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Human gut microbiota/microbiome in health and diseases: a review

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Abstract

The human gut microbiota has received considerable interest in the recent years and our knowledge of the inhabitant species and their potential applications is increased particularly after the development of metagenomic studies. Gut microbiota is highly diverse and harboring trillions of microorganisms in human digestive system. The shaping and multiplication of gut microbiome starts at birth, while the modification of their composition depends mainly on various genetic, nutritional and environmental factors. The modification in the composition and function of the gut microbiota can change intestinal permeability, digestion and metabolism as well as immune responses. The pro inflammatory state caused by alternation of gut microbiota balance lead to the onset of many diseases ranging from gastrointestinal and metabolic conditions to immunological and neuropsychiatric diseases. In this context, the present review clarifies the role of gut microbiota in maintaining host health and investigates how nutritional and environmental factors affect the gut microbial structure and function. In addition, many therapeutic strategies of gut microbiota aimed at modulating and restoring of the intestinal ecosystem balance have been surveyed.

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References

  • Abdollahi-Roodsaz S, Abramson S, Scher J (2016) The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions. Nat Rev Rheum 12:446–455

    Article  CAS  Google Scholar 

  • Abedon S, Kuhl S, Blasdel B, Kutter E (2011) Phage treatment of human infections. Bacteriophage 1:66–85

    Article  PubMed  PubMed Central  Google Scholar 

  • Agans R, Rigsbee L, Kenche H, Michail S, Khamis H, Paliy O (2011) Distal gut microbiota of adolescent children is different from that of adults. FEMS Microbiol Ecol 77:404–412

    Article  CAS  PubMed  Google Scholar 

  • Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA et al (2018) Exercise alters gut microbiota composition and function in lean and obese humans. Med Sci Sport Exer 50:747–757

    Article  Google Scholar 

  • Ambalam P, Raman M, Purama R, Doble M (2016) Probiotics, prebiotics and colorectal cancer prevention. Best Pract Res Clin Gastroenterol 30:119–131

    Article  PubMed  Google Scholar 

  • Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, Kito K, Sugimoto M, Kobayashi T (2016) Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population. J Clin Biochem Nutr 59:65–70

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ann M, Fergus S (2006) The gut flora as a forgotten organ. EMBO Rep 7(7):688–693

    Article  CAS  Google Scholar 

  • Aroniadis O, Brandt L, Oneto C, Feuerstadt P, Sherman A, Wolkoff A, Downs I, Zanetti A, Ramos Y, Cotto C et al (2018) A double-blind, randomized, placebo-controlled trial of fecal microbiota transplantation capsules (FMTC) for the treatment of diarrhea-predominant irritable bowel syndrome (IBS-D). Gastroenterology 154(6):154–155

    Article  Google Scholar 

  • Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende D, Fernandes G, Tap J, Bruls T, Batto J et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Avoli M, Krnjević K (2016) The long and winding road to gamma-amino-butyric acid as neurotransmitter. Can J Neurol Sci 43:219–226

    Article  PubMed  Google Scholar 

  • Azad M, Konya T, Maughan H, Guttman D, Field C, Chari S et al (2013) Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185:385–394

    Article  PubMed  PubMed Central  Google Scholar 

  • Backhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva P et al (2015) Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17:690–703

    Article  PubMed  CAS  Google Scholar 

  • Balious S, Adamakim M, Spandidos D, Kyriakopoulos A, Christodoulou I, Zoumpourlis V (2019) The microbiome, its molecular mechanisms and its potential as a therapeutic strategy against colorectal carcinogenesis (review). World Acad Sci J 1:3–19

    Google Scholar 

  • Bansal T, Alaniz RC, Wood TK, Jayaraman A (2010) The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc Natl Acad Sci USA107:228–233

    Article  Google Scholar 

  • Bennet S, Ohman L, Simren M (2015) Gut microbiota as potential orchestrators of irritable bowel syndrome. Gut Liver 9:318–931

    Article  PubMed  PubMed Central  Google Scholar 

  • Betrapally N, Gillevet P, Bajaj J (2016) Changes in the intestinal microbiome and alcoholic and nonalcoholic liver diseases: causes or effects? Gastroenterology 150:1745–1770

    Article  PubMed  Google Scholar 

  • Biagi E, Rampelli S, Turroni S, Quercia S, Candela M, Brigidi P (2017) The gut microbiota of centenarians: signatures of longevity in the gut microbiota profile. Mech Age Dev 165:180–184

    Article  Google Scholar 

  • Biedermann L, Brulisauer K, Zeitz J et al (2014) Smoking cessation alters intestinal microbiota: insights from quantitative investigations on human fecal samples using FISH. Inflam Bowel Dis 20:1496–1501

    Article  Google Scholar 

  • Biedermann L, Zeitz J, Mwinyi J et al (2013) Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans. PLOS One 8:59–63

    Article  CAS  Google Scholar 

  • Bindels L, Porporato P, Dewulf E, Verrax J, Neyrinck A, Martin J, Scott K, Calderon P, Feron O, Muccioli G et al (2012) Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. Br J Cancer 107:1337–1344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolte ER (1998) Autism and Clostridium tetani. Med Hypotheses 51(2):133–144

    Article  CAS  PubMed  Google Scholar 

  • Breyner NM, Michon C, de Sousa CS, Vilas Boas PB, Chain F, Azevedo VA, Langella P, Chatel JM (2017) Microbial Anti-Inflammatory Molecule (MAM) from Faecalibacterium prausnitzii shows a protective effect on DNBS and DSS-Induced Colitis model in mice through inhibition of NF-B Pathway. Front Microbiol 8:114–129

    Article  PubMed  PubMed Central  Google Scholar 

  • Bron P, Kleerebezem M, Brummer R, Cani P, Mercenier A, MacDonald T, Garcia-Rodenas C, Wells J (2017) Can probiotics modulate human disease by impacting intestinal barrier function? Br J Nutr 117(1):93–107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung D, Sampson H, Sicherer S, Clemente J (2016) Early-life gut microbiome composition and milk allergy resolution. J Allergy Clin Immunol 138(4):1122–1130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cammarota G, Ianiro G, Bibbò S, Gasbarrini A (2014) Fecal microbiota transplantation: A new old kid on the block for the management of gut microbiota-related disease. J Clin Gastroenterol 48:80–84

    Article  Google Scholar 

  • Cammarota G, Ianiro G, Tilg H, Rajilić-Stojanović M, Kump P, Satokari R, Sokol H, Arkkila P, Pintus C, Hart A, et al (2017) European FMT Working Group. European consensus conference on faecal microbiota transplantation in clinical practice. Gut 66:569–580

    Article  PubMed  Google Scholar 

  • Cani PD, Everard A (2017) Akkermansia muciniphila: A novel target controlling obesity, type 2 diabetes and inflammation? Front Microbiol 8:1226–1240

    Article  Google Scholar 

  • Carolina M (2018) Bone and the gut microbiome: a new dimension. J Lab Prec Med 3:96–106

    Article  Google Scholar 

  • Chang P, Hao L, Offermanns S, Medzhitov R (2014) The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci USA 111:2247–2252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen C, Huang X, Fang S, Yang H, He M, Zhao Y, Huang L (2018) Contribution of host genetics to the variation of microbial composition of cecum lumen and feces in pigs. Front Microbiol 9:2626–2639

    Article  PubMed  PubMed Central  Google Scholar 

  • Chimerel C, Emery E, Summers DK, Keyser U, Gribble FM, Reimann F (2014) Bacterial metabolite indole modulates incretin secretion from intestinal enteroendocrine L cells. Cell Report 9:1202–1208

    Article  CAS  Google Scholar 

  • Chu D, Ma J, Prince A, Antony K, Seferovic M, Aagaard K (2017) Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med 23(3):314–326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ciarlo E, Heinonen T, Herderschee J, Fenwick C, Mombelli M, Le Roy D, Roger T (2016) Impact of the microbial derived short chain fatty acid propionate on host susceptibility to bacterial and fungal infections in vivo. Sci Rep 6:37944–37962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD, Shanahan F, Dinan TG, Cryan JF (2013) The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol Psychiatry 18(6):666–673

    Article  CAS  PubMed  Google Scholar 

  • Clarke SF, Murphy EF, O’Sullivan O et al (2014) Exercise and associated dietary extremes impact on gut microbial diversity. Gut 63(12):1913–1920

    Article  CAS  PubMed  Google Scholar 

  • Clemente J, Ursell L, Parfrey L, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148(6):1258–1270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • David L, Maurice C, Carmody R, Gootenberg D, Button J, Wolfe B, Ling A, Devlin A, Varma Y, Fischbach M et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563

    Article  CAS  PubMed  Google Scholar 

  • Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Pratic G et al (2015) Phylogenetic and metabolic tracking of gut microbiota during perinatal development. PLoS One 10:137–247

    Google Scholar 

  • den Besten G, Bleeker A, Gerding A, van Eunen K, Havinga R, van Dijk TH, Oosterveer MH, Jonker JW, Groen AK, Reijngoud DJ, Bakker BM (2015) Short-chain fatty acids protect against high-fat diet–induced obesity via a PPARγ-dependent switch from lipogenesis to fat oxidation. Diabetes 64:2398–2408

    Article  CAS  Google Scholar 

  • Dethlefsen L, Relman DA (2010) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA 108:4554–4561

    Article  PubMed  PubMed Central  Google Scholar 

  • Dolan K, Chang E (2017) Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases. Mol Nutr Food Res 61–80

  • Durack J, Kimes N, Lin D, Rauch M, McKean M, McCauley K, Panzer A, Mar J, Cabana M, Lynch SV (2018) Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat Commun 9:707–720

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Estaki M, Pither J, Baumeister P et al (2016) Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. FASEB J 30(1):1027–1035

    Google Scholar 

  • Estruch R, Ros E, Salas-Salvado J, Covas M, Corella D, Aros F, Gomez- Gracia E, Ruiz-Gutierrez V, Fiol M, Lapetra J et al (2018) Primary prevention of cardiovascular disease with a mediterranean diet supplemented with extra-virgin olive oil or nuts. N Engl J Med 378:34–50

    Article  Google Scholar 

  • Fernández-Murga ML, Sanz Y (2016) Safety assessment of bacteroides uniformis CECT 7771 isolated from stools of healthy breast-fed infants. PLoS ONE 11:e0145503

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Firouzi S, Haghighatdoost F (2018) The effects of prebiotic, probiotic, and synbiotic supplementation on blood parameters of renal function: a systematic review and meta-analysis of clinical trials. Nutrition 51–52:104–113

    Article  PubMed  CAS  Google Scholar 

  • Flint H, Duncan S, Louis P (2017) The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 38:59–65

    Article  CAS  PubMed  Google Scholar 

  • Forouhi N, Krauss R, Taubes G, Willett W (2018) Dietary fat and cardiometabolic health: evidence, controversies, and consensus for guidelines. BMJ 361:21–39

    Google Scholar 

  • Forsythe P, Sudo N, Dinan T, Taylor V, Bienenstock J (2010) Mood and gut feelings. Brain Behav Immunol 24:9–16

    Article  Google Scholar 

  • Fouhy F, Watkins C, Hill C, O’Shea C, Nagle B, Dempsey E, O’Toole P, Ross R, Ryan CA, Stanton C (2019) Microbiome memory of perinatal factors that affect the gut microbiota four years after birth. Nat Commun 10:151–167

    Article  CAS  Google Scholar 

  • Frati F, Salvatori C, Incorvaia C, Bellucci A, Di G, Marcucci F, Esposito S (2019) The role of the microbiome in asthma: the gut–lung axis. Int J Mol Sci 20:123–135

    Article  CAS  Google Scholar 

  • Garcia-Rios A, Torres-Pena J, Perez-Jimenez F, Perez-Martinez P (2017) Gut microbiota: a new marker of cardiovascular disease. Curr Pharm Des 23(22):3233–3238

    Article  CAS  PubMed  Google Scholar 

  • Gaykema RP, Goehler LE, Lyte M (2004) Brain response to cecal infection with Campylobacter jejuni: analysis with Fos immunohistochemistry. Brain Behav Immunol 18(3):238–245

    Article  CAS  Google Scholar 

  • Ghoshal U, Shukla R, Ghoshal U, Gwee K, Ng S, Quigley E (2012) The gut microbiota and irritable bowel syndrome friend or foe? Int J Inflam: 151–185

  • Gianotti R, Moss A (2017) Fecal microbiota transplantation from Clostridium difficile to inflammatory bowel disease. Gastroenterol Hepatol 13:209–213

    Google Scholar 

  • Grant M, Baker J (2016) An overview of the effect of probiotics and exercise on mood and associated health conditions. Crit Rev Food Sci Nutr 23–47

  • Griffin J, Wang X, Stanley E (2015) Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. Circ Cardiovasc Genet 8:187–191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grivennikov S, Wang K, Mucida D, Stewart C, Schnabl B, Jauch D (2012) Adenoma-linked barrier defects and microbial products drive IL-23/ IL-17-mediated tumour growth. Nature 491:254–258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guarner F, Malagelada J (2003) Gut flora in health and disease. Lancet 361(9356):512–519

    Article  PubMed  Google Scholar 

  • Gupta S, Allen-Vercoe E, Petrof E (2016) Fecal microbiota transplantation in perspective. Ther Adv Gastroenterol 9(2):229–239

    Article  Google Scholar 

  • Hadi A, Mohammadi H, Miraghajani M, Ghaedi E (2018) Efficacy of synbiotic supplementation in patients with nonalcoholic fatty liver disease: a systematic review and meta-analysis of clinical trials synbiotic supplementation and NAFLD. Crit Rev Food Sci Nutr 27:1–12

    Google Scholar 

  • Hansen J, Sartor R (2015) Therapeutic manipulation of the microbiome in IBD: current results and future approaches. Curr Treat Opt Gastroenterol 13:105–120

    Article  Google Scholar 

  • Harsch I, Konturek P (2019) Adhesion ileus after fecal microbiota transplantation in longstanding radiation colitis. Case Rep Gastroint Med 6:1–4

    Google Scholar 

  • Harte A, Varma M, Tripathi G, McGee K, Al-Daghri N, Al-Attas O, Sabico S, O’Hare J, Ceriello A, Saravanan P (2012) High fat intake leads to acute postprandial exposure to circulating endotoxin in type 2 diabetic subjects. Diabetes Care 35:375–382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hasan N, Yang H (2019) Factors affecting the composition of the gut microbiota, and its modulation. Peer J: 7–38

  • Haynes M, Rohwer F (2011) The human virome. In: Nelson K, metagenomics of the human body 63–77

  • Hendijani F, Akbari V (2018) Probiotic supplementation for management of cardiovascular risk factors in adults with type II diabetes: a systematic review and meta-analysis. Clin Nutr 37(2):532–541

    Article  PubMed  Google Scholar 

  • Hills R, Pontefract B, Mishcon H, Black C, Sutton S, Theberge C (2019) Gut microbiome profound implications for diet and disease. Nutrition 11:1613–1653

    CAS  Google Scholar 

  • Hold G (2016) Gastrointestinal microbiota and colon cancer. Dig Dis 34:244–250

    Article  PubMed  Google Scholar 

  • Hollister E, Riehle K, Luna R, Weidler E, Rubio-Gonzales M, Mistretta T, Raza S, Doddapaneni H, Metcalf G, Muzny D (2015) Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome 3:36–45

    Article  PubMed  PubMed Central  Google Scholar 

  • Holvoet T, Joossens M, Wang J, Boelens J, Verhasselt B, Laukens D, Van Vlierberghe H, Hindryckx P, De Vos M, De Looze D, Raes J (2017) Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating. Gut: 66 (5) 980–982

  • Hsieh M (2014) The microbiome and probiotics in childhood. Semin Reprod Med 32:23–27

    Article  PubMed  PubMed Central  Google Scholar 

  • Hughes RL (2020) A review of the role of the gut microbiome in personalized sports nutrition. Front Nutr 6:191–218

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hwang IK, Yoo KY, Li H, Park OK, Lee CH, Choi JH, Jeong YG, Lee YL, Kim YM, Kwon YG, Won MH (2009) Indole-3-propionic acid attenuates neuronal damage and oxidative stress in the ischemic hippocampus. J Neurosci Res 87:2126–2137

    Article  CAS  PubMed  Google Scholar 

  • Iebba V, Totino V, Gagliardi A, Santangelo F, Cacciotti F, Trancassini M, Mancini C, Cicerone C, Corazziari E, Pantanella F, Schippa S (2016) Eubiosis and dysbiosis: the two sides of the microbiota. New Microbiol 39:1–12

    CAS  PubMed  Google Scholar 

  • Ikram S, Hassan N, Raffat M, Mirza S, Akram Z (2018) Systematic review and meta-analysis of double-blind, placebo-controlled, randomized clinical trials using probiotics in chronic periodontitis. J Invest Clin Dent 9(3):123–138

    Article  Google Scholar 

  • Isaac S, Scher J, Djukovic A, Jime´nez N, Littman D, Abramson S, Pamer E, Ubeda C (2016) Short-and long-term effects of oral vancomycin on the human intestinal microbiota. J Antimicrob Chem 72(1):128–136

    Article  CAS  Google Scholar 

  • Jakobsson H, Jernberg C, Andersson A, Sjolund-Karlsson M, Jansson J, Engstrand L (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLOS ONE 5(3):983–996

    Article  CAS  Google Scholar 

  • Jeffery I, O‘Toole P, Öhman L, Claesson M, Deane J, Quigley E, Simrén M (2012) An irritable bowel syndrome subtype defined by species- specific alterations in faecal microbiota. Gut 61:997–1006

    Article  PubMed  Google Scholar 

  • Jernberg C, Lo¨fmark S, Edlund C, Jansson J (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1(1):56–66

    Article  CAS  PubMed  Google Scholar 

  • Jethwani P, Grover K (2019) Gut microbiota in health and diseases—a review. Int J Curr Microbiol Appl Sci 8(8):1586–1599

    Article  CAS  Google Scholar 

  • Jiang C, Li G, Huang P, Liu Z, Zhao B (2017) The gut microbiota and Alzheimer’s disease. J Alzheimer's Dis 58:1–15

    Article  CAS  Google Scholar 

  • Jie Z, Xia H, Zhong S, Feng Q, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, Zhang D, Su Z, Fang Z, Lan Z, Li J, Xiao L, Li J et al (2017) The gut microbiome in atherosclerotic cardiovascular disease. Nat Commun 8(1):845–860

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johnsen P, Hilpusch F, Cavanagh J, Leikanger I, Kolstad C, Valle P, Goll R (2018) Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial. Lancet Gastroenterol Hepatol 3(1):17–24

    Article  PubMed  Google Scholar 

  • Kadooka Y, Sato M, Imaizumi K, Ogawa A, Ikuyama K, Akai Y, Okano M, Kagoshima M, Tsuchida T (2010) Regulation of abdominal adiposity by probiotics (Lactobacillus gasseri SBT2055) in adults with obese tendencies in a randomized controlled trial. Eur J Clin Nutr 64:636–643

    Article  CAS  PubMed  Google Scholar 

  • Kaikiri H, Miyamoto J, Kawakami T, Park SB, Kitamura N, Kishino S, Yonejima Y, Hisa K, Watanabe J, Ogita T et al (2017) Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice. Int J Food Sci Nutr 68:941–951

    Article  CAS  PubMed  Google Scholar 

  • Kang DW, Adams JB, Gregory AC et al (2017) Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome 5:10–22

    Article  PubMed  PubMed Central  Google Scholar 

  • Kang S, Denman S, Morrison M, Yu Z, Dore J, Leclerc M et al (2010) Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis 16:2034–2042

    Article  PubMed  Google Scholar 

  • Karczewski J, Troost F, Konings I, Dekker J, Kleerebezem M, Brummer R, Wells J (2010) Regulation of human epithelial tight junction proteins by Lactobacillus plantarum in vivo and protective effects on the epithelial barrier. Am J Physiol Gastrointest Liver Physiol 298(6):851–859

    Article  CAS  Google Scholar 

  • Karlsson F, Tremaroli V, Nielsen J, Backhed F (2013) Assessing the human gut microbiota in metabolic diseases. Diabetes 62(10):3341–3349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelly C, Zheng L, Campbell E, Saeedi B, Scholz C, Bayless A, Wilson K, Glover L, Kominsky D, Magnuson A, Weir T et al (2015a) Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17(5):662–671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP (2015b) Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 9:392–411

    PubMed  PubMed Central  Google Scholar 

  • Kelly JR, Borre Y, O’ Brien C, Patterson E, El Aidy S, Deane J et al (2016) Transferring the blues: depression associated gut microbiota induces neurobehavioural changes in the rat. J Psychiatry Res 82:109–118

    Article  Google Scholar 

  • Khan S, Jena G (2016) Sodium butyrate reduces insulin-resistance, fat accumulation and dyslipidemia in type-2 diabetic rat: A comparative study with metformin. Chem Biol Interact 254:124–134

    Article  CAS  PubMed  Google Scholar 

  • Khoruts A, Sadowsky M (2016) Understanding the mechanisms of faecal microbiota transplantation. Nat Rev Gastroenterol Hepatol 13(9):508–516

    Article  PubMed  PubMed Central  Google Scholar 

  • Klingensmith N, Coopersmith C (2016) The gut as the motor of multiple organ dysfunction in critical illness. Crit Care Clin 32(2):203–212

    Article  PubMed  PubMed Central  Google Scholar 

  • Knip M, Siljander H (2016) The role of the intestinal microbiota in type 1 diabetes mellitus. Nat Rev Endocrinol 12:154–167

    Article  CAS  PubMed  Google Scholar 

  • Kostic A, Gevers D, Pedamallu C, Michaud M, Duke F, Earl A et al (2012) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22:292–298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kristensen N, Bryrup T, Allin K, Nielsen T, Hansen T, Pedersen O (2016) Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Gen Med 8(1):52–63

    Google Scholar 

  • Kudelka M, Hinrichs B, Darby T, Moreno C, Nishio H, Cutler C, Wang J, Wu H, Zeng J, Wang Y et al (2016) Cosmc is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk. Proc Natl Acad Sci USA 113:14787–14792

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurilshikov A, Wijmenga C, Fu JY, Zhernakova A (2017) Host genetics and gut microbiome: challenges and perspectives. Trend Immunol 38:633–647

    Article  CAS  Google Scholar 

  • La Fata G, Weber P, Mohajeri M (2017) Probiotics and the gut immune system: indirect regulation. Probiot Antimicrob Proteins 10(1):11–21

    Article  CAS  Google Scholar 

  • Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM et al (2016) CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med 22:598–605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lane E, Zisman T, Suskind D (2017) The microbiota in inflammatory bowel disease: current and therapeutic insights. J Inflamm Res 10:63–73

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langdon A, Crook N, Dantas G (2016) The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Gen Med 8–17

  • Le Chatelier E, Nielsen T, Qin J et al (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546

    Article  PubMed  CAS  Google Scholar 

  • Le D (2017) 4th microbiome R&D and business collaboration forum and probiotics congress, the Netherlands. EBioMedicine 19:2–3

    Article  PubMed  PubMed Central  Google Scholar 

  • LeBlanc J, Milani C, de Giori G, Sesma F, van Sinderen D, Ventura M (2013) Bacteria as vitamin suppliers to their host: a gut bacteria perspective. Curr Opin Biotechnol 24:160–168

    Article  CAS  PubMed  Google Scholar 

  • Lee B, Bak Y (2011) Irritable bowel syndrome, gut microbiota and probiotics. J Neurogastroenterol Motil 17(3):252–266

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee S, Lim J, Kim B, Cho S, Kim N, Kim O et al (2015) Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing. Nutr Res Pract 9:242–257

    Article  PubMed  Google Scholar 

  • Leung C, Rivera L, Furness J, Angus P (2016) The role of the gut microbiota in NAFLD. Nat Rev Gastroenterol Hepatol 13:412–425

    Article  CAS  PubMed  Google Scholar 

  • Li S, Zhu A, Benes V, Costea P, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Saloja¨rvi J, Voigt A, Zeller G, Sunagawa S, de Vos W, Bork P (2016) Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 352(6285):586–589

    Article  CAS  PubMed  Google Scholar 

  • Lin L, Zhang J (2017) Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol 18:837–850

    Article  CAS  Google Scholar 

  • Louis P, Flint H (2017) Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 19:29–41

    Article  CAS  PubMed  Google Scholar 

  • Lv G, Cheng N, Wang H (2017) The gut microbiota, tumorigenesis, and liver diseases. Engineering 3:110–114

    Article  Google Scholar 

  • Ma Y, Liu J, Rhodes C, Nie Y, Zhang F (2017) Ethical issues in fecal microbiota transplantation in practice. Am J Bioeth 17:34–45

    Article  PubMed  Google Scholar 

  • Mariat D, Firmesse O, Levenez F, Guimaraes V, Sokol H, Dore et al (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123–137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Markowiak P, Slizewska K (2017) Effects of probiotics, prebiotics, and synbiotics on human health. Nutrition 9:1021–1039

    Google Scholar 

  • Martinez I, Stegen J, Maldonado-Gomez M, Eren A, Siba P, Greenhill A, Walter J (2015) The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes. Cell Rep 11:527–538

    Article  CAS  PubMed  Google Scholar 

  • McCoy A, Araujo-Perez F, Azcarate-Peril A, Yeh J, Sandler R, Keku T (2013) Fusobacterium is associated with colorectal adenomas. PLoS One 8:536–549

    Google Scholar 

  • McKean J, Naug H, Nikbakht E, Amiet B, Colson N (2017) Probiotics and subclinical psychological symptoms in healthy participants: a systematic review and meta-analysis. J Altern Complement Med 23:249–258

    Article  PubMed  Google Scholar 

  • Mezzelani A, Landini M, Facchiano F et al (2015) Environment, dysbiosis, immunity and sex-specific susceptibility: a translational hypothesis for regressive autism pathogenesis. Nutr Neurosci 18:145–161

    Article  PubMed  PubMed Central  Google Scholar 

  • Michael S (2016) Gut microbiota and host evolution scaling up symbiosis. Trends Ecol Evol 31(7):539–549

    Article  Google Scholar 

  • Mika A, Fleshner M (2016) Early-life exercise may promote lasting brain and metabolic health through gut bacterial metabolites. Immunol Cell Biol 94:151–157

    Article  CAS  PubMed  Google Scholar 

  • Mills S, Stanton C, Lane J, Smith G, Ross R (2019) Precision nutrition and the microbiome, Part I current state of the science nutrients 11: 923–968

  • Miyamoto J, Mizukure T, Park SB, Kishino S, Kimura I, Hirano K, Bergamo P, Rossi M, Suzuki T, Arita M et al (2015) A gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, ameliorates intestinal epithelial barrier impairment partially via GPR40-MEK-ERKpathway. J Biol Chem 290:2902–2918

    Article  CAS  PubMed  Google Scholar 

  • Mohajeri M, La Fata G, Steinert R, Weber P (2018) Relationship between gut microbiome and brain function. Nutr Rev 76(7):481–496

    Article  PubMed  Google Scholar 

  • Morris A, Beck J, Schloss P et al (2013) Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Res Crit Care Med 187:1067–1075

    Article  Google Scholar 

  • Morrison D, Preston T (2016) Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microb 7:189–200

    Article  Google Scholar 

  • Muscogiuri G, Balercia G, Barrea L, Cignarelli A, Giorgino F, Holst J, Laudisio D, Orio F, Tirabassi G, Colao A (2016) Gut A key player in the pathogenesis of type 2 diabetes? Crit Rev Food Sci Nutr 1–16

  • Nagpal R, Tsuji H, Takahashi T, Nomoto K, Kawashima K, Nagata S, Yamashiro Y (2017) Ontogenesis of the gut microbiota composition in healthy, full-term, vaginally born and breast-fed infants over the first 3 years of life: a quantitative bird’s-eye view. Front Microbiol 8:1388–1400

    Article  PubMed  PubMed Central  Google Scholar 

  • Neef A, Sanz Y (2013) Future for probiotic science in functional food and dietary supplement development. Curr Opin Clin Nutr Metab Care 16:679–687

    Article  CAS  PubMed  Google Scholar 

  • Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, Naito Y, Andoh A (2018) Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. J Gastroenterol 53(1):95–106

    Article  PubMed  Google Scholar 

  • O’Connor G, Lynch S, Bloomberg G, Kattan M, Wood R, Gergen P, Jaffee K, Calatroni A, Bacharier L, Beigelman A et al (2018) Early- life home environment and risk of asthma among inner-city children. J Allergy Clin Immunol 141:1468–1475

    Article  PubMed  Google Scholar 

  • Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao J, Abe F, Osawa R (2016) Age-related changes in gut microbiota composition from newborn to centenarian: a cross sectional study. BMC Microbiol 16(1):90–112

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ohland CL, Kish L, Bell H, Thiesen A, Hotte N, Pankiv E, Madsen KL (2013) Effects of Lactobacillus helveticus on murine behavior are dependent on diet and genotype and correlate with alterations in the gut microbiome. Psychoneuroendocrinology 38(9):1738–1747

    Article  CAS  PubMed  Google Scholar 

  • Parekh P, Balart L, Johnson D (2015) The influence of the gut microbiome on obesity, metabolic syndrome and gastrointestinal disease. Clin Trans Gastroent 6–15

  • Parracho H, Burrowes B, Enright M, McConville M, Harper D (2012) The role of regulated clinical trials in the development of bacteriophage therapeutics. J Mol Gen Med 6:279–286

    CAS  Google Scholar 

  • Parvaneh M, Karimi G, Jamaluddin R et al (2018) Lactobacillus helveticus (ATCC 27558) upregulates Runx2 and Bmp2 and modulates bone mineral density in ovariectomy-induced bone loss rats. Clin Int Aging 13:1555–1564

    Article  CAS  Google Scholar 

  • Pasco JA, Holloway K, Dobbin A, Kotowicz M, Williams L, Brennan S (2014) Body mass index and measures of body fat for defining obesity and underweight: a cross-sectional, population-based study. BMC Obes 1:9–16

    Article  PubMed  PubMed Central  Google Scholar 

  • Passos MCF, Moraes-Filho JP (2017) Intestinal microbiota in digestive diseases. Arq Gastroenterol 54:255–262

    Article  PubMed  Google Scholar 

  • Patel R, DuPont H (2015) New approaches for bacteriotherapy Prebiotics, new-generation probiotics, and synbiotics. Clin Infect Dis 60:108–121

    Article  Google Scholar 

  • Perry R, Peng L, Barry N, Cline G, Zhang D, Cardone R, Petersen K, Kibbey R, Goodman A, Shulman G (2016) Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. Nature 534:213–217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pevsner-Fischer M, Tuganbaev T, Meijer M, Zhang S, Zeng Z, Chen M, Elinav E (2016) Role of the microbiome in non-gastrointestinal cancers. World J Clin Oncol 7:200–213

    Article  PubMed  PubMed Central  Google Scholar 

  • Pistollato F, Cano S, Elio I et al (2016) Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease. Nutr Rev 74:624–634

    Article  PubMed  Google Scholar 

  • Plaza-Diaz J, Ruiz-Ojeda F, Vilchez-Padial L, Gil A (2017) Evidence of the anti-inflammatory effects of probiotics and synbiotics in intestinal chronic diseases. Nutrition 9:555–570

    Google Scholar 

  • Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D et al (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55–60

    Article  CAS  PubMed  Google Scholar 

  • Quigley E (2013) Gut bacteria in health and disease. Gastroenterol Hepatol 9:560–569

    Google Scholar 

  • Quraishi M, Sergeant M, Kay G, Iqbal T, Constantinidou C, Chan J, Trivedi P, Ferguson J, Adams D, Pallen M (2014) Probing the microbiota in PSC: the gut adherent microbiota of PSC-IBD is distinct to that of IBD and controls. Hepatology 60:264–267

    Google Scholar 

  • Raman M, Ambalam P, Kondepudi K, Pithva S, Kothari C, Patel A, Purama R, Dave JM, Vyas BR (2013) Potential of probiotics, prebiotics and synbiotics for management of colorectal cancer. Gut Microb 4:181–192

    Article  Google Scholar 

  • Ramnani P, Chitarrari R, Tuohy K, Grant J, Hotchkiss S, Philp K, Campbell R, Gill C, Rowland I (2012) In vitro fermentation and prebiotic potential of novel low molecular weight polysaccharides derived from agar and alginate seaweeds. Anaerobe 18(1):1–6

    Article  CAS  PubMed  Google Scholar 

  • Ray K (2015) Gut microbiota the gut virome and bacterial microbiome—the early years. Nat Rev Gastroenterol Hepatol 12:609–611

    Article  PubMed  Google Scholar 

  • Ray K (2018) Gut microbiota filling up on fibre for a healthy gut. Nat Rev Gastroenterol Hepatol 15(2):67–67

    Article  PubMed  Google Scholar 

  • Reyes A, Haynes M, Hanson N et al (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334–338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rhee S, Pothoulakis C, Mayer E (2009) Principles and clinical implications of the brain-gut-enteric microbiota axis. Nat Rev Gastroenterol Hepatol 6:306–314

    Article  CAS  PubMed  Google Scholar 

  • Robles-Alonso V, Guarner F (2013) Progress in the knowledge of the intestinal human microbiota. Nutr Hosp 28:553–557

    PubMed  Google Scholar 

  • Rosa EF, Silva AC, Ihara SS, Mora OA, Aboulafia J, Nouailhetas VL (2005) Habitual exercise program protects murine intestinal, skeletal, and cardiac muscles against aging. J Appl Physiol 99(4):1569–1575

    Article  PubMed  Google Scholar 

  • Rosenfeld CS (2015) Microbiome disturbances and autism spectrum disorders. Drug Metab Dispos Biol Fate Chem 43:1557–1571

    Article  CAS  PubMed  Google Scholar 

  • Roshanravan N, Mahdavi R, Alizadeh E, Jafarabadi M, Hedayati M, Ghavami A, Alipour S, Alamdari N, Barati M, Ostadrahimi A (2017) Effect of butyrate and inulin supplementation on glycemic status, lipid profile and glucagon-like peptide 1 level in patients with type 2 diabetes: a randomized double-blind, placebo-controlled trial. Horm Metab Res 49:886–891

    Article  CAS  PubMed  Google Scholar 

  • Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea P, Godneva A, Kalka I, Bar N, Shilo S, Lador D et al (2018) Environment dominates over host genetics in shaping human gut microbiota. Nature 555:210–215

    Article  CAS  PubMed  Google Scholar 

  • Routy B, Le Chatelier E, Derosa L, Duong CP, Alou M, Daillere R, Fluckiger A, Messaoudene M, Rauber C, Roberti M et al (2018) Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359:91–97

    Article  CAS  PubMed  Google Scholar 

  • Sampson T, Mazmanian S (2015) Control of brain development, function, and behavior by the microbiome. Cell Host Microbe 17(5):565–576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scarpellini E, Ianiro G, Attili F, Bassanelli C, De Santis A, Gasbarrini A (2015) The human gut microbiota and virome: potential therapeutic implications. Dig Liver Dis 47:1007–1012

    Article  PubMed  PubMed Central  Google Scholar 

  • Schanche M, Avershina E, Dotterud C, Øien T, Storrø O, Johnsen R, Rudi K (2015) High-resolution analyses of overlap in the microbiota between mothers and their children. Curr Microbiol 71:283–290

    Article  CAS  PubMed  Google Scholar 

  • Schirmer M, Franzosa E, Lloyd-Price J, McIver R, Schwager T, Poon A, Ananthakrishnan E, Andrews G, Barron K et al (2018) Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol 3:337–346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schnorr S, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G et al (2014) Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5:1–12

    Article  CAS  Google Scholar 

  • Schuijs M, Willart M, Vergote K, Gras D, Deswarte K, Ege M, Madeira F, Beyaert R, van Loo G, Bracher F et al (2015) Farm dust and endotoxin protect against allergy through A20 induction in lung epithelial cell. Sci: 349 1106–1110

  • Schwarcz R, Bruno JP, Muchowski PJ, Wu HQ (2012) Kynurenines in the mammalian brain: when physiology meets pathology. Nat Rev Neurosci 13(7):465–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scotti E, Boué S, Sasso G, Zanetti F, Belcastro V, Poussin C, Sierro N, Battey J, Gimalac A, Ivanov N, Hoen J (2017) Exploring the microbiome in health and disease: Implications for toxicology. Toxicol Res Appl 1:1–37

    Google Scholar 

  • Sherwin E, Rea K, Dinan TG, Cryan JF (2016) A gut (microbiome) feeling about the brain. Curr Opin Gastroenterol 32:96–102

    Article  CAS  PubMed  Google Scholar 

  • Simeoli R, Mattace Raso G, Pirozzi C, Lama A, Santoro A, Russo R, Montero-Melendez T, Berni Canani R, Calignano A, Perretti M, Meli R (2017) An orally administered butyrate-releasing derivative reduces neutrophil recruitment and inflammation in dextran sulphate sodium-induced murine colitis. Br J Pharmacol 174:1484–1496

    Article  CAS  PubMed  Google Scholar 

  • Simpson H, Campbell B (2015) Review article: dietary fibre-microbiota interactions. Aliment Pharmcol Therapeut 42:158–179

    Article  CAS  Google Scholar 

  • Singh R, Chang H, Yan D, Lee K, Ucmak D, Wong K, Abrouk M, Farahnik B, Nakamura M, Zhu T, Bhutani T, Liao W (2017) Influence of diet on the gut microbiome and implications for human health. J Translat Med 15–29

  • Sokol H, Seksik P, Furet J, Firmesse O, Nion- Larmurier I, Beaugerie L et al (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15:1183–1189

    Article  CAS  PubMed  Google Scholar 

  • Soty M, Gautier-Stein A, Rajas F et al (2017) Gut-brain glucose signaling in energy homeostasis. Cell Metab 25:1231–1242

    Article  CAS  PubMed  Google Scholar 

  • Stokholm J, Blaser M, Thorsen J, Rasmussen M, Waage J, Vinding R, Schoos A, Kunoe A, Fink N, Chawes B et al (2018) Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 9:141–152

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Strati F, Cavalieri D, Albanese D et al (2017) New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome 5:24–31

    Article  PubMed  PubMed Central  Google Scholar 

  • Thompson A, Monteagudo-Mera A, Cadenas M, Lampl M, Azcarate-Peril M, Mcgavin MJ, Eckstein T (2015) Milk-and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol 5:3–14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thursby E, Juge N (2017) Introduction to the human gut microbiota. Biochem J 474:1823–1836

    Article  CAS  PubMed  Google Scholar 

  • Tong LC, Wang Y, Wang ZB, Liu WY, Sun S, Li L, Su DF, Zhang LC (2016) Propionate ameliorates dextran sodium sulfate-induced colitis by improving intestinal barrier function and reducing inflammation and oxidative stress. Front Pharmacol 7:253

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ (2014) Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20:159–166

    Article  CAS  PubMed  Google Scholar 

  • Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, Qiu Z, Maher L, Redinbo MR, Phillips RS et al (2014) Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity 41:296–310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Villanueva-Millan M, Perez-Matute P, Oteo J (2015) Gut microbiota a key player in health and disease. A review focused on obesity. J Physiol Biochem 71:509–525

    Article  CAS  PubMed  Google Scholar 

  • Voreades N, Kozil A, Weir T (2014) Diet and the development of the human intestinal microbiome. Front Microbiol 5:1–9

    Article  Google Scholar 

  • Vuitton D, Dalphin J (2017) From farming to engineering: the microbiota and allergic diseases. Engineering 3:98–109

    Article  Google Scholar 

  • Weaver C (2015) Diet, gut microbiome, and bone health. Curr Ost Rep 13:125–130

    Article  Google Scholar 

  • Wei W, Sun W, Yu S, Yang Y, Ai L (2016) Butyrate production from high-fibre diet protects against lymphoma tumor. Leuk Lymph 57:2401–2408

    Article  CAS  Google Scholar 

  • Wiley N, Dinan T, Ross R, Stanton C, Clarke G, Cryan J (2017) The microbiota-gut-brain axis as a key regulator of neural function and the stress response: implications for human and animal health. J Anim Sci 95:3225–3246

    CAS  PubMed  Google Scholar 

  • Windey K, De Preter V, Verbeke K (2012) Relevance of protein fermentation to gut health. Mol Nutr Food Res 56:184–196

    Article  CAS  PubMed  Google Scholar 

  • Wu S, Cao Z, Chang K et al (2017) Intestinal microbial dysbiosis aggravates the progression of Alzheimer’s disease in Drosophila. Nat Commun 8:2–9

    Article  CAS  Google Scholar 

  • Xiyue C, Shabnam E, Luoyun F et al (2017) Maintenance of gastrointestinal glucose homeostasis by the gut-brain axis. Curr Proteins Pept Sci 18:541–547

    Article  CAS  Google Scholar 

  • Yan J, Herzog J, Tsang K et al (2016) Gut microbiota induce IGF-1 and promote bone formation and growth. Proc Natl Acad Sci USA 113:7554–7563

    Google Scholar 

  • Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, Zecchi R, D’Angelo C, Massi-Benedetti C, Fallarino F et al (2013) Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39:372–385

    Article  CAS  PubMed  Google Scholar 

  • Zemel B (2017) Dietary calcium intake recommendations for children: are they too high? Am J Clin Nutr 105:1025–1026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal S, Kim J, Degivry M, Quere G, Garault P, van Hylckama Vlieg J et al (2016) Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J 10:2235–2245

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao L, Zhang F, Ding X, Wu G, Lam Y, Wang X, Fu H, Xue X, Lu C, Ma J et al (2018) Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 359:1151–1156

    Article  CAS  PubMed  Google Scholar 

  • Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y, Liu Y, Cheng K, Zhou C, Wang H, Zhou X, Gui S, Perry S, Wong M, Licinio J, Wei H, Xie P (2019) The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice. Science Adv 5(2):8317–8326

    Article  CAS  Google Scholar 

  • Zhu A, Sunagawa S, Mende D, Bork P (2015) Inter-individual differences in the gene content of human gut bacterial species. Genome Biol 16:82–90

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhu W, Gregory J, Org E, Buffa J, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M et al (2016) Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk. Cell 165:111–124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu W, Winter M, Byndloss M, Spiga L, Duerkop B, Hughes E, Buttner L, de Lima Romao E, Behrendt C, Lopez C et al (2018) Precision editing of the gut microbiota ameliorates colitis. Nature 553:208–211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zitvogel L, Ma Y, Raoult D, Kroemer G, Gajewski T (2018) The microbiome in cancer immunotherapy: diagnostic tools and therapeutic strategies. Science 359:1366–1370

    Article  CAS  PubMed  Google Scholar 

  • Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik R et al (2018) Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174:1388–1405

    Article  CAS  PubMed  Google Scholar 

  • Zoetendal EG, Akkermans AD, Akkermans-van Vliet WM, de Visser JA, De Vos WM (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 13:129–134

    Google Scholar 

  • Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe M, Kumar M, Gewirtz AT (2018) Fiber-mediated nourishment of gut microbiota protects against diet-induced obesity by restoring IL-22-mediated colonic health. Cell Host Microbe 23:41–53

    Article  CAS  PubMed  Google Scholar 

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Gomaa, E.Z. Human gut microbiota/microbiome in health and diseases: a review. Antonie van Leeuwenhoek 113, 2019–2040 (2020). https://doi.org/10.1007/s10482-020-01474-7

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