Madigan MT. Brock biology of microorganisms. 13th ed. San Francisco: Benjamin Cummings; 2012.
Google Scholar
Shulman ST, Friedmann HC, Sims RH. Theodor Escherich: the first pediatric infectious diseases physician? Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2007;45(8):1025–9.
Article
Google Scholar
Podolsky SH. Metchnikoff and the microbiome. Lancet. 2012;380(9856):1810–1.
Article
PubMed
Google Scholar
Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352(6282):189–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tan TZ, Miow QH, Miki Y, Noda T, Mori S, Huang RY, Thiery JP. Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients. EMBO molecular medicine. 2014;6(10):1279–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55–60.
Article
CAS
PubMed
Google Scholar
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 2015;528(7581):262–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut. 2006;55(2):205–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carroll IM, Ringel-Kulka T, Keku TO, Chang YH, Packey CD, Sartor RB, Ringel Y. Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome. American journal of physiology Gastrointestinal and liver physiology. 2011;301(5):G799–807.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Bohm J, Brunetti F, Habermann N, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Molecular systems biology. 2014;10:766.
Article
PubMed
PubMed Central
CAS
Google Scholar
De Angelis M, Francavilla R, Piccolo M, De Giacomo A, Gobbetti M. Autism spectrum disorders and intestinal microbiota. Gut microbes. 2015;6(3):207–13.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rosenfeld CS. Microbiome disturbances and autism spectrum disorders. Drug metabolism and disposition: the biological fate of chemicals. 2015;43(10):1557–71.
Article
CAS
Google Scholar
Winek K, Dirnagl U, Meisel A. The Gut Microbiome as Therapeutic target in central nervous system diseases: implications for stroke. Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics. 2016;13(4):762–74.
Article
CAS
Google Scholar
Collins SM, Surette M, Bercik P. The interplay between the intestinal microbiota and the brain. Nature reviews Microbiology. 2012;10(11):735–42.
Article
CAS
PubMed
Google Scholar
Neunlist M, Van Landeghem L, Mahe MM, Derkinderen P, Des Varannes SB, Rolli-Derkinderen M. The digestive neuronal-glial-epithelial unit: a new actor in gut health and disease. Nature reviews Gastroenterology & Hepatology. 2013;10(2):90–100.
Article
CAS
Google Scholar
Furness JB. The enteric nervous system and neurogastroenterology. Nature Reviews Gastroenterology & Hepatology. 2012;9(5):286–94.
Article
CAS
Google Scholar
Matteoli G, Boeckxstaens GE. The vagal innervation of the gut and immune homeostasis. Gut. 2013;62(8):1214–22.
Article
CAS
PubMed
Google Scholar
Wang Y, Kasper LH. The role of microbiome in central nervous system disorders. Brain, behavior, and immunity. 2014;38:1–12.
Article
PubMed
CAS
Google Scholar
Petra AI, Panagiotidou S, Hatziagelaki E, Stewart JM, Conti P, Theoharides TC. Gut-microbiota-brain axis and its effect on neuropsychiatric disorders with suspected immune dysregulation. Clinical therapeutics. 2015;37(5):984–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, et al. Best practices for analysing microbiomes. Nature reviews Microbiology. 2018;16(7):410–22.
Article
CAS
PubMed
Google Scholar
Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America. 1977;74(11):5088–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woese CR, Stackebrandt E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Systematic and applied microbiology. 1985;6:143–51.
Article
CAS
PubMed
Google Scholar
Wilson KH, Blitchington RB. Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol. 1996;62(7):2273–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(16):5261–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Evaluating the information content of shallow shotgun metagenomics. mSystems. 2018;3(6).
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10(1):5029.
Article
PubMed
PubMed Central
CAS
Google Scholar
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences of the United States of America. 2002;99(22):14250–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Applied and environmental microbiology. 2002;68(9):4301–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37–43.
Article
CAS
PubMed
Google Scholar
Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nature reviews Microbiology. 2016;14(8):508–22.
Article
CAS
PubMed
Google Scholar
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nature reviews Microbiology. 2015;13(6):360–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heyer R, Schallert K, Zoun R, Becher B, Saake G, Benndorf D. Challenges and perspectives of metaproteomic data analysis. Journal of biotechnology. 2017;261:24–36.
Article
CAS
PubMed
Google Scholar
Griffin JL, Wang X, Stanley E. Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. Circulation Cardiovascular genetics. 2015;8(1):187–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smirnov KS, Maier TV, Walker A, Heinzmann SS, Forcisi S, Martinez I, Walter J, Schmitt-Kopplin P. Challenges of metabolomics in human gut microbiota research. International journal of medical microbiology : IJMM. 2016;306(5):266–79.
Article
CAS
PubMed
Google Scholar
Arrieta MC, Finlay BB. The commensal microbiota drives immune homeostasis. Front Immunol. 2012;3:33.
Article
PubMed
PubMed Central
Google Scholar
Okada H, Kuhn C, Feillet H, Bach JF. The 'hygiene hypothesis' for autoimmune and allergic diseases: an update. Clin Exp Immunol. 2010;160(1):1–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Medzhitov R, Janeway C Jr. Innate immune recognition: mechanisms and pathways. Immunological reviews. 2000;173:89–97.
Article
CAS
PubMed
Google Scholar
Janeway CA Jr. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harbor symposia on quantitative biology. 1989;54(Pt 1):1–13.
Article
CAS
PubMed
Google Scholar
Konig J, Wells J, Cani PD, Garcia-Rodenas CL, MacDonald T, Mercenier A, Whyte J, Troost F, Brummer RJ. Human intestinal barrier function in health and disease. Clinical and translational gastroenterology. 2016;7(10):e196.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wells JM, Brummer RJ, Derrien M, MacDonald TT, Troost F, Cani PD, Theodorou V, Dekker J, Meheust A, de Vos WM, et al. Homeostasis of the gut barrier and potential biomarkers. American journal of physiology Gastrointestinal and liver physiology. 2017;312(3):G171–93.
Article
PubMed
Google Scholar
Okun MS. Deep-brain stimulation for Parkinson's disease. The New England journal of medicine. 2012;367(16):1529–38.
Article
CAS
PubMed
Google Scholar
Rolls A, Shechter R, London A, Ziv Y, Ronen A, Levy R, Schwartz M. Toll-like receptors modulate adult hippocampal neurogenesis. Nature cell biology. 2007;9(9):1081–8.
Article
CAS
PubMed
Google Scholar
Shechter R, Ronen A, Rolls A, London A, Bakalash S, Young MJ, Schwartz M. Toll-like receptor 4 restricts retinal progenitor cell proliferation. The Journal of cell biology. 2008;183(3):393–400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Okun E, Griffioen KJ, Son TG, Lee JH, Roberts NJ, Mughal MR, Hutchison E, Cheng A, Arumugam TV, Lathia JD, et al. TLR2 activation inhibits embryonic neural progenitor cell proliferation. Journal of neurochemistry. 2010;114(2):462–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keohane A, Ryan S, Maloney E, Sullivan AM, Nolan YM. Tumour necrosis factor-alpha impairs neuronal differentiation but not proliferation of hippocampal neural precursor cells: role of Hes1. Molecular and cellular neurosciences. 2010;43(1):127–35.
Article
CAS
PubMed
Google Scholar
Okun E, Barak B, Saada-Madar R, Rothman SM, Griffioen KJ, Roberts N, Castro K, Mughal MR, Pita MA, Stranahan AM, et al. Evidence for a developmental role for TLR4 in learning and memory. PloS one. 2012;7(10):e47522.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang S, Zhang X, Zhai L, Sheng X, Zheng W, Chu H, Zhang G. Atorvastatin attenuates cognitive deficits and neuroinflammation induced by Abeta1-42 involving modulation of TLR4/TRAF6/NF-kappaB pathway. Journal of molecular neuroscience : MN. 2018;64(3):363–73.
Article
CAS
PubMed
Google Scholar
Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature. 2016;535(7610):75–84.
Article
CAS
PubMed
Google Scholar
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331(6015):337–41.
Article
CAS
PubMed
Google Scholar
Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, Glickman JN, Garrett WS. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341(6145):569–73.
Article
CAS
PubMed
Google Scholar
Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122(1):107–18.
Article
CAS
PubMed
Google Scholar
Hirota K, Turner JE, Villa M, Duarte JH, Demengeot J, Steinmetz OM, Stockinger B. Plasticity of Th17 cells in Peyer's patches is responsible for the induction of T cell-dependent IgA responses. Nature immunology. 2013;14(4):372–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ivanov II, McKenzie BS, Zhou L, Tadokoro CE, Lepelley A, Lafaille JJ, Cua DJ, Littman DR. The orphan nuclear receptor RORgammat directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell. 2006;126(6):1121–33.
Article
CAS
PubMed
Google Scholar
Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell host & microbe. 2008;4(4):337–49.
Article
CAS
Google Scholar
Ishigame H, Kakuta S, Nagai T, Kadoki M, Nambu A, Komiyama Y, Fujikado N, Tanahashi Y, Akitsu A, Kotaki H, et al. Differential roles of interleukin-17A and -17F in host defense against mucoepithelial bacterial infection and allergic responses. Immunity. 2009;30(1):108–19.
Article
CAS
PubMed
Google Scholar
Horai R, Zarate-Blades CR, Dillenburg-Pilla P, Chen J, Kielczewski JL, Silver PB, Jittayasothorn Y, Chan CC, Yamane H, Honda K, et al. Microbiota-dependent activation of an autoreactive T cell receptor provokes autoimmunity in an immunologically privileged site. Immunity. 2015;43(2):343–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berer K, Mues M, Koutrolos M, Rasbi ZA, Boziki M, Johner C, Wekerle H, Krishnamoorthy G. Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination. Nature. 2011;479(7374):538–41.
Article
CAS
PubMed
Google Scholar
McGeachy MJ, Chen Y, Tato CM, Laurence A, Joyce-Shaikh B, Blumenschein WM, McClanahan TK, O'Shea JJ, Cua DJ. The interleukin 23 receptor is essential for the terminal differentiation of interleukin 17-producing effector T helper cells in vivo. Nature immunology. 2009;10(3):314–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coccia M, Harrison OJ, Schiering C, Asquith MJ, Becher B, Powrie F, Maloy KJ. IL-1beta mediates chronic intestinal inflammation by promoting the accumulation of IL-17A secreting innate lymphoid cells and CD4(+) Th17 cells. The Journal of experimental medicine. 2012;209(9):1595–609.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schulte-Herbruggen O, Quarcoo D, Meisel A, Meisel C. Differential affection of intestinal immune cell populations after cerebral ischemia in mice. Neuroimmunomodulation. 2009;16(3):213–8.
Article
PubMed
CAS
Google Scholar
Diaz Heijtz R, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A, Hibberd ML, Forssberg H, Pettersson S. Normal gut microbiota modulates brain development and behavior. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(7):3047–52.
Article
PubMed
Google Scholar
Obermeier B, Daneman R, Ransohoff RM. Development, maintenance and disruption of the blood-brain barrier. Nature medicine. 2013;19(12):1584–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daneman R, Prat A. The blood-brain barrier. Cold Spring Harbor perspectives in biology. 2015;7(1):a020412.
Article
PubMed
PubMed Central
CAS
Google Scholar
Acharya NK, Levin EC, Clifford PM, Han M, Tourtellotte R, Chamberlain D, Pollaro M, Coretti NJ, Kosciuk MC, Nagele EP, et al. Diabetes and hypercholesterolemia increase blood-brain barrier permeability and brain amyloid deposition: beneficial effects of the LpPLA2 inhibitor darapladib. Journal of Alzheimer’s disease : JAD. 2013;35(1):179–98.
Article
CAS
PubMed
Google Scholar
Fiorentino M, Sapone A, Senger S, Camhi SS, Kadzielski SM, Buie TM, Kelly DL, Cascella N, Fasano A. Blood-brain barrier and intestinal epithelial barrier alterations in autism spectrum disorders. Molecular autism. 2016;7:49.
Article
PubMed
PubMed Central
CAS
Google Scholar
Holmqvist S, Chutna O, Bousset L, Aldrin-Kirk P, Li W, Bjorklund T, Wang ZY, Roybon L, Melki R, Li JY. Direct evidence of Parkinson pathology spread from the gastrointestinal tract to the brain in rats. Acta neuropathologica. 2014;128(6):805–20.
Article
PubMed
Google Scholar
Braniste V, Al-Asmakh M, Kowal C, Anuar F, Abbaspour A, Toth M, Korecka A, Bakocevic N, Ng LG, Kundu P, et al. The gut microbiota influences blood-brain barrier permeability in mice. Science translational medicine. 2014;6(263):263ra158.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lee SW, Kim WJ, Choi YK, Song HS, Son MJ, Gelman IH, Kim YJ, Kim KW. SSeCKS regulates angiogenesis and tight junction formation in blood-brain barrier. Nature medicine. 2003;9(7):900–6.
Article
CAS
PubMed
Google Scholar
Spadoni I, Fornasa G, Rescigno M. Organ-specific protection mediated by cooperation between vascular and epithelial barriers. Nature reviews Immunology. 2017;17(12):761–73.
Article
CAS
PubMed
Google Scholar
Luczynski P, McVey Neufeld KA, Oriach CS, Clarke G, Dinan TG, Cryan JF. Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior. The international journal of neuropsychopharmacology. 2016;19(8).
Article
PubMed
PubMed Central
CAS
Google Scholar
Bao CH, Liu P, Liu HR, Wu LY, Shi Y, Chen WF, Qin W, Lu Y, Zhang JY, Jin XM, et al. Alterations in brain grey matter structures in patients with Crohn's disease and their correlation with psychological distress. Journal of Crohn's & colitis. 2015;9(7):532–40.
Article
Google Scholar
Mrakotsky C AR, Watson C, Vu C, Matos A, Friel S, Rivkin M, Snapper S: New Evidence for structural brain differences in pediatric Crohn's disease: impact of underlying disease factors. Inflammatory bowel diseases 2016, Mar; 22 Suppl 1:S6-S7.
Article
Google Scholar
Fernandez-Real JM, Serino M, Blasco G, Puig J, Daunis-i-Estadella J, Ricart W, Burcelin R, Fernandez-Aranda F, Portero-Otin M. Gut microbiota interacts with brain microstructure and function. The Journal of clinical endocrinology and metabolism. 2015;100(12):4505–13.
Article
CAS
PubMed
Google Scholar
Vipperla K, O'Keefe SJ. The microbiota and its metabolites in colonic mucosal health and cancer risk. Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition. 2012;27(5):624–35.
Article
Google Scholar
Luna RA, Foster JA. Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression. Current opinion in biotechnology. 2015;32:35–41.
Article
CAS
PubMed
Google Scholar
Evrensel A, Ceylan ME. The gut-brain axis: the missing link in depression. Clinical psychopharmacology and neuroscience : the official scientific journal of the Korean College of Neuropsychopharmacology. 2015;13(3):239–44.
Article
CAS
Google Scholar
Pistollato F, Iglesias RC, Ruiz R, Aparicio S, Crespo J, Lopez LD, Manna PP, Giampieri F, Battino M. Nutritional patterns associated with the maintenance of neurocognitive functions and the risk of dementia and Alzheimer's disease: a focus on human studies. Pharmacological research. 2018;131:32–43.
Article
PubMed
Google Scholar
Dominguez LJ, Barbagallo M, Munoz-Garcia M, Godos J, Martinez-Gonzalez MA. Dietary patterns and cognitive decline: key features for prevention. Current pharmaceutical design. 2019;25(22):2428–42.
Article
CAS
PubMed
Google Scholar
Tangney CC, Li H, Wang Y, Barnes L, Schneider JA, Bennett DA, Morris MC. Relation of DASH- and Mediterranean-like dietary patterns to cognitive decline in older persons. Neurology. 2014;83(16):1410–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harrison CA, Taren D. How poverty affects diet to shape the microbiota and chronic disease. Nature reviews Immunology. 2018;18(4):279–87.
Article
CAS
PubMed
Google Scholar
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 2009;137(5):1716–1724 e1711-1712.
Article
CAS
PubMed
Google Scholar
Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, Petersen KF, Kibbey RG, Goodman AL, Shulman GI. Acetate mediates a microbiome-brain-beta-cell axis to promote metabolic syndrome. Nature. 2016;534(7606):213–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Q, Lauber CL, Czarnecki-Maulden G, Pan Y, Hannah SS. Effects of the dietary protein and carbohydrate ratio on gut microbiomes in dogs of different body conditions. MBio. 2017:8(1).
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65(11):1812–21.
Article
PubMed
CAS
Google Scholar
Li JM, Yu R, Zhang LP, Wen SY, Wang SJ, Zhang XY, Xu Q, Kong LD. Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids. Microbiome. 2019;7(1):98.
Article
PubMed
PubMed Central
Google Scholar
Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, Feldstein AE, Britt EB, Fu X, Chung YM, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472(7341):57–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature medicine. 2013;19(5):576–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M, et al. Gut microbial metabolite TMAO ehances platelet hyperreactivity and thrombosis risk. Cell. 2016;165(1):111–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koren O, Spor A, Felin J, Fak F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(Suppl 1):4592–8.
Article
CAS
PubMed
Google Scholar
Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y, Hazen SL. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. The New England journal of medicine. 2013;368(17):1575–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, Gu X, Huang Y, Zamanian-Daryoush M, Culley MK, et al. Non-lethal Inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell. 2015;163(7):1585–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jie Z, Xia H, Zhong SL, Feng Q, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, et al. The gut microbiome in atherosclerotic cardiovascular disease. Nature communications. 2017;8(1):845.
Article
PubMed
PubMed Central
CAS
Google Scholar
Olson CA, Vuong HE, Yano JM, Liang QY, Nusbaum DJ, Hsiao EY. The gut microbiota mediates the anti-seizure effects of the ketogenic diet. Cell. 2018;173(7):1728–1741 e1713.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kelder T, Stroeve JH, Bijlsma S, Radonjic M, Roeselers G. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health. Nutrition & diabetes. 2014;4:e122.
Article
CAS
Google Scholar
He K, Hu Y, Ma H, Zou Z, Xiao Y, Yang Y, Feng M, Li X, Ye X. Rhizoma Coptidis alkaloids alleviate hyperlipidemia in B6 mice by modulating gut microbiota and bile acid pathways. Biochimica et biophysica acta. 2016;1862(9):1696–709.
Article
CAS
PubMed
Google Scholar
Bourassa MW, Alim I, Bultman SJ, Ratan RR. Butyrate, neuroepigenetics and the gut microbiome: can a high fiber diet improve brain health? Neuroscience letters. 2016;625:56–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Topping DL, Clifton PM. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiological reviews. 2001;81(3):1031–64.
Article
CAS
PubMed
Google Scholar
Haghikia A, Jorg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee DH, May C, Wilck N, et al. Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity. 2016;44(4):951–3.
Article
PubMed
Google Scholar
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, et al. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell. 2016;167(4):1125–1136 e1128.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duncan SH, Holtrop G, Lobley GE, Calder AG, Stewart CS, Flint HJ. Contribution of acetate to butyrate formation by human faecal bacteria. The British journal of nutrition. 2004;91(6):915–23.
Article
CAS
PubMed
Google Scholar
Tan J, McKenzie C, Potamitis M, Thorburn AN, Mackay CR, Macia L. The role of short-chain fatty acids in health and disease. Advances in immunology. 2014;121:91–119.
Article
CAS
PubMed
Google Scholar
Macfarlane S, Macfarlane GT. Regulation of short-chain fatty acid production. The Proceedings of the Nutrition Society. 2003;62(1):67–72.
Article
CAS
PubMed
Google Scholar
Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009;461(7268):1282–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kasubuchi M, Hasegawa S, Hiramatsu T, Ichimura A, Kimura I. Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation. Nutrients. 2015;7(4):2839–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM. Diet-microbiota interactions mediate global epigenetic programming in multiple host tissues. Molecular cell. 2016;64(5):982–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rothhammer V, Borucki DM, Tjon EC, Takenaka MC, Chao CC, Ardura-Fabregat A, de Lima KA, Gutierrez-Vazquez C, Hewson P, Staszewski O, et al. Microglial control of astrocytes in response to microbial metabolites. Nature. 2018;557(7707):724–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rothhammer V, Mascanfroni ID, Bunse L, Takenaka MC, Kenison JE, Mayo L, Chao CC, Patel B, Yan R, Blain M, et al. Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor. Nature medicine. 2016;22(6):586–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schroeder JC, Dinatale BC, Murray IA, Flaveny CA, Liu Q, Laurenzana EM, Lin JM, Strom SC, Omiecinski CJ, Amin S, et al. The uremic toxin 3-indoxyl sulfate is a potent endogenous agonist for the human aryl hydrocarbon receptor. Biochemistry. 2010;49(2):393–400.
Article
CAS
PubMed
Google Scholar
Jaglin M, Rhimi M, Philippe C, Pons N, Bruneau A, Goustard B, Dauge V, Maguin E, Naudon L, Rabot S. Indole, a signaling molecule droduced by the gut microbiota, negatively impacts emotional behaviors in rats. Frontiers in neuroscience. 2018;12:216.
Article
PubMed
PubMed Central
Google Scholar
Szczesniak O, Hestad KA, Hanssen JF, Rudi K. Isovaleric acid in stool correlates with human depression. Nutritional neuroscience. 2016;19(7):279–83.
Article
CAS
PubMed
Google Scholar
Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 2016;65(1):63–72.
Article
CAS
PubMed
Google Scholar
Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155(7):1451–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miles C, Green R, Hines M. Estrogen treatment effects on cognition, memory and mood in male-to-female transsexuals. Hormones and behavior. 2006;50(5):708–17.
Article
CAS
PubMed
Google Scholar
Keefer L. Behavioural medicine and gastrointestinal disorders: the promise of positive psychology. Nature reviews Gastroenterology & hepatology. 2018;15(6):378–86.
Article
Google Scholar
Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD, Shanahan F, Dinan TG, Cryan JF. The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Molecular psychiatry. 2013;18(6):666–73.
Article
CAS
PubMed
Google Scholar
Messaoudi M, Lalonde R, Violle N, Javelot H, Desor D, Nejdi A, Bisson JF, Rougeot C, Pichelin M, Cazaubiel M, et al. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. The British journal of nutrition. 2011;105(5):755–64.
Article
CAS
PubMed
Google Scholar
Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(38):16050–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Janik R, Thomason LAM, Stanisz AM, Forsythe P, Bienenstock J, Stanisz GJ. Magnetic resonance spectroscopy reveals oral Lactobacillus promotion of increases in brain GABA, N-acetyl aspartate and glutamate. NeuroImage. 2016;125:988–95.
Article
CAS
PubMed
Google Scholar
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. The Journal of physiology. 2004;558(Pt 1):263–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. 2011;23(3):255–264, e119.
Article
CAS
Google Scholar
Bercik P, Verdu EF, Foster JA, Macri J, Potter M, Huang X, Malinowski P, Jackson W, Blennerhassett P, Neufeld KA, et al. Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice. Gastroenterology. 2010;139(6):2102–2112 e2101.
Article
CAS
PubMed
Google Scholar
Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, Deng Y, Blennerhassett P, Macri J, McCoy KD, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 2011;141(2):599–609 609 e591-593.
Article
CAS
PubMed
Google Scholar
Crumeyrolle-Arias M, Jaglin M, Bruneau A, Vancassel S, Cardona A, Dauge V, Naudon L, Rabot S. Absence of the gut microbiota enhances anxiety-like behavior and neuroendocrine response to acute stress in rats. Psychoneuroendocrinology. 2014;42:207–17.
Article
CAS
PubMed
Google Scholar
Desbonnet L, Clarke G, Shanahan F, Dinan TG, Cryan JF. Microbiota is essential for social development in the mouse. Molecular psychiatry. 2014;19(2):146–8.
Article
CAS
PubMed
Google Scholar
Degroote S, Hunting DJ, Baccarelli AA, Takser L. Maternal gut and fetal brain connection: increased anxiety and reduced social interactions in Wistar rat offspring following peri-conceptional antibiotic exposure. Progress in neuro-psychopharmacology & biological psychiatry. 2016;71:76–82.
Article
CAS
Google Scholar
Frohlich EE, Farzi A, Mayerhofer R, Reichmann F, Jacan A, Wagner B, Zinser E, Bordag N, Magnes C, Frohlich E, et al. Cognitive impairment by antibiotic-induced gut dysbiosis: analysis of gut microbiota-brain communication. Brain, behavior, and immunity. 2016;56:140–55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gareau MG, Wine E, Rodrigues DM, Cho JH, Whary MT, Philpott DJ, Macqueen G, Sherman PM. Bacterial infection causes stress-induced memory dysfunction in mice. Gut. 2011;60(3):307–17.
Article
PubMed
Google Scholar
Mohle L, Mattei D, Heimesaat MM, Bereswill S, Fischer A, Alutis M, French T, Hambardzumyan D, Matzinger P, Dunay IR, et al. Ly6C(hi) monocytes provide a link between antibiotic-induced changes in gut microbiota and adult hippocampal neurogenesis. Cell reports. 2016;15(9):1945–56.
Article
PubMed
CAS
Google Scholar
Lyte M, Li W, Opitz N, Gaykema RP, Goehler LE. Induction of anxiety-like behavior in mice during the initial stages of infection with the agent of murine colonic hyperplasia Citrobacter rodentium. Physiology & behavior. 2006;89(3):350–7.
Article
CAS
Google Scholar
Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, et al. Unlocking the potential of metagenomics through replicated experimental design. Nature biotechnology. 2012;30(6):513–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blaser MJ, Dominguez-Bello MG. The human microbiome before birth. Cell host & microbe. 2016;20(5):558–60.
Article
CAS
Google Scholar
Kostic AD, Gevers D, Siljander H, Vatanen T, Hyotylainen T, Hamalainen AM, Peet A, Tillmann V, Poho P, Mattila I, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell host & microbe. 2015;17(2):260–73.
Article
CAS
Google Scholar
Williamson LL, Sholar PW, Mistry RS, Smith SH, Bilbo SD. Microglia and memory: modulation by early-life infection. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2011;31(43):15511–21.
Article
CAS
Google Scholar
Andre C, Dinel AL, Ferreira G, Laye S, Castanon N. Diet-induced obesity progressively alters cognition, anxiety-like behavior and lipopolysaccharide-induced depressive-like behavior: focus on brain indoleamine 2,3-dioxygenase activation. Brain, behavior, and immunity. 2014;41:10–21.
Article
CAS
PubMed
Google Scholar
Magnusson KR, Hauck L, Jeffrey BM, Elias V, Humphrey A, Nath R, Perrone A, Bermudez LE. Relationships between diet-related changes in the gut microbiome and cognitive flexibility. Neuroscience. 2015;300:128–40.
Article
CAS
PubMed
Google Scholar
O'Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EM, Cryan JF, Dinan TG. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biological psychiatry. 2009;65(3):263–7.
Article
PubMed
Google Scholar
Bangsgaard Bendtsen KM, Krych L, Sorensen DB, Pang W, Nielsen DS, Josefsen K, Hansen LH, Sorensen SJ, Hansen AK. Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse. PloS one. 2012;7(10):e46231.
Article
PubMed
PubMed Central
CAS
Google Scholar
Banerjee A, Sarkhel S, Sarkar R, Dhali GK. Anxiety and depression in irritable bowel syndrome. Indian journal of psychological medicine. 2017;39(6):741–5.
Article
PubMed
PubMed Central
Google Scholar
Owens M, Herbert J, Jones PB, Sahakian BJ, Wilkinson PO, Dunn VJ, Croudace TJ, Goodyer IM. Elevated morning cortisol is a stratified population-level biomarker for major depression in boys only with high depressive symptoms. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(9):3638–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ait-Belgnaoui A, Colom A, Braniste V, Ramalho L, Marrot A, Cartier C, Houdeau E, Theodorou V, Tompkins T. Probiotic gut effect prevents the chronic psychological stress-induced brain activity abnormality in mice. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. 2014;26(4):510–20.
Article
CAS
Google Scholar
de Theije CG, Wopereis H, Ramadan M, van Eijndthoven T, Lambert J, Knol J, Garssen J, Kraneveld AD, Oozeer R. Altered gut microbiota and activity in a murine model of autism spectrum disorders. Brain, behavior, and immunity. 2014;37:197–206.
Article
PubMed
CAS
Google Scholar
Curran LK, Newschaffer CJ, Lee LC, Crawford SO, Johnston MV, Zimmerman AW. Behaviors associated with fever in children with autism spectrum disorders. Pediatrics. 2007;120(6):e1386–92.
Article
PubMed
Google Scholar
Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Vaisanen ML, Nelson MN, Wexler HM. Short-term benefit from oral vancomycin treatment of regressive-onset autism. Journal of child neurology. 2000;15(7):429–35.
Article
CAS
PubMed
Google Scholar
Critchfield JW, van Hemert S, Ash M, Mulder L, Ashwood P. The potential role of probiotics in the management of childhood autism spectrum disorders. Gastroenterology research and practice. 2011;2011:161358.
Article
PubMed
PubMed Central
Google Scholar
Klukowski M, Wasilewska J, Lebensztejn D. Sleep and gastrointestinal disturbances in autism spectrum disorder in children. Developmental period medicine. 2015;19(2):157–61.
PubMed
Google Scholar
Chaidez V, Hansen RL, Hertz-Picciotto I. Gastrointestinal problems in children with autism, developmental delays or typical development. Journal of autism and developmental disorders. 2014;44(5):1117–27.
Article
PubMed
PubMed Central
Google Scholar
Horvath K, Perman JA. Autistic disorder and gastrointestinal disease. Current opinion in pediatrics. 2002;14(5):583–7.
Article
PubMed
Google Scholar
De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PloS one. 2013;8(10):e76993.
Article
PubMed
PubMed Central
CAS
Google Scholar
Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA. Gastrointestinal flora and gastrointestinal status in children with autism--comparisons to typical children and correlation with autism severity. BMC gastroenterology. 2011;11:22.
Article
PubMed
PubMed Central
Google Scholar
Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Applied and environmental microbiology. 2011;77(18):6718–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16(4):444–53.
Article
CAS
PubMed
Google Scholar
Parracho HM, Bingham MO, Gibson GR, McCartney AL. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. Journal of medical microbiology. 2005;54(Pt 10):987–91.
Article
PubMed
Google Scholar
Saulnier DM, Ringel Y, Heyman MB, Foster JA, Bercik P, Shulman RJ, Versalovic J, Verdu EF, Dinan TG, Hecht G, et al. The intestinal microbiome, probiotics and prebiotics in neurogastroenterology. Gut microbes. 2013;4(1):17–27.
Article
PubMed
PubMed Central
Google Scholar
Theodorou V, Ait Belgnaoui A, Agostini S, Eutamene H. Effect of commensals and probiotics on visceral sensitivity and pain in irritable bowel syndrome. Gut microbes. 2014;5(3):430–6.
Article
PubMed
PubMed Central
Google Scholar
Sachdev AH, Pimentel M. Gastrointestinal bacterial overgrowth: pathogenesis and clinical significance. Therapeutic advances in chronic disease. 2013;4(5):223–31.
Article
PubMed
PubMed Central
Google Scholar
Faraji F, Zarinfar N, Zanjani AT, Morteza A. The effect of Helicobacter pylori eradication on migraine: a randomized, double blind, controlled trial. Pain physician. 2012;15(6):495–8.
PubMed
Google Scholar
Smilowicz A. An osteopathic approach to gastrointestinal disease: somatic clues for diagnosis and clinical challenges associated with Helicobacter pylori antibiotic resistance. The Journal of the American Osteopathic Association. 2013;113(5):404–16.
PubMed
Google Scholar
Aguilera M, Cerda-Cuellar M, Martinez V. Antibiotic-induced dysbiosis alters host-bacterial interactions and leads to colonic sensory and motor changes in mice. Gut microbes. 2015;6(1):10–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amaral FA, Sachs D, Costa VV, Fagundes CT, Cisalpino D, Cunha TM, Ferreira SH, Cunha FQ, Silva TA, Nicoli JR, et al. Commensal microbiota is fundamental for the development of inflammatory pain. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(6):2193–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Su J, Zhou XY, Zhang GX. Association between Helicobacter pylori infection and migraine: a meta-analysis. World journal of gastroenterology. 2014;20(40):14965–72.
Article
PubMed
PubMed Central
Google Scholar
Tang Y, Liu S, Shu H, Yanagisawa L, Tao F. Gut microbiota dysbiosis enhances migraine-like pain via TNFalpha upregulation. Molecular neurobiology. 2019.
Rousseaux C, Thuru X, Gelot A, Barnich N, Neut C, Dubuquoy L, Dubuquoy C, Merour E, Geboes K, Chamaillard M, et al. Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors. Nature medicine. 2007;13(1):35–7.
Article
CAS
PubMed
Google Scholar
McKernan DP, Fitzgerald P, Dinan TG, Cryan JF. The probiotic Bifidobacterium infantis 35624 displays visceral antinociceptive effects in the rat. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. 2010;22(9):1029–1035, e1268.
Article
CAS
Google Scholar
Ait-Belgnaoui A, Eutamene H, Houdeau E, Bueno L, Fioramonti J, Theodorou V. Lactobacillus farciminis treatment attenuates stress-induced overexpression of Fos protein in spinal and supraspinal sites after colorectal distension in rats. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. 2009;21(5):567–73 e518-569.
Article
CAS
Google Scholar
O'Mahony L, McCarthy J, Kelly P, Hurley G, Luo F, Chen K, O'Sullivan GC, Kiely B, Collins JK, Shanahan F, et al. Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology. 2005;128(3):541–51.
Article
PubMed
Google Scholar
Pellegrini C, Antonioli L, Colucci R, Blandizzi C, Fornai M. Interplay among gut microbiota, intestinal mucosal barrier and enteric neuro-immune system: a common path to neurodegenerative diseases? Acta neuropathologica. 2018;136(3):345–61.
Article
CAS
PubMed
Google Scholar
Spielman LJ, Gibson DL, Klegeris A. Unhealthy gut, unhealthy brain: the role of the intestinal microbiota in neurodegenerative diseases. Neurochemistry international. 2018;120:149–63.
Article
CAS
PubMed
Google Scholar
Tilvis RS, Kahonen-Vare MH, Jolkkonen J, Valvanne J, Pitkala KH, Strandberg TE. Predictors of cognitive decline and mortality of aged people over a 10-year period. The journals of gerontology Series A, Biological sciences and medical sciences. 2004;59(3):268–74.
Article
PubMed
Google Scholar
Serres S, Anthony DC, Jiang Y, Broom KA, Campbell SJ, Tyler DJ, van Kasteren SI, Davis BG, Sibson NR. Systemic inflammatory response reactivates immune-mediated lesions in rat brain. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2009;29(15):4820–8.
Article
CAS
Google Scholar
Reeve A, Simcox E, Turnbull D. Ageing and Parkinson's disease: why is advancing age the biggest risk factor? Ageing research reviews. 2014;14:19–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Felice VD, Quigley EM, Sullivan AM, O'Keeffe GW, O'Mahony SM. Microbiota-gut-brain signalling in Parkinson's disease: implications for non-motor symptoms. Parkinsonism & related disorders. 2016;27:1–8.
Article
Google Scholar
Fasano A, Visanji NP, Liu LW, Lang AE, Pfeiffer RF. Gastrointestinal dysfunction in Parkinson's disease. The Lancet Neurology. 2015;14(6):625–39.
Article
CAS
PubMed
Google Scholar
Chiang HL, Lin CH. Altered gut microbiome and intestinal pathology in Parkinson's disease. Journal of movement disorders. 2019;12(2):67–83.
Article
PubMed
PubMed Central
Google Scholar
Ulusoy A, Phillips RJ, Helwig M, Klinkenberg M, Powley TL, Di Monte DA. Brain-to-stomach transfer of alpha-synuclein via vagal preganglionic projections. Acta neuropathologica. 2017;133(3):381–93.
Article
CAS
PubMed
Google Scholar
Villaran RF, Espinosa-Oliva AM, Sarmiento M, De Pablos RM, Arguelles S, Delgado-Cortes MJ, Sobrino V, Van Rooijen N, Venero JL, Herrera AJ, et al. Ulcerative colitis exacerbates lipopolysaccharide-induced damage to the nigral dopaminergic system: potential risk factor in Parkinson`s disease. Journal of neurochemistry. 2010;114(6):1687–700.
Article
CAS
PubMed
Google Scholar
Forsyth CB, Shannon KM, Kordower JH, Voigt RM, Shaikh M, Jaglin JA, Estes JD, Dodiya HB, Keshavarzian A. Increased intestinal permeability correlates with sigmoid mucosa alpha-synuclein staining and endotoxin exposure markers in early Parkinson's disease. PloS one. 2011;6(12):e28032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salat-Foix D, Tran K, Ranawaya R, Meddings J, Suchowersky O. Increased intestinal permeability and Parkinson disease patients: chicken or egg? The Canadian journal of neurological sciences Le journal canadien des sciences neurologiques. 2012;39(2):185–8.
Article
CAS
PubMed
Google Scholar
Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, Mutlu E, Shannon KM. Colonic bacterial composition in Parkinson's disease. Movement disorders : official journal of the Movement Disorder Society. 2015;30(10):1351–60.
Article
CAS
Google Scholar
Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M, et al. Gut microbiota are related to Parkinson's disease and clinical phenotype. Movement disorders : official journal of the Movement Disorder Society. 2015;30(3):350–8.
Article
Google Scholar
Barichella M, Pacchetti C, Bolliri C, Cassani E, Iorio L, Pusani C, Pinelli G, Privitera G, Cesari I, Faierman SA, et al. Probiotics and prebiotic fiber for constipation associated with Parkinson disease: an RCT. Neurology. 2016;87(12):1274–80.
Article
CAS
PubMed
Google Scholar
Peter I, Dubinsky M, Bressman S, Park A, Lu C, Chen N, Wang A. Anti-tumor necrosis factor therapy and incidence of Parkinson disease among patients with inflammatory bowel disease. JAMA neurology. 2018;75(8):939–46.
Article
PubMed
PubMed Central
Google Scholar
Camacho-Soto A, Gross A, Searles Nielsen S, Dey N, Racette BA. Inflammatory bowel disease and risk of Parkinson's disease in Medicare beneficiaries. Parkinsonism & related disorders. 2018;50:23–8.
Article
Google Scholar
Alzheimer's A. 2016 Alzheimer's disease facts and figures. Alzheimer's & dementia : the journal of the Alzheimer's Association. 2016;12(4):459–509.
Article
Google Scholar
Wang MM, Miao D, Cao XP, Tan L, Tan L. Innate immune activation in Alzheimer's disease. Annals of translational medicine. 2018;6(10):177.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bagyinszky E, Giau VV, Shim K, Suk K, An SSA, Kim S. Role of inflammatory molecules in the Alzheimer's disease progression and diagnosis. Journal of the neurological sciences. 2017;376:242–54.
Article
CAS
PubMed
Google Scholar
Asti A, Gioglio L. Can a bacterial endotoxin be a key factor in the kinetics of amyloid fibril formation? Journal of Alzheimer's disease : JAD. 2014;39(1):169–79.
Article
CAS
PubMed
Google Scholar
Allen HB. Alzheimer's disease: assessing the role of Spirochetes, biofilms, the immune system, and amyloid-beta with regard to potential treatment and prevention. Journal of Alzheimer's disease : JAD. 2016;53(4):1271–6.
Article
CAS
PubMed
Google Scholar
Schwartz K, Boles BR. Microbial amyloids--functions and interactions within the host. Current opinion in microbiology. 2013;16(1):93–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou Y, Smith D, Leong BJ, Brannstrom K, Almqvist F, Chapman MR. Promiscuous cross-seeding between bacterial amyloids promotes interspecies biofilms. The Journal of biological chemistry. 2012;287(42):35092–103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hill JM, Lukiw WJ. Microbial-generated amyloids and Alzheimer's disease (AD). Frontiers in aging neuroscience. 2015;7:9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roubaud-Baudron C, Krolak-Salmon P, Quadrio I, Megraud F, Salles N. Impact of chronic Helicobacter pylori infection on Alzheimer's disease: preliminary results. Neurobiology of aging. 2012;33(5):1009 e1011–09.
Article
CAS
Google Scholar
Bu XL, Yao XQ, Jiao SS, Zeng F, Liu YH, Xiang Y, Liang CR, Wang QH, Wang X, Cao HY, et al. A study on the association between infectious burden and Alzheimer's disease. European journal of neurology. 2015;22(12):1519–25.
Article
PubMed
Google Scholar
Wang XL, Zeng J, Yang Y, Xiong Y, Zhang ZH, Qiu M, Yan X, Sun XY, Tuo QZ, Liu R, et al. Helicobacter pylori filtrate induces Alzheimer-like tau hyperphosphorylation by activating glycogen synthase kinase-3beta. JAD. 2015;43(1):153–65.
Article
PubMed
CAS
Google Scholar
Friedland RP, Chapman MR. The role of microbial amyloid in neurodegeneration. PLoS pathogens. 2017;13(12):e1006654.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schwartz K, Syed AK, Stephenson RE, Rickard AH, Boles BR. Functional amyloids composed of phenol soluble modulins stabilize Staphylococcus aureus biofilms. PLoS pathogens. 2012;8(6):e1002744.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harach T, Marungruang N, Duthilleul N, Cheatham V, Mc Coy KD, Frisoni G, Neher JJ, Fak F, Jucker M, Lasser T, et al. Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota. Scientific reports. 2017;7:41802.
Article
CAS
PubMed
PubMed Central
Google Scholar
Al-Atrache Z, Lopez DB, Hingley ST, Appelt DM. Astrocytes infected with Chlamydia pneumoniae demonstrate altered expression and activity of secretases involved in the generation of beta-amyloid found in Alzheimer disease. BMC neuroscience. 2019;20(1):6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Athari Nik Azm S, Djazayeri A, Safa M, Azami K, Ahmadvand B, Sabbaghziarani F, Sharifzadeh M, Vafa M. Lactobacilli and bifidobacteria ameliorate memory and learning deficits and oxidative stress in beta-amyloid (1-42) injected rats. Applied physiology, nutrition, and metabolism = Physiologie appliquee, nutrition et metabolisme. 2018;43(7):718–26.
Article
CAS
PubMed
Google Scholar
Wang T, Hu X, Liang S, Li W, Wu X, Wang L, Jin F. Lactobacillus fermentum NS9 restores the antibiotic induced physiological and psychological abnormalities in rats. Beneficial microbes. 2015;6(5):707–17.
Article
CAS
PubMed
Google Scholar
Liang S, Wang T, Hu X, Luo J, Li W, Wu X, Duan Y, Jin F. Administration of Lactobacillus helveticus NS8 improves behavioral, cognitive, and biochemical aberrations caused by chronic restraint stress. Neuroscience. 2015;310:561–77.
Article
CAS
PubMed
Google Scholar
Akbari E, Asemi Z, Daneshvar Kakhaki R, Bahmani F, Kouchaki E, Tamtaji OR, Hamidi GA, Salami M. Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer's disease: a randomized, double-blind and controlled trial. Frontiers in aging neuroscience. 2016;8:256.
Article
PubMed
PubMed Central
Google Scholar
Kountouras J, Boziki M, Gavalas E, Zavos C, Grigoriadis N, Deretzi G, Tzilves D, Katsinelos P, Tsolaki M, Chatzopoulos D, et al. Eradication of Helicobacter pylori may be beneficial in the management of Alzheimer's disease. Journal of neurology. 2009;256(5):758–67.
Article
PubMed
Google Scholar
Abraham D, Feher J, Scuderi GL, Szabo D, Dobolyi A, Cservenak M, Juhasz J, Ligeti B, Pongor S, Gomez-Cabrera MC, et al. Exercise and probiotics attenuate the development of Alzheimer's disease in transgenic mice: role of microbiome. Experimental gerontology. 2019;115:122–31.
Article
CAS
PubMed
Google Scholar
Alonso A, Logroscino G, Jick SS, Hernan MA. Incidence and lifetime risk of motor neuron disease in the United Kingdom: a population-based study. European journal of neurology. 2009;16(6):745–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang MD, Little J, Gomes J, Cashman NR, Krewski D. Identification of risk factors associated with onset and progression of amyotrophic lateral sclerosis using systematic review and meta-analysis. Neurotoxicology. 2017;61:101–30.
Article
CAS
PubMed
Google Scholar
Nguyen MD, D'Aigle T, Gowing G, Julien JP, Rivest S. Exacerbation of motor neuron disease by chronic stimulation of innate immunity in a mouse model of amyotrophic lateral sclerosis. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2004;24(6):1340–9.
Article
CAS
Google Scholar
Zhang R, Miller RG, Gascon R, Champion S, Katz J, Lancero M, Narvaez A, Honrada R, Ruvalcaba D, McGrath MS. Circulating endotoxin and systemic immune activation in sporadic amyotrophic lateral sclerosis (sALS). Journal of neuroimmunology. 2009;206(1-2):121–4.
Article
CAS
PubMed
Google Scholar
Longstreth WT Jr, Meschke JS, Davidson SK, Smoot LM, Smoot JC, Koepsell TD. Hypothesis: a motor neuron toxin produced by a clostridial species residing in gut causes ALS. Medical hypotheses. 2005;64(6):1153–6.
Article
CAS
PubMed
Google Scholar
Kaneko K, Hachiya NS. Hypothesis: gut as source of motor neuron toxin in the development of ALS. Medical hypotheses. 2006;66(2):438–9.
Article
CAS
PubMed
Google Scholar
Al-Asmakh M, Hedin L. Microbiota and the control of blood-tissue barriers. Tissue barriers. 2015;3(3):e1039691.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu S, Yi J, Zhang YG, Zhou J, Sun J. Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model. Physiological reports. 2015:3(4).
Article
PubMed
PubMed Central
CAS
Google Scholar
Fang X, Wang X, Yang S, Meng F, Wang X, Wei H, Chen T. Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing. Frontiers in microbiology. 2016;7:1479.
PubMed
PubMed Central
Google Scholar
Brenner D, Hiergeist A, Adis C, Mayer B, Gessner A, Ludolph AC, Weishaupt JH. The fecal microbiome of ALS patients. Neurobiology of aging. 2018;61:132–7.
Article
PubMed
Google Scholar
Zhang YG, Wu S, Yi J, Xia Y, Jin D, Zhou J, Sun J. Target intestinal microbiota to alleviate disease progression in amyotrophic lateral sclerosis. Clinical therapeutics. 2017;39(2):322–36.
Article
PubMed
PubMed Central
Google Scholar
Mazzini L, Mogna L, De Marchi F, Amoruso A, Pane M, Aloisio I, Cionci NB, Gaggia F, Lucenti A, Bersano E, et al. Potential role of gut microbiota in ALS pathogenesis and possible novel therapeutic strategies, Journal of clinical gastroenterology. 52 Suppl 1, Proceedings from the 9th Probiotics, Prebiotics and New Foods, Nutraceuticals and Botanicals for Nutrition & Human and Microbiota Health Meeting, held in Rome, Italy from September 10 to 12, 2017:2018, S68–S70.
Tremlett H, Bauer KC, Appel-Cresswell S, Finlay BB, Waubant E. The gut microbiome in human neurological disease: a review. Annals of neurology. 2017;81(3):369–82.
Article
PubMed
Google Scholar
Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Scientific reports. 2016;6:28484.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buscarinu MC, Cerasoli B, Annibali V, Policano C, Lionetto L, Capi M, Mechelli R, Romano S, Fornasiero A, Mattei G, et al. Altered intestinal permeability in patients with relapsing-remitting multiple sclerosis: A pilot study. Multiple sclerosis. 2017;23(3):442–6.
Article
PubMed
Google Scholar
Dendrou CA, Fugger L, Friese MA. Immunopathology of multiple sclerosis. Nat Rev Immunol. 2015;15(9):545–58.
Article
CAS
PubMed
Google Scholar
Chu F, Shi M, Lang Y, Shen D, Jin T, Zhu J, Cui L. Gut microbiota in multiple sclerosis and experimental autoimmune encephalomyelitis: current applications and future perspectives. Mediators of inflammation. 2018;2018:8168717.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ezendam J, de Klerk A, Gremmer ER, van Loveren H. Effects of Bifidobacterium animalis administered during lactation on allergic and autoimmune responses in rodents. Clinical and experimental immunology. 2008;154(3):424–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takata K, Kinoshita M, Okuno T, Moriya M, Kohda T, Honorat JA, Sugimoto T, Kumanogoh A, Kayama H, Takeda K, et al. The lactic acid bacterium Pediococcus acidilactici suppresses autoimmune encephalomyelitis by inducing IL-10-producing regulatory T cells. PloS one. 2011;6(11):e27644.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Lynch S, Waubant E. Centers USNoPM: Gut microbiota composition and relapse risk in pediatric MS: a pilot study. Journal of the neurological sciences. 2016;363:153–7.
Article
PubMed
PubMed Central
Google Scholar
Adamczyk-Sowa M, Medrek A, Madej P, Michlicka W, Dobrakowski P. Does the gut microbiota influence immunity and inflammation in multiple sclerosis pathophysiology? Journal of immunology research. 2017;2017:7904821.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ochoa-Reparaz J, Mielcarz DW, Ditrio LE, Burroughs AR, Foureau DM, Haque-Begum S, Kasper LH. Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. Journal of immunology. 2009;183(10):6041–50.
Article
CAS
Google Scholar
Bron PA, Kleerebezem M, Brummer RJ, Cani PD, Mercenier A, MacDonald TT, Garcia-Rodenas CL, Wells JM. Can probiotics modulate human disease by impacting intestinal barrier function? The British journal of nutrition. 2017;117(1):93–107.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wing AC, Kremenchutzky M. Multiple sclerosis and faecal microbiome transplantation: are you going to eat that? Beneficial microbes. 2019;10(1):27–32.
Article
CAS
PubMed
Google Scholar
Fernandes CP, Oliveira FA, Silva PG, Alves AP, Mota MR, Montenegro RC, Burbano RM, Seabra AD, Lobo Filho JG, Lima DL, et al. Molecular analysis of oral bacteria in dental biofilm and atherosclerotic plaques of patients with vascular disease. International journal of cardiology. 2014;174(3):710–2.
Article
PubMed
Google Scholar
Apfalter P, Hammerschlag MR, Boman J. Reliability of nested PCR for the detection of Chlamydia pneumoniae in carotid artery atherosclerosis. Stroke. 2003;34(7):e73–5 author reply e73-75.
Article
CAS
PubMed
Google Scholar
Mitra S, Drautz-Moses DI, Alhede M, Maw MT, Liu Y, Purbojati RW, Yap ZH, Kushwaha KK, Gheorghe AG, Bjarnsholt T, et al. In silico analyses of metagenomes from human atherosclerotic plaque samples. Microbiome. 2015;3:38.
Article
PubMed
PubMed Central
Google Scholar
Karlsson FH, Fak F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, Backhed F, Nielsen J. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature communications. 2012;3:1245.
Article
PubMed
CAS
Google Scholar
Ufnal M, Zadlo A, Ostaszewski R. TMAO: a small molecule of great expectations. Nutrition. 2015;31(11-12):1317–23.
Article
CAS
PubMed
Google Scholar
Skagen K, Troseid M, Ueland T, Holm S, Abbas A, Gregersen I, Kummen M, Bjerkeli V, Reier-Nilsen F, Russell D, et al. The carnitine-butyrobetaine-trimethylamine-N-oxide pathway and its association with cardiovascular mortality in patients with carotid atherosclerosis. Atherosclerosis. 2016;247:64–9.
Article
CAS
PubMed
Google Scholar
Lau K, Srivatsav V, Rizwan A, Nashed A, Liu R, Shen R, Akhtar M. Bridging the gap between gut microbial dysbiosis and cardiovascular diseases. Nutrients. 2017:9(8).
Tang WHW, Backhed F, Landmesser U, Hazen SL. Intestinal microbiota in cardiovascular health and disease: JACC State-of-the-Art Review. Journal of the American College of Cardiology. 2019;73(16):2089–105.
Article
PubMed
PubMed Central
Google Scholar
Kiessling G, Schneider J, Jahreis G. Long-term consumption of fermented dairy products over 6 months increases HDL cholesterol. European journal of clinical nutrition. 2002;56(9):843–9.
Article
CAS
PubMed
Google Scholar
Rerksuppaphol S, Rerksuppaphol L. A randomized double-blind controlled trial of Lactobacillus acidophilus plus Bifidobacterium bifidum versus placebo in patients with hypercholesterolemia. Journal of clinical and diagnostic research : JCDR. 2015;9(3):KC01–4.
PubMed
PubMed Central
Google Scholar
Qiu L, Tao X, Xiong H, Yu J, Wei H. Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice. Food & function. 2018;9(8):4299–309.
Article
CAS
Google Scholar
Benakis C, Brea D, Caballero S, Faraco G, Moore J, Murphy M, Sita G, Racchumi G, Ling L, Pamer EG, et al. Commensal microbiota affects ischemic stroke outcome by regulating intestinal gammadelta T cells. Nature medicine. 2016;22(5):516–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pussinen PJ, Alfthan G, Jousilahti P, Paju S, Tuomilehto J. Systemic exposure to Porphyromonas gingivalis predicts incident stroke. Atherosclerosis. 2007;193(1):222–8.
Article
CAS
PubMed
Google Scholar
Kawato T, Tanaka H, Tabuchi M, Ooshima K, Nakai K, Yamashita Y, Maeno M. Continual Gram-negative bacterial challenge accelerates stroke onset in stroke-prone spontaneously hypertensive rats. Clinical and experimental hypertension. 2013;35(1):28–34.
Article
CAS
PubMed
Google Scholar
Zhu W, Wang Z, Tang WHW, Hazen SL. Gut microbe-generated trimethylamine N-oxide from dietary choline is prothrombotic in subjects. Circulation. 2017;135(17):1671–3.
Article
PubMed
PubMed Central
Google Scholar
Yin J, Liao SX, He Y, Wang S, Xia GH, Liu FT, Zhu JJ, You C, Chen Q, Zhou L, et al. Dysbiosis of gut microbiota with reduced trimethylamine-N-oxide level in patients with large-artery atherosclerotic stroke or transient ischemic attack. Journal of the American Heart Association. 2015:4(11).
Shikata F, Shimada K, Sato H, Ikedo T, Kuwabara A, Furukawa H, Korai M, Kotoda M, Yokosuka K, Makino H, et al. Potential influences of gut microbiota on the formation of intracranial aneurysm. Hypertension. 2019;73(2):491–6.
Article
CAS
PubMed
Google Scholar
Fischer A, Zalvide J, Faurobert E, Albiges-Rizo C, Tournier-Lasserve E. Cerebral cavernous malformations: from CCM genes to endothelial cell homeostasis. Trends in molecular medicine. 2013;19(5):302–8.
Article
CAS
PubMed
Google Scholar
Tang AT, Choi JP, Kotzin JJ, Yang Y, Hong CC, Hobson N, Girard R, Zeineddine HA, Lightle R, Moore T, et al. Endothelial TLR4 and the microbiome drive cerebral cavernous malformations. Nature. 2017;545(7654):305–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Winek K, Engel O, Koduah P, Heimesaat MM, Fischer A, Bereswill S, Dames C, Kershaw O, Gruber AD, Curato C, et al. Depletion of cultivatable gut microbiota by broad-spectrum antibiotic pretreatment worsens outcome after murine stroke. Stroke. 2016;47(5):1354–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boumis E, Capone A, Galati V, Venditti C, Petrosillo N. Probiotics and infective endocarditis in patients with hereditary hemorrhagic` telangiectasia: a clinical case and a review of the literature. BMC Infect Dis. 2018;18(1):65.
Article
PubMed
PubMed Central
Google Scholar
Sun Y, Zhang M, Chen CC, Gillilland M, 3rd, Sun X, El-Zaatari M, Huffnagle GB, Young VB, Zhang J, Hong SC et al: Stress-induced corticotropin-releasing hormone-mediated NLRP6 inflammasome inhibition and transmissible enteritis in mice. Gastroenterology 2013, 144(7):1478-1487, 1487 e1471-1478.
Article
CAS
Google Scholar
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, et al. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560–4.
Article
CAS
PubMed
Google Scholar
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555(7695):210–5.
Article
CAS
PubMed
Google Scholar
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016;352(6285):565–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jonsson AL, Backhed F. Role of gut microbiota in atherosclerosis. Nature reviews Cardiology. 2017;14(2):79–87.
Article
CAS
PubMed
Google Scholar
Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, et al. Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(48):17224–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mouse Genome Sequencing C, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420(6915):520–62.
Article
CAS
Google Scholar
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS biology. 2009;7(5):e1000112.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cellular and molecular life sciences : CMLS. 2018;75(1):149–60.
Article
CAS
PubMed
Google Scholar
Scholtens PA, Oozeer R, Martin R, Amor KB, Knol J. The early settlers: intestinal microbiology in early life. Annual review of food science and technology. 2012;3:425–47.
Article
CAS
PubMed
Google Scholar
Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, Ben-Yacov O, Lador D, Avnit-Sagi T, Lotan-Pompan M, et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell. 2015;163(5):1079–94.
Article
CAS
PubMed
Google Scholar
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, et al. Towards standards for human fecal sample processing in metagenomic studies. Nature biotechnology. 2017;35(11):1069–76.
Article
CAS
PubMed
Google Scholar
Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, et al. Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(22):E2329–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S. Microbiome Quality Control Project C et al: Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nature biotechnology. 2017;35(11):1077–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shah N, Tang H, Doak TG, Ye Y. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2011:165–76.
Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR. Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environmental microbiology reports. 2012;4(2):248–56.
Article
PubMed
Google Scholar
Poretsky R, Rodriguez RL, Luo C, Tsementzi D, Konstantinidis KT. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PloS one. 2014;9(4):e93827.
Article
PubMed
PubMed Central
CAS
Google Scholar
Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, Grice EA. Skin microbiome surveys are strongly influenced by experimental design. The Journal of investigative dermatology. 2016;136(5):947–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nature methods. 2016;13(5):435–8.
Article
CAS
PubMed
Google Scholar
Winek K, Meisel A, Dirnagl U. Gut microbiota impact on stroke outcome: fad or fact? Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism. 2016;36(5):891–8.
Article
Google Scholar