicenter analysis of fecal microbiota profiles in Japanese patients with Crohn’s disease. J Gastroenterol 47(12):1298–1307CrossRefGoogle Scholar
  7. Angelberger S, Reinisch W, Makristathis A, Lichtenberger C, Dejaco C, Papay P, Novacek G, Trauner M, Loy A, Berry D (2013) Temporal bacterial community dynamics vary among ulcerative colitis patients after fecal microbiota transplantation. Am J Gastroenterol 108(10):1620CrossRefGoogle Scholar
  8. Anstee QM, McPherson S, Day CP (2011) How big a problem is non-alcoholic fatty liver disease? BMJ 343:d3897CrossRefGoogle Scholar
  9. Artis D (2008) Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat Rev Immunol 8(6):411–420CrossRefGoogle Scholar
  10. Atkinson M, Chervonsky A (2012) Does the gut microbiota have a role in type 1 diabetes? Early evidence from humans and animal models of the disease. Diabetologia 55(11):2868–2877CrossRefPubMedPubMedCentralGoogle Scholar
  11. Bach J-F (2002) The effect of infections on susceptibility to autoimmune and allergic diseases. N Engl J Med 347(12):911–920CrossRefGoogle Scholar
  12. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci 101(44):15718–15723CrossRefGoogle Scholar
  13. Bakken J, Borody T, Brandt L, Brill J, Demarco D, Franzos M, Kelly C, Khoruts A, Louie T, Martinelli L et al (2011) Treating Clostridium difficile infection with fecal microbiota transplantation. Clinical Gastroenterol hepatol: official Clin Pract J Am Gastroenterol Assoc 9:1044–1049CrossRefGoogle Scholar
  14. Balin BJ, Hudson AP (2014) Etiology and pathogenesis of late-onset Alzheimer’s disease. Curr Allergy Asthma Rep 14(3):417CrossRefGoogle Scholar
  15. Banjoko IO, Adeyanju MM, Ademuyiwa O, Adebawo OO, Olalere RA, Kolawole MO, Adegbola IA, Adesanmi TA, Oladunjoye TO, Ogunnowo AA (2012) Hypolipidemic effects of lactic acid bacteria fermented cereal in rats. Lipids Health Dis 11(1):170CrossRefPubMedPubMedCentralGoogle Scholar
  16. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG et al (2007) Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of clostridiales in Crohn’s disease involving the ileum. ISME J 1(5):403–418CrossRefGoogle Scholar
  17. Behera SK, Praharaj AB, Dehury B, Negi S (2015) Exploring the role and diversity of mucins in health and disease with special insight into non-communicable diseases. Glycoconj J 32(8):575–613CrossRefGoogle Scholar
  18. Bekkering P, Jafri I, Van Overveld FJ, Rijkers GT (2013) The intricate association between gut microbiota and development of type 1, type 2 and type 3 diabetes. Expert Rev Clin Immunol 9(11):1031–1041CrossRefGoogle Scholar
  19. Belmonte L, Youmba SB, Bertiaux-Vandaele N, Antonietti M, Lecleire S, Zalar A, Gourcerol G, Leroi A-M, Déchelotte P, Coëffier M (2012) Role of toll like receptors in irritable bowel syndrome: differential mucosal immune activation according to the disease subtype. PLoS One 7(8):e42777CrossRefPubMedPubMedCentralGoogle Scholar
  20. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkïla J, Monti D, Satokari R, Franceschi C (2010) Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One 5(5):e10667CrossRefPubMedPubMedCentralGoogle Scholar
  21. Blaecher C, Smet A, Flahou B, Pasmans F, Ducatelle R, Taylor D, Weller C, Bjarnason I, Charlett A, Lawson A (2013) Significantly higher frequency of H elicobacter suis in patients with idiopathic parkinsonism than in control patients. Aliment Pharmacol Ther 38(11–12):1347–1353CrossRefPubMedPubMedCentralGoogle Scholar
  22. Boesten RJ, de Vos WM (2008) Interactomics in the human intestine: lactobacilli and bifidobacteria make a difference. J Clin Gastroenterol 42:S163–S167CrossRefGoogle Scholar
  23. Boursier J, Diehl AM (2015) Implication of gut microbiota in nonalcoholic fatty liver disease. PLoS Pathog 11(1):e1004559CrossRefPubMedPubMedCentralGoogle Scholar
  24. Brandl K, Schnabl B (2017) Intestinal microbiota and nonalcoholic steatohepatitis. Curr Opin Gastroenterol 33(3):128–133CrossRefPubMedPubMedCentralGoogle Scholar
  25. Brown K, DeCoffe D, Molcan E, Gibson DL (2012) Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 4(8):1095–1119CrossRefPubMedPubMedCentralGoogle Scholar
  26. Bull TJ, McMinn EJ, Sidi-Boumedine K, Skull A, Durkin D, Neild P, Rhodes G, Pickup R, Hermon-Taylor J (2003) Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn’s disease. J Clin Microbiol 41(7):2915–2923CrossRefPubMedPubMedCentralGoogle Scholar
  27. Burrows MP, Volchkov P, Kobayashi KS, Chervonsky AV (2015) Microbiota regulates type 1 diabetes through toll-like receptors. Proc Natl Acad Sci U S A 112(32):9973–9977CrossRefPubMedPubMedCentralGoogle Scholar
  28. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, Neyrinck AM, Fava F, Tuohy KM, Chabo C et al (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56(7):1761–1772CrossRefGoogle Scholar
  29. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, Burcelin R (2008) Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet–induced obesity and diabetes in mice. Diabetes 57(6):1470–1481CrossRefGoogle Scholar
  30. Cani PD, Daubioul CA, Reusens B, Remacle C, Catillon GG, Delzenne NM (2005) Involvement of endogenous glucagon-like peptide-1(7–36) amide on glycaemia-lowering effect of oligofructose in streptozotocin-treated rats. J Endocrinol 185(3):457CrossRefGoogle Scholar
  31. Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ (2015) Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 26:26191–26191PubMedGoogle Scholar
  32. Caselli M, Cassol F, Calò G, Holton J, Zuliani G, Gasbarrini A (2013) Actual concept of “probiotics”: is it more functional to science or business? World J Gastroenterol: WJG 19(10):1527CrossRefGoogle Scholar
  33. Cenit MC, Olivares M, Codoñer-Franch P, Sanz Y (2015) Intestinal microbiota and celiac disease: cause, consequence or co-evolution? Nutrients 7(8):6900–6923CrossRefPubMedPubMedCentralGoogle Scholar
  34. Chalasani N, Younossi Z, Lavine JE, Diehl AM, Brunt EM, Cusi K, Charlton M, Sanyal AJ (2012) The diagnosis and management of non-alcoholic fatty liver disease: practice guideline by the American Association for the Study of Liver Diseases, American College of Gastroenterology, and the American Gastroenterological Association. Hepatology 55(6):2005–2023CrossRefGoogle Scholar
  35. Cheng J, Palva AM, de Vos WM, Satokari R (2011) Contribution of the intestinal microbiota to human health: from birth to 100 years of age. In: Between pathogenicity and commensalism. Springer, Berlin, Heidelberg, pp 323–346Google Scholar
  36. Clarke JL, Daniell H (2011) Plastid biotechnology for crop production: present status and future perspectives. Plant Mol Biol 76(3–5):211–220CrossRefPubMedPubMedCentralGoogle Scholar
  37. Collado MC, Isolauri E, Laitinen K, Salminen S (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88(4):894–899CrossRefGoogle Scholar
  38. Collins M, Lawson P, Willems A, Cordoba J, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow J (1994) The phylogeny of the genus clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Evol Microbiol 44(4):812–826Google Scholar
  39. Cope K, Risby T, Diehl AM (2000) Increased gastrointestinal ethanol production in obese mice: implications for fatty liver disease pathogenesis. Gastroenterology 119(5):1340–1347CrossRefGoogle Scholar
  40. Corbin KD, Zeisel SH (2012) Choline metabolism provides novel insights into non-alcoholic fatty liver disease and its progression. Curr Opin Gastroenterol 28(2):159CrossRefPubMedPubMedCentralGoogle Scholar
  41. Crost EH, Tailford LE, Le Gall G, Fons M, Henrissat B, Juge N (2013) Utilisation of mucin glycans by the human gut symbiont ruminococcus gnavus is strain-dependent. PLoS One 8(10):e76341CrossRefPubMedPubMedCentralGoogle Scholar
  42. Crow JR, Davis SL, Chaykosky DM, Smith TT, Smith JM (2015) Probiotics and fecal microbiota transplant for primary and secondary prevention of C lostridium difficile infection. Pharmacother: J Hum Pharmacol Drug Ther 35(11):1016–1025CrossRefGoogle Scholar
  43. Cuervo A, Hevia A, López P, Suárez A, Sánchez B, Margolles A, González S (2015) Association of polyphenols from oranges and apples with specific intestinal microorganisms in systemic lupus erythematosus patients. Nutrients 7(2):1301–1317CrossRefPubMedPubMedCentralGoogle Scholar
  44. de Goffau MC, Luopajärvi K, Knip M, Ilonen J, Ruohtula T, Härkönen T, Orivuori L, Hakala S, Welling GW, Harmsen HJ (2013) Fecal microbiota composition differs between children with β-cell autoimmunity and those without. Diabetes 62(4):1238–1244CrossRefPubMedPubMedCentralGoogle Scholar
  45. Derrien M, Vaughan EE, Plugge CM, de Vos WM (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54(5):1469–1476CrossRefGoogle Scholar
  46. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature 487(7405):104CrossRefPubMedPubMedCentralGoogle Scholar
  47. Diamant M, Blaak E, De Vos W (2011) Do nutrient–gut–microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes? Obes Rev 12(4):272–281CrossRefGoogle Scholar
  48. Dicksved J, Halfvarson J, Rosenquist M, Järnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK (2008) Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J 2(7):716CrossRefGoogle Scholar
  49. Dobbs S, Dobbs R, Weller C, Charlett A (2000) Link between helicobacter pylori infection and idiopathic parkinsonism. Med Hypotheses 55(2):93–98CrossRefGoogle Scholar
  50. Dumas M-E, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC (2006) Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci 103(33):12511–12516CrossRefGoogle Scholar
  51. Duncan SH, Lobley G, Holtrop G, Ince J, Johnstone A, Louis P, Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes 32(11):1720CrossRefGoogle Scholar
  52. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefPubMedPubMedCentralGoogle Scholar
  53. Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI (2011) NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145(5):745–757CrossRefPubMedPubMedCentralGoogle Scholar
  54. Ermund A, Schütte A, Johansson MEV, Gustafsson JK, Hansson GC (2013) Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer’s patches. Am J Physiol Gastrointest Liver Physiol 305(5):G341–G347CrossRefPubMedPubMedCentralGoogle Scholar
  55. Finegold SM (2011) State of the art; microbiology in health and disease. Intestinal bacterial flora in autism. Anaerobe 17(6):367–368CrossRefGoogle Scholar
  56. Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, Pace NR (2007a) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci 104(34):13780–13785CrossRefGoogle Scholar
  57. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR (2007b) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104(34):13780–13785CrossRefPubMedPubMedCentralGoogle Scholar
  58. Furet J-P, Kong L-C, Tap J, Poitou C, Basdevant A, Bouillot J-L, Mariat D, Corthier G, Doré J, Henegar C et al (2010) Differential adaptation of human gut microbiota to bariatric surgery–induced weight loss. Links with metabolic and low-grade inflammation markers. Diabetes 59(12):3049–3057CrossRefPubMedPubMedCentralGoogle Scholar
  59. Gao Z, Yin J, Zhang J, Ward RE, Martin RJ, Lefevre M, Cefalu WT, Ye J (2009) Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 58(7):1509–1517CrossRefPubMedPubMedCentralGoogle Scholar
  60. Gomes AC, Bueno AA, de Souza RGM, Mota JF (2014) Gut microbiota, probiotics and diabetes. Nutr J 13(1):60CrossRefPubMedPubMedCentralGoogle Scholar
  61. Goso Y, Ishihara K, Sugawara S, Hotta K (2001) Purification and characterization of α-l-fucosidases from Streptomyces sp. OH11242. Comp Biochem Physiol B: Biochem Mol Biol 130(3):375–383CrossRefGoogle Scholar
  62. Guo Y, Mah E, Davis C, Jalili T, Ferruzzi M, Chun O, Bruno R (2013) Dietary fat increases quercetin bioavailability in overweight adults. Mol Nutr Food Res 57:896–905CrossRefGoogle Scholar
  63. Hedin CR, McCarthy NE, Louis P, Farquharson FM, McCartney S, Taylor K, Prescott NJ, Murrells T, Stagg AJ, Whelan K et al (2014) Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn’s disease and their unaffected siblings. Gut 63(10):1578–1586CrossRefGoogle Scholar
  64. Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ (2012) Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482(7384):179CrossRefPubMedPubMedCentralGoogle Scholar
  65. Hevia A, Milani C, López P, Cuervo A, Arboleya S, Duranti S, Turroni F, González S, Suárez A, Gueimonde M et al (2014) Intestinal dysbiosis associated with systemic lupus erythematosus. MBio 5(5):e01548–e01514CrossRefPubMedPubMedCentralGoogle Scholar
  66. Hida M, Aiba Y, Sawamura S, Suzuki N, Satoh T, Koga Y (1996) Inhibition of the accumulation of uremic toxins in the blood and their precursors in the feces after oral administration of Lebenin®, a lactic acid bacteria preparation, to uremic patients undergoing hemodialysis. Nephron 74(2):349–355CrossRefPubMedPubMedCentralGoogle Scholar
  67. Honda K, Littman DR (2012) The microbiome in infectious disease and inflammation. Annu Rev Immunol 30:759–795CrossRefPubMedPubMedCentralGoogle Scholar
  68. Hoskins LC, Boulding ET, Larson G (1997) Purification and characterization of blood group A-degrading isoforms of α-N-acetylgalactosaminidase from ruminococcus torques strain IX-70. J Biol Chem 272(12):7932–7939CrossRefGoogle Scholar
  69. Hur KY, Lee M-S (2015) Gut microbiota and metabolic disorders. Diabetes Metab J 39(3):198–203CrossRefPubMedPubMedCentralGoogle Scholar
  70. Jia W, Li H, Zhao L, Nicholson JK (2008) Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 7(2):123CrossRefGoogle Scholar
  71. Jiang W, Wu N, Wang X, Chi Y, Zhang Y, Qiu X, Hu Y, Li J, Liu Y (2015) Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease. Sci Rep 5:8096CrossRefPubMedPubMedCentralGoogle Scholar
  72. Johansson ME, Larsson JMH, Hansson GC (2011) The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host–microbial interactions. Proc Natl Acad Sci 108(Supplement 1):4659–4665CrossRefGoogle Scholar
  73. Jumpertz R, Le DS, Turnbaugh PJ, Trinidad C, Bogardus C, Gordon JI, Krakoff J (2011) Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr 94(1):58–65CrossRefPubMedPubMedCentralGoogle Scholar
  74. Kang D-W, Park JG, Ilhan ZE, Wallstrom G, Labaer J, Adams JB, Krajmalnik-Brown R (2013) Reduced incidence of prevotella and other fermenters in intestinal microflora of autistic children. PLoS One 8(7):e68322–e68322CrossRefPubMedPubMedCentralGoogle Scholar
  75. Kasubuchi M, Hasegawa S, Hiramatsu T, Ichimura A, Kimura I (2015) Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation. Nutrients 7(4):2839–2849CrossRefPubMedPubMedCentralGoogle Scholar
  76. Kelly D, Campbell JI, King TP, Grant G, Jansson EA, Coutts AG, Pettersson S, Conway S (2004) Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-γ and RelA. Nat Immunol 5(1):104CrossRefGoogle Scholar
  77. Kelly T, Yang W, Chen C-S, Reynolds K, He J (2008) Global burden of obesity in 2005 and projections to 2030. Int J Obes 32(9):1431CrossRefGoogle Scholar
  78. Kieffer DA, Piccolo BD, Vaziri ND, Liu S, Lau WL, Khazaeli M, Nazertehrani S, Moore ME, Marco ML, Martin RJ (2016) Resistant starch alters gut microbiome and metabolomic profiles concurrent with amelioration of chronic kidney disease in rats. Am J Physiol Renal Physiol 310(9):F857–F871CrossRefPubMedPubMedCentralGoogle Scholar
  79. Kimura I, Ozawa K, Inoue D, Imamura T, Kimura K, Maeda T, Terasawa K, Kashihara D, Hirano K, Tani T (2013) The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43. Nat Commun 4:1829CrossRefPubMedPubMedCentralGoogle Scholar
  80. Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R (2011) Human-associated microbial signatures: examining their predictive value. Cell Host Microbe 10(4):292–296CrossRefGoogle Scholar
  81. Kondo S, Xiao J-Z, Satoh T, Odamaki T, Takahashi S, Sugahara H, Yaeshima T, Iwatsuki K, Kamei A, Abe K (2010) Antiobesity effects of bifidobacterium breve strain B-3 supplementation in a mouse model with high-fat diet-induced obesity. Biosci Biotechnol Biochem 74(8):1656–1661CrossRefGoogle Scholar
  82. Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (2010) Bergey’s manual of systematic bacteriology, vol 4. Springer Science+ Business Media, New York, NYCrossRefGoogle Scholar
  83. Kumar A, Agarwal S, Phadke SR, Jaiswal Y (2014) Genetic insight of schizophrenia: past and future perspectives. Gene 535(2):97–100CrossRefGoogle Scholar
  84. Langley-Evans S (2015) Nutrition in early life and the programming of adult disease: a review. J Hum Nutr Diet 28:1–14CrossRefGoogle Scholar
  85. Larsson JMH, Karlsson H, Crespo JG, Johansson ME, Eklund L, Sjövall H, Hansson GC (2011) Altered O-glycosylation profile of MUC2 mucin occurs in active ulcerative colitis and is associated with increased inflammation. Inflamm Bowel Dis 17(11):2299–2307CrossRefGoogle Scholar
  86. Levine MJ, Reddy MS, Tabak LA, Loomis RE, Bergey EJ, Jones PC, Cohen RE, Stinson MW, Al-Hashimi I (1987) Structural aspects of salivary glycoproteins. J Dent Res 66(2):436–441CrossRefGoogle Scholar
  87. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444(7122):1022CrossRefPubMedPubMedCentralGoogle Scholar
  88. Lim GB (2015) Heart failure: gut flora—pathogenic role in chronic heart failure. Nat Rev Cardiol 13(2):61CrossRefGoogle Scholar
  89. Macfarlane S, Hopkins MJ, Macfarlane GT (2001) Toxin synthesis and mucin breakdown are related to swarming phenomenon in clostridium septicum. Infect Immun 69(2):1120–1126CrossRefPubMedPubMedCentralGoogle Scholar
  90. Mafra D, Lobo JC, Barros AF, Koppe L, Vaziri ND, Fouque D (2014) Role of altered intestinal microbiota in systemic inflammation and cardiovascular disease in chronic kidney disease. Future Microbiol 9(3):399–410CrossRefGoogle Scholar
  91. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci 106(14):5859–5864CrossRefGoogle Scholar
  92. Malinen E, Krogius-Kurikka L, Lyra A, Nikkilä J, Jääskeläinen A, Rinttilä T, Vilpponen-Salmela T, von Wright AJ, Palva A (2010) Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol: WJG 16(36):4532CrossRefGoogle Scholar
  93. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P et al (2006) Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55(2):205–211CrossRefPubMedPubMedCentralGoogle Scholar
  94. Mao Y, Nobaek S, Kasravi B, Adawi D, Stenram U, Molin G, Jeppsson B (1996) The effects of lactobacillus strains and oat fiber on methotrexate-induced enterocolitis in rats. Gastroenterology 111(2):334–344CrossRefGoogle Scholar
  95. Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet J (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9(1):123CrossRefPubMedPubMedCentralGoogle Scholar
  96. Martínez I, Perdicaro DJ, Brown AW, Hammons S, Carden TJ, Carr TP, Eskridge KM, Walter J (2013) Diet-induced alterations of host cholesterol metabolism are likely to affect the gut microbiota composition in hamsters. Appl Environ Microbiol 79(2):516–524CrossRefPubMedPubMedCentralGoogle Scholar
  97. Martinez RCR, Bedani R, Saad SMI (2015) Scientific evidence for health effects attributed to the consumption of probiotics and prebiotics: an update for current perspectives and future challenges. Br J Nutr 114(12):1993–2015CrossRefGoogle Scholar
  98. Matsuoka K, Kanai T (2015) The gut microbiota and inflammatory bowel disease. In: Seminars in immunopathology: 2015. Springer, Berlin, pp 47–55Google Scholar
  99. McPhee JB, Schertzer JD (2015) Immunometabolism of obesity and diabetes: microbiota link compartmentalized immunity in the gut to metabolic tissue inflammation. Clin Sci 129(12):1083–1096CrossRefGoogle Scholar
  100. Mejía-León ME, Barca AM (2015) Diet, microbiota and immune system in type 1 diabetes development and evolution. Nutrients 7(11):9171–9184CrossRefPubMedPubMedCentralGoogle Scholar
  101. Miklossy J (2011, Sep 20) Emerging roles of pathogens in Alzheimer disease. Expert Rev Mol Med 13:e30.
  102. Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B, Raoult D (2012a) Obesity-associated gut microbiota is enriched in lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. Int J Obes 36(6):817–825CrossRefGoogle Scholar
  103. Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B, Raoult D (2012b) Obesity-associated gut microbiota is enriched in lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. Int J Obes 36(6):817CrossRefGoogle Scholar
  104. Molloy MJ, Bouladoux N, Belkaid Y (2012) Intestinal microbiota: shaping local and systemic immune responses. In: Seminars in immunology: 2012. Elsevier, pp 58–66Google Scholar
  105. Moos WH, Maneta E, Pinkert CA, Irwin MH, Hoffman ME, Faller DV, Steliou K (2016) Epigenetic treatment of neuropsychiatric disorders: autism and schizophrenia. Drug Dev Res 77(2):53–72CrossRefGoogle Scholar
  106. Mulak A, Bonaz B (2015) Brain-gut-microbiota axis in Parkinson’s disease. World J Gastroenterol 21(37):10609–10620CrossRefPubMedPubMedCentralGoogle Scholar
  107. Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, Queipo-Ortuño MI (2013) Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med 11(1):46CrossRefPubMedPubMedCentralGoogle Scholar
  108. Murugesan S, Nirmalkar K, García-Espitia M, Pizano-Zárate ML, Hoyo-Vadillo C, Garcia-Mena J (2017) Current insight into the role of gut microbiota in Mexican childhood obesity. SOJ Pharm Pharm Sci 4:1–5CrossRefGoogle Scholar
  109. Musso G, Gambino R, Cassader M (2011) Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annu Rev Med 62:361–380CrossRefGoogle Scholar
  110. Nicholson JK, Holmes E, Wilson ID (2005) Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3(5):431CrossRefGoogle Scholar
  111. Nielsen HH, Qiu J, Friis S, Wermuth L, Ritz B (2012) Treatment for helicobacter pylori infection and risk of Parkinson’s disease in Denmark. Eur J Neurol 19(6):864–869CrossRefPubMedPubMedCentralGoogle Scholar
  112. Nisbet RM, Polanco J-C, Ittner LM, Götz J (2015) Tau aggregation and its interplay with amyloid-β. Acta Neuropathol 129(2):207–220CrossRefGoogle Scholar
  113. Nishikawa J, Kudo T, Sakata S, Benno Y, Sugiyama T (2009) Diversity of mucosa-associated microbiota in active and inactive ulcerative colitis. Scand J Gastroenterol 44(2):180–186CrossRefGoogle Scholar
  114. O’Mahony D, Murphy S, Boileau T, Park J, O’Brien F, Groeger D, Konieczna P, Ziegler M, Scully P, Shanahan F et al (2010) Bifidobacterium animalis AHC7 protects against pathogen-induced NF-κB activation in vivo. BMC Immunol 11:63–63CrossRefPubMedPubMedCentralGoogle Scholar
  115. O’Toole PW, Jeffery IB (2015) Gut microbiota and aging. Science 350(6265):1214–1215CrossRefGoogle Scholar
  116. Oishi K, Sato T, Yokoi W, Yoshida Y, Ito M, Sawada H (2008) Effect of probiotics, Bifidobacterium breve and lactobacillus casei, on bisphenol a exposure in rats. Biosci Biotechnol Biochem 72(6):1409–1415CrossRefGoogle Scholar
  117. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Fölsch UR, Timmis KN, Schreiber S (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53(5):685–693CrossRefPubMedPubMedCentralGoogle Scholar
  118. Patil DP, Dhotre DP, Chavan SG, Sultan A, Jain DS, Lanjekar VB, Gangawani J, Shah PS, Todkar JS, Shah S (2012) Molecular analysis of gut microbiota in obesity among Indian individuals. J Biosci 37(4):647–657CrossRefGoogle Scholar
  119. Pellegrini S, Sordi V, Bolla AM, Saita D, Ferrarese R, Canducci F, Clementi M, Invernizzi F, Mariani A, Bonfanti R et al (2017a) Duodenal mucosa of patients with type 1 diabetes shows distinctive inflammatory profile and microbiota. J Clin Endocrinol Metabol 102(5):1468–1477CrossRefGoogle Scholar
  120. Pellegrini S, Sordi V, Bolla AM, Saita D, Ferrarese R, Canducci F, Clementi M, Invernizzi F, Mariani A, Bonfanti R (2017b) Duodenal mucosa of patients with type 1 diabetes shows distinctive inflammatory profile and microbiota. J Clin Endocrinol Metabol 102(5):1468–1477CrossRefGoogle Scholar
  121. Peterson DA, Frank DN, Pace NR, Gordon JI (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3(6):417–427CrossRefPubMedPubMedCentralGoogle Scholar
  122. Png CW, Lindén SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin TH (2010) Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 105(11):2420CrossRefGoogle Scholar
  123. Pozzilli P, Signore A, Williams AJK, Beales PE (1993) NOD mouse colonies around the world- recent facts and figures. Immunol Today 14(5):193–196CrossRefGoogle Scholar
  124. Prandota J (2014) Possible link between toxoplasma gondii and the anosmia associated with neurodegenerative diseases. Am J Alzheimers Dis Other Dement 29(3):205–214CrossRefGoogle Scholar
  125. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418):55CrossRefGoogle Scholar
  126. Radilla-Vázquez RB, Parra-Rojas I, Martínez-Hernández NE, Márquez-Sandoval YF, Illades-Aguiar B, Castro-Alarcón N (2016) Gut microbiota and metabolic endotoxemia in young obese Mexican subjects. Obes Facts 9(1):1–11CrossRefPubMedPubMedCentralGoogle Scholar
  127. Rahne K-E, Tagesson C, Nyholm D (2013) Motor fluctuations and helicobacter pylori in Parkinson’s disease. J Neurol 260(12):2974–2980CrossRefGoogle Scholar
  128. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P (2013) Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol 11(7):868–875. e863CrossRefGoogle Scholar
  129. Reunanen J, Kainulainen V, Huuskonen L, Ottman N, Belzer C, Huhtinen H, de Vos WM, Satokari R (2015) Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of the epithelial cell layer. Appl Environ Microbiol 81(11):3655–3662CrossRefPubMedPubMedCentralGoogle Scholar
  130. Roberton AM, Corfield AP (1999) Mucin degradation and its significance in inflammatory conditions of the gastrointestinal tract. In: Medical importance of the normal microflora. Springer, pp 222–261Google Scholar
  131. Robinson CV, Elkins MR, Bialkowski KM, Thornton DJ, Kertesz MA (2012) Desulfurization of mucin by Pseudomonas aeruginosa: influence of sulfate in the lungs of cystic fibrosis patients. J Med Microbiol 61(12):1644–1653CrossRefGoogle Scholar
  132. Rogers G, Keating D, Young R, Wong M, Licinio J, Wesselingh S (2016) From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol Psychiatry 21(6):738CrossRefPubMedPubMedCentralGoogle Scholar
  133. Rogier R, Koenders MI, Abdollahi-Roodsaz S (2015) Toll-like receptor mediated modulation of T cell response by commensal intestinal microbiota as a trigger for autoimmune arthritis. J Immunol Res 2015:527696–527696CrossRefPubMedPubMedCentralGoogle Scholar
  134. Rojo D, Hevia A, Bargiela R, López P, Cuervo A, González S, Suárez A, Sánchez B, Martínez-Martínez M, Milani C et al (2015) Ranking the impact of human health disorders on gut metabolism: systemic lupus erythematosus and obesity as study cases. Sci Rep 5:8310–8310CrossRefPubMedPubMedCentralGoogle Scholar
  135. Ruotolo G, Howard BV (2002) Dyslipidemia of the metabolic syndrome. Curr Cardiol Rep 4(6):494–500CrossRefGoogle Scholar
  136. Sandberg MEC, Bengtsson C, Klareskog L, Alfredsson L, Saevarsdottir S (2015) Recent infections are associated with decreased risk of rheumatoid arthritis: a population-based case-control study. Ann Rheum Dis 74(5):904–907CrossRefGoogle Scholar
  137. Sandek A, Bauditz J, Swidsinski A, Buhner S, Weber-Eibel J, von Haehling S, Schroedl W, Karhausen T, Doehner W, Rauchhaus M (2007) Altered intestinal function in patients with chronic heart failure. J Am Coll Cardiol 50(16):1561–1569CrossRefGoogle Scholar
  138. Sandhya P, Danda D, Sharma D, Scaria V (2016) Does the buck stop with the bugs?: an overview of microbial dysbiosis in rheumatoid arthritis. Int J Rheum Dis 19(1):8–20CrossRefGoogle Scholar
  139. Sanz Y (2010) Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes 1(3):135–137CrossRefPubMedPubMedCentralGoogle Scholar
  140. Sato J, Kanazawa A, Ikeda F, Yoshihara T, Goto H, Abe H, Komiya K, Kawaguchi M, Shimizu T, Ogihara T et al (2014) Gut dysbiosis and detection of “live gut bacteria” in blood of Japanese patients with type 2 diabetes. Diabetes Care 37(8):2343–2350CrossRefGoogle Scholar
  141. Saulnier DM, Gibson GR, Kolida S (2008) In vitro effects of selected synbiotics on the human faecal microbiota composition. FEMS Microbiol Ecol 66(3):516–527CrossRefGoogle Scholar
  142. Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M (2015) Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov Disord 30(3):350–358CrossRefGoogle Scholar
  143. Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB et al (2013) Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. elife 2:e01202–e01202CrossRefPubMedPubMedCentralGoogle Scholar
  144. Schultsz C, van den Berg FM, Fiebo W, Tytgat GN, Dankert J (1999) The intestinal mucus layer from patients with inflammatory bowel disease harbors high numbers of bacteria compared with controls. Gastroenterology 117(5):1089–1097CrossRefGoogle Scholar
  145. Schwabe RF, Jobin C (2013) The microbiome and cancer. Nat Rev Cancer 13(11):800CrossRefPubMedPubMedCentralGoogle Scholar
  146. Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SSK, Sakamoto J, Boothe D et al (2012) Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS One 7(3):e33387–e33387CrossRefPubMedPubMedCentralGoogle Scholar
  147. Serino M, Fernández-Real JM, García-Fuentes E, Queipo-Ortuño M, Moreno-Navarrete JM, Sánchez A, Burcelin R, Tinahones F (2013) The gut microbiota profile is associated with insulin action in humans. Acta Diabetol 50(5):753–761CrossRefGoogle Scholar
  148. Serre CBL, Ellis CL, Lee J, Hartman AL, Rutledge JC, Raybould HE (2010) Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am J Physiol Gastrointest Liver Physiol 299(2):G440–G448CrossRefGoogle Scholar
  149. Sheridan PO, Bindels LB, Saulnier DM, Reid G, Nova E, Holmgren K, O’Toole PW, Bunn J, Delzenne N, Scott KP: Can prebiotics and probiotics improve therapeutic outcomes for undernourished individuals?; 201474-82Google Scholar
  150. Shin N-R, Lee J-C, Lee H-Y, Kim M-S, Whon TW, Lee M-S, Bae J-W (2014) An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 63(5):727–735CrossRefGoogle Scholar
  151. Silberberg D, Anand NP, Michels K, Kalaria RN (2015) Brain and other nervous system disorders across the lifespan — global challenges and opportunities. Nature 527:S151CrossRefGoogle Scholar
  152. Sipos F, Leiszter K, Tulassay Z (2011) Effect of ageing on colonic mucosal regeneration. World J Gastroenterol: WJG 17(25):2981CrossRefGoogle Scholar
  153. Sokol H, Cosnes J, Chazouilleres O, Beaugerie L, Tiret E, Poupon R, Seksik P (2008) Disease activity and cancer risk in inflammatory bowel disease associated with primary sclerosing cholangitis. World J Gastroenterol: WJG 14(22):3497CrossRefGoogle Scholar
  154. Sommer F, Bäckhed F (2013) The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 11(4):227CrossRefGoogle Scholar
  155. Song X, Fan X, Song X, Zhang J, Zhang W, Li X, Gao J, Harrington A, Ziedonis D, Lv L (2013) Elevated levels of adiponectin and other cytokines in drug naive, first episode schizophrenia patients with normal weight. Schizophr Res 150(1):269–273CrossRefGoogle Scholar
  156. Spencer MD, Hamp TJ, Reid RW, Fischer LM, Zeisel SH, Fodor AA (2011) Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140(3):976–986CrossRefGoogle Scholar
  157. Stewart-Tull D, Ollar R, SCOBIE TS (1986) Studies on the vibrio cholerae mucinase complex. I. Enzymic activities associated with the complex325. J Med Microbiol 22(4):325–333CrossRefGoogle Scholar
  158. Sun J, Chang EB (2014) Exploring gut microbes in human health and disease: pushing the envelope. Genes Dis 1(2):132–139CrossRefPubMedPubMedCentralGoogle Scholar
  159. Tailford LE, Crost EH, Kavanaugh D, Juge N (2015) Mucin glycan foraging in the human gut microbiome. Front Genet 6:81CrossRefPubMedPubMedCentralGoogle Scholar
  160. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DL, Nalin R (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11(10):2574–2584CrossRefGoogle Scholar
  161. Tilg H, Moschen AR (2014) Microbiota and diabetes: an evolving relationship. Gut 63(9):1513–1521CrossRefGoogle Scholar
  162. Tlaskalová-Hogenová H, Stěpánková R, Kozáková H, Hudcovic T, Vannucci L, Tučková L, Rossmann P, Hrnčíř T, Kverka M, Zákostelská Z et al (2011) The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cell Mol Immunol 8(2):110–120CrossRefPubMedPubMedCentralGoogle Scholar
  163. Tomova A, Husarova V, Lakatosova S, Bakos J, Vlkova B, Babinska K, Ostatnikova D (2015) Gastrointestinal microbiota in children with autism in Slovakia. Physiol Behav 138:179–187CrossRefGoogle Scholar
  164. Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DPB, Frank DN, Li E et al (2013) A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One 8(11):e80702–e80702CrossRefPubMedPubMedCentralGoogle Scholar
  165. Toshikuni N, Tsutsumi M, Arisawa T (2014) Clinical differences between alcoholic liver disease and nonalcoholic fatty liver disease. World J Gastroenterol: WJG 20(26):8393CrossRefGoogle Scholar
  166. Tuohy KM, Fava F, Viola R (2014) ‘The way to a man’s heart is through his gut microbiota’–dietary pro-and prebiotics for the management of cardiovascular risk. Proc Nutr Soc 73(2):172–185CrossRefGoogle Scholar
  167. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP (2009) A core gut microbiome in obese and lean twins. Nature 457(7228):480CrossRefGoogle Scholar
  168. Vaahtovuo J, Munukka E, Korkeamäki M, Luukkainen R, Toivanen P (2008) Fecal microbiota in early rheumatoid arthritis. J Rheumatol 35(8):1500–1505PubMedGoogle Scholar
  169. Veerappan G, Betteridge J, Young P (2012) Probiotics for the treatment of inflammatory bowel disease. Curr Gastroenterol Rep 14:324–333CrossRefGoogle Scholar
  170. Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM, Rensen SS (2013) Human intestinal microbiota composition is associated with local and systemic inflammation in obesity. Obesity 21(12):E607–E615CrossRefGoogle Scholar
  171. Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT (2010) Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5. Science 328(5975):228–231CrossRefPubMedPubMedCentralGoogle Scholar
  172. Vindigni SM, Zisman TL, Suskind DL, Damman CJ (2016) The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions. Ther Adv Gastroenterol 9(4):606–625CrossRefGoogle Scholar
  173. Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L (2011) High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 11:7–7CrossRefPubMedPubMedCentralGoogle Scholar
  174. Wallace BD, Redinbo MR (2013) The human microbiome is a source of therapeutic drug targets. Curr Opin Chem Biol 17(3):379–384CrossRefPubMedPubMedCentralGoogle Scholar
  175. Walters WA, Xu Z, Knight R (2014) Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett 588(22):4223–4233CrossRefPubMedPubMedCentralGoogle Scholar
  176. Wang I-K, Lai H-C, Yu C-J, Liang C-C, Chang C-T, Kuo H-L, Yang Y-F, Lin C-C, Lin H-H, Liu Y-L (2012) Real-time PCR analysis of the intestinal microbiotas in peritoneal dialysis patients. Appl Environ Microbiol 78(4):1107–1112CrossRefPubMedPubMedCentralGoogle Scholar
  177. Wang W, Chen L, Zhou R, Wang X, Song L, Huang S, Wang G, Xia B (2014) Increased proportions of bifidobacterium and the lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease. J Clin Microbiol 52(2):398–406CrossRefPubMedPubMedCentralGoogle Scholar
  178. Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan EP (2013) Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One 8(8):e70803CrossRefPubMedPubMedCentralGoogle Scholar
  179. Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA et al (2008) Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455(7216):1109–1113CrossRefPubMedPubMedCentralGoogle Scholar
  180. West CE, Jenmalm M, Prescott S (2015) The gut microbiota and its role in the development of allergic disease: a wider perspective. Clin Exp Allergy 45(1):43–53CrossRefGoogle Scholar
  181. Wexler HM (2007) Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev 20(4):593–621CrossRefPubMedPubMedCentralGoogle Scholar
  182. Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, Järnerot G, Tysk C, Jansson JK, Engstrand L (2010) A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Commentary. Gastroenterology 139(6):1844–1854. e1CrossRefGoogle Scholar
  183. Winer DA, Luck H, Tsai S, Winer S (2016) The intestinal immune system in obesity and insulin resistance. Cell Metab 23(3):413–426CrossRefGoogle Scholar
  184. Wing MR, Patel SS, Ramezani A, Raj DS (2016) Gut microbiome in chronic kidney disease. Exp Physiol 101(4):471–477CrossRefGoogle Scholar
  185. Woting A, Blaut M (2016) The intestinal microbiota in metabolic disease. Nutrients 8(4):202CrossRefPubMedPubMedCentralGoogle Scholar
  186. Wright IC, Rabe-Hesketh S, Woodruff PW, David AS, Murray RM, Bullmore ET (2000) Meta-analysis of regional brain volumes in schizophrenia. Am J Psychiatr 157(1):16–25CrossRefGoogle Scholar
  187. Wu C-C, Weng W-L, Lai W-L, Tsai H-P, Liu W-H, Lee M-H, Tsai Y-C (2015) Effect of lactobacillus plantarum strain K21 on high-fat diet-fed obese mice. Evid Based Complement Alternat Med 2015Google Scholar
  188. Xu J, Gordon JI (2003) Honor thy symbionts. Proc Natl Acad Sci 100(18):10452–10459CrossRefGoogle Scholar
  189. Yang J-Y, Kweon M-N (2016) The gut microbiota: a key regulator of metabolic diseases. BMB Rep 49(10):536CrossRefPubMedPubMedCentralGoogle Scholar
  190. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222CrossRefPubMedPubMedCentralGoogle Scholar
  191. Yeoh N, Burton J, Suppiah P, Reid G, Stebbings S (2013) The role of the microbiome in rheumatic diseases. Curr Rheumatol Rep 15:314CrossRefGoogle Scholar
  192. Yolken R, Dickerson F (2014) The microbiome-the missing link in the pathogenesis of schizophrenia. Schizophr Res 153:S16CrossRefGoogle Scholar
  193. Zeng MY, Cisalpino D, Varadarajan S, Hellman J, Warren HS, Cascalho M, Inohara N, Núñez G (2016) Gut microbiota-induced immunoglobulin G controls systemic infection by symbiotic bacteria and pathogens. Immunity 44(3):647–658CrossRefPubMedPubMedCentralGoogle Scholar
  194. Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y, Ji L (2013) Human gut microbiota changes reveal the progression of glucose intolerance. PLoS One 8(8):e71108–e71108CrossRefPubMedPubMedCentralGoogle Scholar
  195. Zhang M, Fan X, Fang B, Zhu C, Zhu J, Ren F (2015) Effects of lactobacillus salivarius Ren on cancer prevention and intestinal microbiota in 1, 2-dimethylhydrazine-induced rat model. J Microbiol 53(6):398–405CrossRefGoogle Scholar
  196. Zhu L, Baker SS, Gill C, Liu W, Alkhouri R, Baker RD, Gill SR (2013) Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 57(2):601–609CrossRefGoogle Scholar
  197. Zigra P, Maipa V, Alamanos Y (2008) Probiotics and remission of ulcerative colitis: a systematic review. Neth J Med 65:411–418Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Santosh Kumar Behera
    • 1
  • Ardhendu Bhusan Praharaj
    • 2
  • Gayathri Chalikonda
    • 3
  • Gowru Srivani
    • 4
  • Namita Mahapatra
    • 1
  1. 1.Biomedical Informatics Centre, ICMR-Regional Medical Research CentreChandrasekharpur, BhubaneswarIndia
  2. 2.Department of Human Genetics, ICMR-Regional Medical Research CentreChandrasekharpur, BhubaneswarIndia
  3. 3.Department of Bioscience and BiotechnologyBanasthali UniversityVanasthaliIndia
  4. 4.Department of Hematology and Medical OncologyWinship Cancer Institute, Emory UniversityAtlantaUSA

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