Man and the Microbiome: A New Theory of Everything?

Literature Cited

1. Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J et al. 2017. Gut microbiome in ADHD and its relation to neural reward anticipation. PLOS ONE 12:9e0183509
   [Google Scholar]
2. Ackerman HD, Gerhard GS 2016. Bile acids in neurodegenerative disorders. Front. Aging Neurosci. 8:263
   [Google Scholar]
3. Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA 2011. Gastrointestinal flora and gastrointestinal status in children with autism—comparisons to typical children and correlation with autism severity. BMC Gastroenterol 11:22
   [Google Scholar]
4. Akira S, Takeda K 2004. Toll-like receptor signalling. Nat. Rev. Immunol. 4:7499–511
   [Google Scholar]
5. Akkasheh G, Kashani-Poor Z, Tajabadi-Ebrahimi M, Jafari P, Akbari H et al. 2016. Clinical and metabolic response to probiotic administration in patients with major depressive disorder: a randomized, double-blind, placebo-controlled trial. Nutrition 32:3315–20
   [Google Scholar]
6. Albuquerque EX, Schwarcz R 2013. Kynurenic acid as an antagonist of α7 nicotinic acetylcholine receptors in the brain: facts and challenges. Biochem. Pharmacol. 85:81027–32
   [Google Scholar]
7. Allen AP, Hutch W, Borre YE, Kennedy PJ, Temko A et al. 2016. Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers. Transl. Psychiatry 6:11e939
   [Google Scholar]
8. Badawy AAB 2017. Kynurenine pathway of tryptophan metabolism: regulatory and functional aspects. Int. J. Tryptophan Res. 10:1178646917691938
   [Google Scholar]
9. Bailey MT, Dowd SE, Galley JD, Hufnagle AR, Allen RG, Lyte M 2011. Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain Behav. Immun. 25:3397–407
   [Google Scholar]
10. Bangsgaard Bendtsen KM, Krych L, Sorensen DB, Pang W, Nielsen DS et al. 2012. Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse. PLOS ONE 7:10e46231
    [Google Scholar]
11. Begley M, Gahan CG, Hill C 2005. The interaction between bacteria and bile. FEMS Microbiol. Rev. 29:4625–51
    [Google Scholar]
12. Benton D, Williams C, Brown A 2007. Impact of consuming a milk drink containing a probiotic on mood and cognition. Eur. J. Clin. Nutr. 61:3355–61
    [Google Scholar]
13. Berger M, Gray JA, Roth BL 2009. The expanded biology of serotonin. Annu. Rev. Med. 60:355–66
    [Google Scholar]
14. Boffa LC, Vidali G, Mann RS, Allfrey VG 1978. Suppression of histone deacetylation in vivo and in vitro by sodium butyrate. J. Biol. Chem. 253:103364–66
    [Google Scholar]
15. Bolognini D, Tobin AB, Milligan G, Moss CE 2016. The pharmacology and function of receptors for short-chain fatty acids. Mol. Pharmacol. 89:3388–98
    [Google Scholar]
16. Bonaz B, Bazin T, Pellissier S 2018. The vagus nerve at the interface of the microbiota–gut–brain axis. Front. Neurosci. 12:49
    [Google Scholar]
17. Bonda DJ, Mailankot M, Stone JG, Garrett MR, Staniszewska M et al. 2010. Indoleamine 2,3-dioxygenase and 3-hydroxykynurenine modifications are found in the neuropathology of Alzheimer's disease. Redox Rep 15:4161–68
    [Google Scholar]
18. Bonini JA, Anderson SM, Steiner DF 1997. Molecular cloning and tissue expression of a novel orphan G protein–coupled receptor from rat lung. Biochem. Biophys. Res. Commun. 234:1190–93
    [Google Scholar]
19. Borovikova LV, Ivanova S, Zhang M, Yang H, Botchkina GI et al. 2000. Vagus nerve stimulation attenuates the systemic inflammatory response to endotoxin. Nature 405:6785458–62
    [Google Scholar]
20. Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM et al. 2011. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. PNAS 108:3816050–55
    [Google Scholar]
21. Breuer J, Freud S 2004 (1895). Studies in Hysteria London: Penguin
    [Google Scholar]
22. Castren E, Voikar V, Rantamaki T 2007. Role of neurotrophic factors in depression. Curr. Opin. Pharmacol. 7:118–21
    [Google Scholar]
23. Castro-Nallar E, Bendall ML, Perez-Losada M, Sabuncyan S, Severance EG et al. 2015. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ 3:e1140
    [Google Scholar]
24. Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM et al. 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149:71578–93
    [Google Scholar]
25. Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD et al. 2013. The microbiome–gut–brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol. Psychiatry 18:6666–73
    [Google Scholar]
26. Clarke G, Stilling RM, Kennedy PJ, Stanton C, Cryan JF, Dinan TG 2014. Gut microbiota: the neglected endocrine organ. Mol. Endocrinol. 28:81221–38
    [Google Scholar]
27. Cryan JF, Kaupmann K 2005. Don't worry ‘B’ happy!: a role for GABA_B receptors in anxiety and depression. Trends Pharmacol. Sci. 26:136–43
    [Google Scholar]
28. Cummings JH, Pomare EW, Branch WJ, Naylor CP, Macfarlane GT 1987. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28:101221–27
    [Google Scholar]
29. Dapoigny M, Piche T, Ducrotte P, Lunaud B, Cardot J-M, Bernalier-Donadille A 2012. Efficacy and safety profile of LCR35 complete freeze-dried culture in irritable bowel syndrome: a randomized, double-blind study. World J. Gastroenterol. 18:172067–75
    [Google Scholar]
30. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:7484559–63
    [Google Scholar]
31. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A et al. 2013. Fecal microbiota and metabolome of children with autism and Pervasive Developmental Disorder Not Otherwise Specified. PLOS ONE 8:10e76993
    [Google Scholar]
32. Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan JF, Dinan TG 2010. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience 170:41179–88
    [Google Scholar]
33. Dickerson FB, Adamos M, Katsafanas E, Khushalani S, Origoni A et al. 2018. Adjunctive probiotic microorganisms to prevent rehospitalization in patients with acute mania: a randomized controlled trial. Bipolar Disord 20:7614–21
    [Google Scholar]
34. Dickerson FB, Stallings C, Origoni A, Katsafanas E, Savage CL et al. 2014. Effect of probiotic supplementation on schizophrenia symptoms and association with gastrointestinal functioning: a randomized, placebo-controlled trial. Prim. Care Companion CNS Disord. 16:1 https://dx.doi.org/10.4088/PCC.13m01579
    [Crossref] [Google Scholar]
35. Dlugos A, Childs E, Stuhr KL, Hillard CJ, de Wit H 2012. Acute stress increases circulating anandamide and other N-acylethanolamines in healthy humans. Neuropsychopharmacology 37:112416–27
    [Google Scholar]
36. Emanuele E, Orsi P, Boso M, Broglia D, Brondino N et al. 2010. Low-grade endotoxemia in patients with severe autism. Neurosci. Lett. 471:3162–65
    [Google Scholar]
37. Erny D, Hrabe de Angelis AL, Jaitin D, Wieghofer P, Staszewski O et al. 2015. Host microbiota constantly control maturation and function of microglia in the CNS. Nat. Neurosci. 18:7965–77
    [Google Scholar]
38. Evans SJ, Bassis CM, Hein R, Assari S, Flowers SA et al. 2017. The gut microbiome composition associates with bipolar disorder and illness severity. J. Psychiatr. Res. 87:23–29
    [Google Scholar]
39. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C et al. 2013. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. PNAS 110:229066–71
    [Google Scholar]
40. Ferrante RJ, Kubilus JK, Lee J, Ryu H, Beesen A et al. 2003. Histone deacetylase inhibition by sodium butyrate chemotherapy ameliorates the neurodegenerative phenotype in Huntington's disease mice. J. Neurosci. 23:289418–27
    [Google Scholar]
41. Finegold SM, Molitoris D, Song Y, Liu C, Vaisanen ML et al. 2002. Gastrointestinal microflora studies in late-onset autism. Clin. Infect. Dis. 35:Suppl. 1S6–16
    [Google Scholar]
42. Fremont M, Coomans D, Massart S, De Meirleir K 2013. High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients. Anaerobe 22:50–56
    [Google Scholar]
43. Fu SP, Liu BR, Wang JF, Xue WJ, Liu HM et al. 2015. β-Hydroxybutyric acid inhibits growth hormone–releasing hormone synthesis and secretion through the GPR109A/extracellular signal-regulated 1/2 signalling pathway in the hypothalamus. J. Neuroendocrinol. 27:3212–22
    [Google Scholar]
44. Ganapathy V, Thangaraju M, Gopal E, Martin PM, Itagaki S et al. 2008. Sodium-coupled monocarboxylate transporters in normal tissues and in cancer. AAPS J 10:1193–99
    [Google Scholar]
45. Gatta-Cherifi B, Cota D 2015. New insights on the role of the endocannabinoid system in the regulation of energy balance. Int. J. Obes. 40:210–19
    [Google Scholar]
46. Gaykema RP, Goehler LE, Lyte M 2004. Brain response to cecal infection with Campylobacter jejuni: analysis with Fos immunohistochemistry. Brain Behav. Immun. 18:3238–45
    [Google Scholar]
47. Ge H, Li X, Weiszmann J, Wang P, Baribault H et al. 2008. Activation of G protein–coupled receptor 43 in adipocytes leads to inhibition of lipolysis and suppression of plasma free fatty acids. Endocrinology 149:94519–26
    [Google Scholar]
48. Goehler LE, Park SM, Opitz N, Lyte M, Gaykema RP 2008. Campylobacter jejuni infection increases anxiety-like behavior in the holeboard: possible anatomical substrates for viscerosensory modulation of exploratory behavior. Brain Behav. Immun. 22:3354–66
    [Google Scholar]
49. Golubeva AV, Joyce SA, Moloney G, Burokas A, Sherwin E et al. 2017. Microbiota-related changes in bile acid & tryptophan metabolism are associated with gastrointestinal dysfunction in a mouse model of autism. EBioMedicine 24:166–178
    [Google Scholar]
50. Gonzalez-Regueiro JA, Moreno-Castaneda L, Uribe M, Chavez-Tapia NC 2017. The role of bile acids in glucose metabolism and their relation with diabetes. Ann. Hepatol. 16:Suppl. 116–21
    [Google Scholar]
51. Govindarajan N, Agis-Balboa RC, Walter J, Sananbenesi F, Fischer A 2011. Sodium butyrate improves memory function in an Alzheimer's disease mouse model when administered at an advanced stage of disease progression. J. Alzheimer's Dis. 26:1187–97
    [Google Scholar]
52. Graff LA, Walker JR, Bernstein CN 2009. Depression and anxiety in inflammatory bowel disease: a review of comorbidity and management. Inflamm. Bowel Dis. 15:71105–18
    [Google Scholar]
53. Han K, Wang J, Seo JG, Kim H 2017. Efficacy of double-coated probiotics for irritable bowel syndrome: a randomized double-blind controlled trial. J. Gastroenterol. 52:4432–43
    [Google Scholar]
54. Hegstrand LR, Hine RJ 1986. Variations of brain histamine levels in germ-free and nephrectomized rats. Neurochem. Res. 11:2185–91
    [Google Scholar]
55. Hemmings SMJ, Malan-Müller S, van den Heuvel LL, Demmitt BA, Stanislawski MA et al. 2017. The microbiome in posttraumatic stress disorder and trauma-exposed controls: an exploratory study. Psychosom. Med. 79:8936–46
    [Google Scholar]
56. Hill MN, Miller GE, Ho WS, Gorzalka BB, Hillard CJ 2008. Serum endocannabinoid content is altered in females with depressive disorders: a preliminary report. Pharmacopsychiatry 41:248–53
    [Google Scholar]
57. Hill MN, Patel S 2013. Translational evidence for the involvement of the endocannabinoid system in stress-related psychiatric illnesses. Biol. Mood Anxiety Disord. 3:19
    [Google Scholar]
58. Holsboer F 2000. The corticosteroid receptor hypothesis of depression. Neuropsychopharmacology 23:5477–501
    [Google Scholar]
59. Holzer P, Farzi A 2014. Neuropeptides and the microbiota–gut–brain axis. Adv. Exp. Med. Biol. 817:195–219
    [Google Scholar]
60. Ichimura A, Hirasawa A, Hara T, Tsujimoto G 2009. Free fatty acid receptors act as nutrient sensors to regulate energy homeostasis. Prostaglandins Other Lipid Mediat 89:3–482–88
    [Google Scholar]
61. Jacka FN, O'Neil A, Opie R, Itsiopoulos C, Cotton S et al. 2017. A randomised controlled trial of dietary improvement for adults with major depression (the ‘SMILES’ trial). BMC Med 15:23
    [Google Scholar]
62. Jia H-M, Li Q, Zhou C, Yu M, Yang Y et al. 2016. Chronic unpredictive mild stress leads to altered hepatic metabolic profile and gene expression. Sci. Rep. 6:23441
    [Google Scholar]
63. Jiang H, Ling Z, Zhang Y, Mao H, Ma Z et al. 2015. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav. Immun. 48:186–94
    [Google Scholar]
64. Kaluzna-Czaplinska J, Blaszczyk S 2012. The level of arabinitol in autistic children after probiotic therapy. Nutrition 28:2124–26
    [Google Scholar]
65. Kang DW, Park JG, Ilhan ZE, Wallstrom G, Labaer J et al. 2013. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLOS ONE 8:7e68322
    [Google Scholar]
66. Keller J, Gomez R, Williams G, Lembke A, Lazzeroni L et al. 2017. HPA axis in major depression: cortisol, clinical symptomatology, and genetic variation predict cognition. Mol. Psychiatry 22:4527–36
    [Google Scholar]
67. Kelly JR, Allen AP, Temko A, Hutch W, Kennedy PJ et al. 2017. Lost in translation? The potential psychobiotic Lactobacillus rhamnosus (JB-1) fails to modulate stress or cognitive performance in healthy male subjects. Brain Behav. Immun. 61:50–59
    [Google Scholar]
68. Kelly JR, Borre Y, O'Brien C, Patterson E, El Aidy S et al. 2016. Transferring the blues: depression-associated gut microbiota induces neurobehavioural changes in the rat. J. Psychiatr. Res. 82:109–18
    [Google Scholar]
69. Kessler RC, Petukhova M, Sampson NA, Zaslavsky AM, Wittchen HU 2012. Twelve-month and lifetime prevalence and lifetime morbid risk of anxiety and mood disorders in the United States. Int. J. Methods Psychiatr. Res. 21:3169–84
    [Google Scholar]
70. Kim CH, Park J, Kim M 2014. Gut microbiota–derived short-chain fatty acids, T cells, and inflammation. Immune Netw 14:6277–88
    [Google Scholar]
71. Kir S, Beddow SA, Samuel VT, Miller P, Previs SF et al. 2011. FGF19 as a postprandial, insulin-independent activator of hepatic protein and glycogen synthesis. Science 331:60241621–24
    [Google Scholar]
72. Kirchner A, Birklein F, Stefan H, Handwerker HO 2000. Left vagus nerve stimulation suppresses experimentally induced pain. Neurology 55:81167–71
    [Google Scholar]
73. Kratsman N, Getselter D, Elliott E 2016. Sodium butyrate attenuates social behavior deficits and modifies the transcription of inhibitory/excitatory genes in the frontal cortex of an autism model. Neuropharmacology 102:136–45
    [Google Scholar]
74. Lim GY, Tam WW, Lu Y, Ho CS, Zhang MW, Ho RC 2018. Prevalence of depression in the community from 30 countries between 1994 and 2014. Sci. Rep. 8:12861
    [Google Scholar]
75. Lim WY, Subramaniam M, Abdin E, Vaingankar J, Chong SA 2014. Peptic ulcer disease and mental illnesses. Gen. Hosp. Psychiatry 36:163–67
    [Google Scholar]
76. Liu S, Marcelin G, Blouet C, Jeong JH, Jo YH et al. 2018. A gut–brain axis regulating glucose metabolism mediated by bile acids and competitive fibroblast growth factor actions at the hypothalamus. Mol. Metab. 8:37–50
    [Google Scholar]
77. Lyte M 2011. Probiotics function mechanistically as delivery vehicles for neuroactive compounds: microbial endocrinology in the design and use of probiotics. BioEssays 33:8574–81
    [Google Scholar]
78. Macer BJ, Prady SL, Mikocka-Walus A 2017. Antidepressants in inflammatory bowel disease: a systematic review. Inflamm. Bowel Dis. 23:4534–50
    [Google Scholar]
79. Maes M, Kubera M, Leunis JC 2008. The gut–brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of LPS from Gram negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression. Neuroendocrinol. Lett. 29:1117–24
    [Google Scholar]
80. Maes M, Leonard BE, Myint AM, Kubera M, Verkerk R 2011. The new ‘5-HT’ hypothesis of depression: cell-mediated immune activation induces indoleamine 2,3-dioxygenase, which leads to lower plasma tryptophan and an increased synthesis of detrimental tryptophan catabolites (TRYCATs), both of which contribute to the onset of depression. Prog. Neuropsychopharmacol. Biol. Psychiatry 35:3702–21
    [Google Scholar]
81. Maes M, Melzer HY 1995. The serotonin hypothesis of major depression. Psychopharmacology: The Fourth Generation of Progress FE Bloom, DJ Kupfer 933–44 New York: Raven Press
    [Google Scholar]
82. Maniam J, Antoniadis C, Morris MJ 2014. Early-life stress, HPA axis adaptation, and mechanisms contributing to later health outcomes. Front. Endocrinol. 5:73
    [Google Scholar]
83. Marcos A, Warnberg J, Nova E, Gomez S, Alvarez A et al. 2004. The effect of milk fermented by yogurt cultures plus Lactobacillus casei DN-114001 on the immune response of subjects under academic examination stress. Eur. J. Nutr. 43:6381–89
    [Google Scholar]
84. Messaoudi M, Lalonde R, Violle N, Javelot H, Desor D et al. 2011. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br. J. Nutr. 105:5755–64
    [Google Scholar]
85. Morena M, Patel S, Bains JS, Hill MN 2016. Neurobiological interactions between stress and the endocannabinoid system. Neuropsychopharmacology 41:180–102
    [Google Scholar]
86. Muccioli GG, Naslain D, Backhed F, Reigstad CS, Lambert DM et al. 2010. The endocannabinoid system links gut microbiota to adipogenesis. Mol. Syst. Biol. 6:392
    [Google Scholar]
87. Myint AM, Kim YK, Verkerk R, Scharpe S, Steinbusch H, Leonard B 2007. Kynurenine pathway in major depression: evidence of impaired neuroprotection. J. Affect. Disord. 98:1–2143–51
    [Google Scholar]
88. Naccache PH, Faucher N, Caon AC, McColl SR 1988. Propionic acid–induced calcium mobilization in human neutrophils. J. Cell. Physiol. 136:1118–24
    [Google Scholar]
89. Naseribafrouei A, Hestad K, Avershina E, Sekelja M, Linlokken A et al. 2014. Correlation between the human fecal microbiota and depression. Neurogastroenterol. Motil. 26:81155–62
    [Google Scholar]
90. Neufeld KM, Kang N, Bienenstock J, Foster JA 2011. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol. Motil. 23:3255–64
    [Google Scholar]
91. Nishihira J, Kagami-Katsuyama H, Tanaka A, Nishimura M, Kobayashi T, Kawasaki Y 2014. Elevation of natural killer cell activity and alleviation of mental stress by the consumption of yogurt containing Lactobacillus gasseri SBT2055 and Bifidobacterium longum SBT2928 in a double-blind, placebo-controlled clinical trial. J. Funct. Foods 11:261–68
    [Google Scholar]
92. O'Brien SM, Scott LV, Dinan TG 2004. Cytokines: abnormalities in major depression and implications for pharmacological treatment. Hum. Psychopharmacol. 19:6397–403
    [Google Scholar]
93. O'Hara AM, Shanahan F 2006. The gut flora as a forgotten organ. EMBO Rep 7:7688–93
    [Google Scholar]
94. O'Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM et al. 2009. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol. Psychiatry 65:3263–67
    [Google Scholar]
95. O'Mahony L, McCarthy J, Kelly P, Hurley G, Luo F et al. 2005. Lactobacillus and Bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 128:3541–51
    [Google Scholar]
96. Panek M, Čipčić Paljetak H, Barešić A, Perić M, Matijašić M et al. 2018. Methodology challenges in studying human gut microbiota—effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci. Rep. 8:15143
    [Google Scholar]
97. Parracho HMRT, Bingham MO, Gibson GR, McCartney AL 2005. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J. Med. Microbiol. 54:987–71
    [Google Scholar]
98. Parracho HMRT, Gibson GR, Knott F, Bosscher D, Kleerebezem M, McCartney AL 2010. A double-blind, placebo-controlled crossover-designed probiotic feeding study in children diagnosed with autistic spectrum disorders. Int. J. Probiotics Prebiotics 5:269–74
    [Google Scholar]
99. Pearson JP, Brownlee IA 2010. The interaction of large bowel microflora with the colonic mucus barrier. Int. J. Inflamm. 2010:321426
    [Google Scholar]
100. Pinto-Sanchez MI, Hall GB, Ghajar K, Nardelli A, Bolino C et al. 2017. Probiotic Bifidobacterium longum NCC3001 reduces depression scores and alters brain activity: a pilot study in patients with irritable bowel syndrome. Gastroenterology 153:2448–459.e8
     [Google Scholar]
101. Psaltopoulou T, Sergentanis TN, Panagiotakos DB, Sergentanis IN, Kosti R, Scarmeas N 2013. Mediterranean diet, stroke, cognitive impairment, and depression: a meta-analysis. Ann. Neurol. 74:4580–71
     [Google Scholar]
102. Rao AV, Bested AC, Beaulne TM, Katzman MA, Iorio C et al. 2009. A randomized, double-blind, placebo-controlled pilot study of a probiotic in emotional symptoms of chronic fatigue syndrome. Gut Pathog 1:6
     [Google Scholar]
103. Raybould HE 2010. Gut chemosensing: interactions between gut endocrine cells and visceral afferents. Auton. Neurosci. 153:1–241–46
     [Google Scholar]
104. Reale M, Boscolo P, Bellante V, Tarantelli C, Di Nicola M et al. 2012. Daily intake of Lactobacillus casei Shirota increases natural killer cell activity in smokers. Br. J. Nutr. 108:2308–14
     [Google Scholar]
105. Réus GZ, Jansen K, Titus S, Carvalho AF, Gabbay V, Quevedo J 2015. Kynurenine pathway dysfunction in the pathophysiology and treatment of depression: evidences from animal and human studies. J. Psychiatr. Res. 68:316–28
     [Google Scholar]
106. Ridlon JM, Kang DJ, Hylemon PB 2006. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47:2241–59
     [Google Scholar]
107. Roberts E, Frankel S 1950. γ-Aminobutyric acid in brain: its formation from glutamic acid. J. Biol. Chem. 187:155–63
     [Google Scholar]
108. Romijn AR, Rucklidge JJ, Kuijer RG, Frampton C 2017. A double-blind, randomized, placebo-controlled trial of Lactobacillus helveticus and Bifidobacterium longum for the symptoms of depression. Aust. N. Z. J. Psychiatry 51:8810–21
     [Google Scholar]
109. Rosenblat JD, McIntyre RS 2017. Bipolar disorder and immune dysfunction: epidemiological findings, proposed pathophysiology and clinical implications. Brain Sci 7:11144
     [Google Scholar]
110. Roshchina V 2010. Evolutionary considerations of neurotransmitters in microbial, plant, and animal cells. Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health M Lyte, PPE Freestone 17–52 New York: Springer
     [Google Scholar]
111. Rousseaux C, Thuru X, Gelot A, Barnich N, Neut C et al. 2007. Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors. Nat. Med. 13:135–37
     [Google Scholar]
112. Ruddick JP, Evans AK, Nutt DJ, Lightman SL, Rook GA, Lowry CA 2006. Tryptophan metabolism in the central nervous system: medical implications. Expert Rev. Mol. Med. 8:201–27
     [Google Scholar]
113. Sackeim HA, Rush AJ, George MS, Marangell LB, Husain MM et al. 2001. Vagus nerve stimulation (VNS) for treatment-resistant depression: efficacy, side effects, and predictors of outcome. Neuropsychopharmacology 25:5713–28
     [Google Scholar]
114. Sam AH, Salem V, Ghatei MA 2011. Rimonabant: from RIO to ban. J. Obes. 2011:432607
     [Google Scholar]
115. Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP et al. 2000. Short-term benefit from oral vancomycin treatment of regressive-onset autism. J. Child Neurol. 15:7429–35
     [Google Scholar]
116. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D et al. 2011. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 141:51782–91
     [Google Scholar]
117. Sayin SI, Wahlstrom A, Felin J, Jantti S, Marschall HU et al. 2013. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-β-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 17:2225–35
     [Google Scholar]
118. Schmidt HD, Shelton RC, Duman RS 2011. Functional biomarkers of depression: diagnosis, treatment, and pathophysiology. Neuropsychopharmacology 36:122375–94
     [Google Scholar]
119. Schmidt K, Cowen PJ, Harmer CJ, Tzortzis G, Errington S, Burnet PW 2015. Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers. Psychopharmacology 232:101793–801
     [Google Scholar]
120. Schroeder FA, Lin CL, Crusio WE, Akbarian S 2007. Antidepressant-like effects of the histone deacetylase inhibitor, sodium butyrate, in the mouse. Biol. Psychiatry 62:155–64
     [Google Scholar]
121. Schwarcz R, Pellicciari R 2002. Manipulation of brain kynurenines: glial targets, neuronal effects, and clinical opportunities. J. Pharmacol. Exp. Ther. 303:11–10
     [Google Scholar]
122. Shaaban SY, El Gendy YG, Mehanna NS, El-Senousy WM, El-Feki HSA et al. 2017. The role of probiotics in children with autism spectrum disorder: a prospective, open-label study. Nutr. Neurosci. 21:9676–71
     [Google Scholar]
123. Sharma S, Taliyan R, Singh S 2015. Beneficial effects of sodium butyrate in 6-OHDA induced neurotoxicity and behavioral abnormalities: Modulation of histone deacetylase activity. Behav. Brain Res. 291:306–71
     [Google Scholar]
124. Simren M, Ohman L, Olsson J, Svensson U, Ohlson K et al. 2010. Clinical trial: the effects of a fermented milk containing three probiotic bacteria in patients with irritable bowel syndrome—a randomized, double-blind, controlled study. Aliment Pharmacol. Ther. 31:2218–27
     [Google Scholar]
125. Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R et al. 2014. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 40:1128–39
     [Google Scholar]
126. Song Y, Liu C, Finegold SM 2004. Real-time PCR quantitation of Clostridia in feces of autistic children. Appl. Environ. Microbiol. 70:116459–65
     [Google Scholar]
127. Staley C, Weingarden AR, Khoruts A, Sadowsky MJ 2017. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl. Microbiol. Biotechnol. 101:147–64
     [Google Scholar]
128. Steenbergen L, Sellaro R, van Hemert S, Bosch JA, Colzato LS 2015. A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood. Brain Behav. Immun. 48:258–64
     [Google Scholar]
129. Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N et al. 2004. Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. J. Physiol. 558:Pt. 1263–75
     [Google Scholar]
130. Tack J, Broekaert D, Fischler B, Van Oudenhove L, Gevers AM, Janssens J 2006. A controlled crossover study of the selective serotonin reuptake inhibitor citalopram in irritable bowel syndrome. Gut 55:81095–103
     [Google Scholar]
131. Takada M, Nishida K, Kataoka-Kato A, Gondo Y, Ishikawa H et al. 2016. Probiotic Lactobacillus casei strain Shirota relieves stress-associated symptoms by modulating the gut–brain interaction in human and animal models. Neurogastroenterol. Motil. 28:71027–36
     [Google Scholar]
132. Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J et al. 2013. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology 144:71394–401.e4
     [Google Scholar]
133. Tomova A, Husarova V, Lakatosova S, Bakos J, Vlkova B et al. 2015. Gastrointestinal microbiota in children with autism in Slovakia. Physiol. Behav. 138:179–87
     [Google Scholar]
134. Topping DL, Clifton PM 2001. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81:31031–64
     [Google Scholar]
135. Udina M, Castellvi P, Moreno-Espana J, Navines R, Valdes M et al. 2012. Interferon-induced depression in chronic hepatitis C: a systematic review and meta-analysis. J. Clin. Psychiatry 73:81128–38
     [Google Scholar]
136. van Kesteren CF, Gremmels H, de Witte LD, Hol EM, Van Gool AR et al. 2017. Immune involvement in the pathogenesis of schizophrenia: a meta-analysis on postmortem brain studies. Transl. Psychiatry 7:3e1075
     [Google Scholar]
137. Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA 2012. Elevated fecal short chain fatty acid and ammonia concentrations in children with autism spectrum disorder. Dig. Dis. Sci. 57:82096–102
     [Google Scholar]
138. Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA 2013. Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder. Mol. Autism 4:42
     [Google Scholar]
139. Wang X, Wang BR, Zhang XJ, Xu Z, Ding YQ, Ju G 2002. Evidences for vagus nerve in maintenance of immune balance and transmission of immune information from gut to brain in STM-infected rats. World J. Gastroenterol. 8:3540–45
     [Google Scholar]
140. Whitehead WE, Palsson O, Jones KR 2002. Systematic review of the comorbidity of irritable bowel syndrome with other disorders: What are the causes and implications?. Gastroenterology 122:41140–56
     [Google Scholar]
141. Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D et al. 2006. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome. Am. J. Gastroenterol. 101:71581–90
     [Google Scholar]
142. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA et al. 2009. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. PNAS 106:103698–703
     [Google Scholar]
143. Williams BL, Hornig M, Parekh T, Lipkin WI 2012. Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. mBio 3:1e00261–11
     [Google Scholar]
144. Yang H, Zhao X, Tang S, Huang H, Ning Z et al. 2016. Probiotics reduce psychological stress in patients before laryngeal cancer surgery. Asia Pac. J. Clin. Oncol. 12:1e92–96
     [Google Scholar]
145. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P et al. 2015. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 161:2264–76
     [Google Scholar]
146. Yolken RH, Severance EG, Sabunciyan S, Gressitt KL, Chen O et al. 2015. Metagenomic sequencing indicates that the oropharyngeal phageome of individuals with schizophrenia differs from that of controls. Schizophr Bull 41:51153–61
     [Google Scholar]
147. Zhang R, Miller RG, Gascon R, Champion S, Katz J et al. 2009. Circulating endotoxin and systemic immune activation in sporadic amyotrophic lateral sclerosis (sALS). J. Neuroimmunol. 206:1–2121–24
     [Google Scholar]
148. Zingone F, Swift GL, Card TR, Sanders DS, Ludvigsson JF, Bai JC 2015. Psychological morbidity of celiac disease: a review of the literature. United Eur. Gastroenterol. J. 3:2136–45
     [Google Scholar]