Wu X, Xia Y, He F, et al. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. Microbiome. 2021;9:60.
Article
Google Scholar
Li XV, Leonardi I, Iliev ID. Gut mycobiota in immunity and inflammatory disease. Immunity. 2019;50:1365–79.
Article
Google Scholar
Woo V, Alenghat T. Epigenetic regulation by gut microbiota. Gut Microbes. 2022;14:2022407.
Article
Google Scholar
Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30:492–506.
Article
Google Scholar
Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med. 2016;375:2369–79.
Article
Google Scholar
Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19:55–71.
Article
Google Scholar
Jakobsson HE, Abrahamsson TR, Jenmalm MC, et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut. 2014;63:559–66.
Article
Google Scholar
Rodríguez JM, Murphy K, Stanton C, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26:26050.
Google Scholar
Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.
Article
Google Scholar
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Article
Google Scholar
Valdes AM, Walter J, Segal E, et al. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.
Article
Google Scholar
Shafquat A, Joice R, Simmons SL, et al. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 2014;22:261–6.
Article
Google Scholar
Allegretti JR, Kassam Z, Osman M, et al. The 5D framework: a clinical primer for fecal microbiota transplantation to treat Clostridium difficile infection. Gastrointest Endosc. 2018;87:18–29.
Article
Google Scholar
van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407–15.
Article
Google Scholar
Allegretti JR, Mullish BH, Kelly C, et al. The evolution of the use of faecal microbiota transplantation and emerging therapeutic indications. Lancet. 2019;394(10196):420–31.
Article
Google Scholar
Rossen NG, Fuentes S, van der Spek MJ, et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology. 2015;149:110-118.e4.
Article
Google Scholar
Moayyedi P, Surette MG, Kim PT, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149:102–9.
Article
Google Scholar
Paramsothy S, Kamm MA, Kaakoush NO, et al. Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet. 2017;389:1218–28.
Article
Google Scholar
Costello SP, Hughes PA, Waters O, et al. Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial. JAMA. 2019;321:156–64.
Article
Google Scholar
Bajaj JS, Fagan A, Gavis EA, et al. Long-term outcomes of fecal microbiota transplantation in patients with cirrhosis. Gastroenterology. 2019;156:1921-1923.e3.
Article
Google Scholar
Bajaj JS, Salzman NH, Acharya C, et al. Fecal microbial transplant capsules are safe in hepatic encephalopathy: a phase 1, randomized, placebo-controlled trial. Hepatology. 2019;70:1690–703.
Article
Google Scholar
Shah A, Macdonald GA, Morrison M, et al. Targeting the gut microbiome as a treatment for primary sclerosing cholangitis: a conceptional framework. Am J Gastroenterol. 2020;115:814–22.
Article
Google Scholar
Mocanu V, Zhang Z, Deehan EC, et al. Fecal microbial transplantation and fiber supplementation in patients with severe obesity and metabolic syndrome: a randomized double-blind, placebo-controlled phase 2 trial. Nat Med. 2021;27:1272–9.
Article
Google Scholar
Yu EW, Gao L, Stastka P, et al. Fecal microbiota transplantation for the improvement of metabolism in obesity: the FMT-TRIM double-blind placebo-controlled pilot trial. PLoS Med. 2020;17:e1003051.
Article
Google Scholar
Zhao Z, Ning J, Bao XQ, et al. Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis. Microbiome. 2021;9:226.
Article
Google Scholar
Hou YF, Shan C, Zhuang SY, et al. Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease. Microbiome. 2021;9:34.
Article
Google Scholar
Kang DW, Adams JB, Gregory AC, et al. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017;5:10.
Article
Google Scholar
Yang J, Fu X, Liao X, et al. Effects of gut microbial-based treatments on gut microbiota, behavioral symptoms, and gastrointestinal symptoms in children with autism spectrum disorder: a systematic review. Psychiatry Res. 2020;293:113471.
Article
Google Scholar
Sorboni SG, Moghaddam HS, Jafarzadeh-Esfehani R, et al. A comprehensive review on the role of the gut microbiome in human neurological disorders. Clin Microbiol Rev. 2022;35:e0033820.
Article
Google Scholar
Aria M, Cuccurullo C. Bibliometrix: an R-tool for comprehensive science mapping analysis. J Informetrics. 2017;11:959–75.
Article
Google Scholar
Chen C. Searching for intellectual turning points: progressive knowledge domain visualization. Proc Natl Acad Sci USA. 2004;101(Suppl 1(Suppl 1)):5303–10.
Article
Google Scholar
Chen C, Dubin R, Kim MC. Emerging trends and new developments in regenerative medicine: a scientometric update (2000–2014). Expert Opin Biol Ther. 2014;14:1295–317.
Article
Google Scholar
Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis. 2011;53:994–1002.
Article
Google Scholar
McDonald LC, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis. 2018;66:e1–48.
Article
Google Scholar
Bakken JS, Borody T, Brandt LJ, et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2011;9:1044–9.
Article
Google Scholar
Routy B, Le Chatelier E, Derosa L, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science. 2018;359:91–7.
Article
Google Scholar
Quraishi MN, Widlak M, Bhala N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017;46:479–93.
Article
Google Scholar
Kao D, Roach B, Silva M, et al. Effect of oral capsule– vs. colonoscopy-delivered fecal microbiota transplantation on recurrent Clostridium difficile infection: a randomized clinical trial. JAMA. 2017;318:1985–93.
Article
Google Scholar
Cammarota G, Ianiro G, Tilg H, et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017;66:569–80.
Article
Google Scholar
Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108:500–8.
Article
Google Scholar
Surawicz CM, Brandt LJ, Binion DG, et al. Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am J Gastroenterol. 2013;108(4):478–99.
Article
Google Scholar
Gopalakrishnan V, Spencer CN, Nezi L, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018;359:97–103.
Article
Google Scholar
Kootte RS, Levin E, Salojärvi J, et al. Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition. Cell Metab. 2017;26:611-619.e6.
Article
Google Scholar
Bajaj JS, Kassam Z, Fagan A, et al. Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: a randomized clinical trial. Hepatology. 2017;66:1727–38.
Article
Google Scholar
Shono Y, Docampo MD, Peled JU, et al. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med. 2016;8:339ra71.
Article
Google Scholar
Chen C, Hu Z, Liu S, et al. Emerging trends in regenerative medicine: a scientometric analysis in CiteSpace. Expert Opin Biol Ther. 2012;12:593–608.
Article
Google Scholar
Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–9.
Article
Google Scholar
Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc. 2013;78:240–9.
Article
Google Scholar
Kelly CR, Kahn S, Kashyap P, et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology. 2015;149:223–37.
Article
Google Scholar
Leshem A, Horesh N, Elinav E. Fecal microbial transplantation and its potential application in cardiometabolic syndrome. Front Immunol. 2019;10:1341.
Article
Google Scholar
Brandt LJ. Fecal microbiota therapy with a focus on Clostridium difficile infection. Psychosom Med. 2017;79:868–73.
Article
Google Scholar
Sokol H, Landman C, Seksik P, et al. Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study. Microbiome. 2020;8:12.
Article
Google Scholar
El-Salhy M, Hatlebakk JG, Gilja OH, et al. Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study. Gut. 2020;69:859–67.
Article
Google Scholar
Cammarota G, Ianiro G, Kelly CR, et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice. Gut. 2019;68:2111–21.
Article
Google Scholar
DeFilipp Z, Bloom PP, Torres Soto M, et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N Engl J Med. 2019;381:2043–50.
Article
Google Scholar
Jiang ZD, Ajami NJ, Petrosino JF, et al. Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection—fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy. Aliment Pharmacol Ther. 2017;45:899–908.
Article
Google Scholar
Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–80.
Article
Google Scholar
Wen L, Ley RE, Volchkov PY, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature. 2008;455:1109–13.
Article
Google Scholar
Rosvall M, Bergstrom CT. Mapping change in large networks. PLoS ONE. 2010;5:e8694.
Article
Google Scholar
Haifer C, Paramsothy S, Kaakoush NO, et al. Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial. Lancet Gastroenterol Hepatol. 2022;7:141–51.
Article
Google Scholar
Yao Y, Cai X, Fei W, et al. The role of short-chain fatty acids in immunity, inflammation and metabolism. Crit Rev Food Sci Nutr. 2022;62:1–12.
Article
Google Scholar
Parada Venegas D, De la Fuente MK, Landskron G, et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019;10:277.
Article
Google Scholar
Rios-Covian D, González S, Nogacka AM, et al. An overview on fecal branched short-chain fatty acids along human life and as related with body mass index: associated dietary and anthropometric factors. Front Microbiol. 2020;11:973.
Article
Google Scholar
Cook SI, Sellin JH. Review article: short chain fatty acids in health and disease. Aliment Pharmacol Ther. 1998;12:499–507.
Article
Google Scholar
Gill PA, van Zelm MC, Muir JG, et al. Review article: short chain fatty acids as potential therapeutic agents in human gastrointestinal and inflammatory disorders. Aliment Pharmacol Ther. 2018;48:15–34.
Article
Google Scholar
Pluznick JL. Microbial short-chain fatty acids and blood pressure regulation. Curr Hypertens Rep. 2017;19:25.
Article
Google Scholar
Tahara Y, Yamazaki M, Sukigara H, et al. Gut microbiota-derived short chain fatty acids induce circadian clock entrainment in mouse peripheral tissue. Sci Rep. 2018;8:1395.
Article
Google Scholar
Erny D, de Angelis ALH, Prinz M. Communicating systems in the body: how microbiota and microglia cooperate. Immunology. 2017;150:7–15.
Article
Google Scholar
Bell KJ, Saad S, Tillett BJ, et al. Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation. Microbiome. 2022;10:9.
Article
Google Scholar
Dąbek-Drobny A, Kaczmarczyk O, Woźniakiewicz M, et al. Association between fecal short-chain fatty acid levels, diet, and body mass index in patients with inflammatory bowel disease. Biology. 2022;11:108.
Article
Google Scholar
Chen SJ, Chen CC, Liao HY, et al. Association of fecal and plasma levels of short-chain fatty acids with gut microbiota and clinical severity in Parkinson disease patients. Neurology. 2022. https://doi.org/10.1212/WNL.0000000000013225.
Article
Google Scholar
De Pablo-Fernandez E, Gebeyehu GG, Flain L, et al. The faecal metabolome and mycobiome in Parkinson’s disease. Parkinsonism Relat Disord. 2022;95:65–9.
Article
Google Scholar
Derrien M, Vaughan EE, Plugge CM, et al. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol. 2004;54:1469–76.
Article
Google Scholar
Collado MC, Derrien M, Isolauri E, et al. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007;73:7767–70.
Article
Google Scholar
Derrien M, Collado MC, Ben-Amor K, et al. The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol. 2008;74:1646–8.
Article
Google Scholar
Yan J, Sheng L, Li H. Akkermansia muciniphila: is it the Holy Grail for ameliorating metabolic diseases? Gut Microbes. 2021;13:1984104.
Article
Google Scholar
Zhang J, Ni Y, Qian L, et al. Decreased abundance of Akkermansia muciniphila leads to the impairment of insulin secretion and glucose homeostasis in lean type 2 diabetes. Adv Sci. 2021;8:e2100536.
Article
Google Scholar
Dao MC, Belda E, Prifti E, et al. Akkermansia muciniphila abundance is lower in severe obesity, but its increased level after bariatric surgery is not associated with metabolic health improvement. Am J Physiol Endocrinol Metab. 2019;317:E446–59.
Article
Google Scholar
Borgo F, Verduci E, Riva A, et al. Relative abundance in bacterial and fungal gut microbes in obese children: a case control study. Child Obes. 2017;13:78–84.
Article
Google Scholar
Thingholm LB, Rühlemann MC, Koch M, et al. Obese individuals with and without type 2 diabetes show different gut microbial functional capacity and composition. Cell Host Microbe. 2019;26:252-264.e10.
Article
Google Scholar
Leyrolle Q, Cserjesi R, Mulders MDGH, et al. Specific gut microbial, biological, and psychiatric profiling related to binge eating disorders: a cross-sectional study in obese patients. Clin Nutr. 2021;40:2035–44.
Article
Google Scholar
Valentini V, Silvestri V, Marraffa F, et al. Gut microbiome profile in psoriatic patients treated and untreated with biologic therapy. J Dermatol. 2021;48:786–93.
Article
Google Scholar
Beaumont W. Nutrition Classics. Experiments and observations on the gastric juice and the physiology of digestion. By William Beaumont. Plattsburgh. Printed by F. P. Allen. 1833. Nutr Rev. 1977;35:144–5.
Article
Google Scholar
Cleary JL, Condren AR, Zink KE, et al. Calling all hosts: Bacterial communication in situ. Chem. 2017;2:334–58.
Article
Google Scholar
Clemente JC, Ursell LK, Parfrey LW, et al. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148:1258–70.
Article
Google Scholar
Karst SM. The influence of commensal bacteria on infection with enteric viruses. Nat Rev Microbiol. 2016;14:197–204.
Article
Google Scholar
Turroni S, Brigidi P, Cavalli A, et al. Microbiota-host transgenomic metabolism, bioactive molecules from the inside. J Med Chem. 2018;61:47–61.
Article
Google Scholar
Cryan JF, O’Riordan KJ, Cowan CSM, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013.
Article
Google Scholar
Tillisch K, Labus J, Kilpatrick L, et al. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology. 2013;144:1394-1401.e14014.
Article
Google Scholar
Smith AP, Sutherland D, Hewlett P. An investigation of the acute effects of oligofructose-enriched inulin on subjective wellbeing, Mood and Cognitive Performance. Nutrients. 2015;7:8887–96.
Article
Google Scholar
Lew LC, Hor YY, Yusoff NAA, et al. Probiotic Lactobacillus plantarum P8 alleviated stress and anxiety while enhancing memory and cognition in stressed adults: a randomised, double-blind, placebo-controlled study. Clin Nutr. 2019;38:2053–64.
Article
Google Scholar
Akbari E, Asemi Z, Daneshvar Kakhaki R, et al. Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind and controlled trial. Front Aging Neurosci. 2016;8:256.
Article
Google Scholar
Grimaldi R, Gibson GR, Vulevic J, et al. A prebiotic intervention study in children with autism spectrum disorders (ASDs). Microbiome. 2018;6:133.
Article
Google Scholar
Miyaoka T, Kanayama M, Wake R, et al. Clostridium butyricum MIYAIRI 588 as adjunctive therapy for treatment-resistant major depressive disorder: a prospective open-label trial. Clin Neuropharmacol. 2018;41:151–5.
Article
Google Scholar
Colica C, Avolio E, Bollero P, et al. Evidences of a new psychobiotic formulation on body composition and anxiety. Mediators Inflamm. 2017;2017:5650627.
Article
Google Scholar
Chong HX, Yusoff NAA, Hor YY, et al. Lactobacillus plantarum DR7 alleviates stress and anxiety in adults: a randomised, double-blind, placebo-controlled study. Benef Microbes. 2019;10:355–73.
Article
Google Scholar
Castro-Nallar E, Bendall ML, Pérez-Losada M, et al. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ. 2015;3:e1140.
Article
Google Scholar