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

Antonie van Leeuwenhoek - Tập 113 Số 12 - Trang 2019-2040 - 2020
Eman Zakaria Gomaa1
1Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt

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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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