Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65. https://doi.org/10.1038/nature08821

Article  CAS  PubMed  PubMed Central  Google Scholar 

Consortium THMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14. https://doi.org/10.1038/nature11234

Article  CAS  Google Scholar 

Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306. https://doi.org/10.4161/gmic.19897

Article  PubMed  PubMed Central  Google Scholar 

Koropatkin NM, Cameron EA, Martens EC. How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol. 2012;10(5):323–35. https://doi.org/10.1038/nrmicro2746

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1–24. https://doi.org/10.1007/s00394-017-1445-8

Article  CAS  PubMed  Google Scholar 

Silva YP, Bernardi A, Frozza RL. The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front Endocrinol. 2020;11. https://doi.org/10.3389/fendo.2020.00025

Kaplan JL, Shi HN, Walker WA. The role of microbes in developmental immunologic programming. Pediatr Res. 2011;69(6):465–72. https://doi.org/10.1203/PDR.0b013e318217638a

Article  PubMed  Google Scholar 

Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492–506. https://doi.org/10.1038/s41422-020-0332-7

Article  PubMed  PubMed Central  Google Scholar 

Panwar RB, Sequeira RP, Clarke TB. Microbiota-mediated protection against antibiotic-resistant pathogens. Genes Immun. 2021;22(5):255–67. https://doi.org/10.1038/s41435-021-00129-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ubeda C, Djukovic A, Isaac S. Roles of the intestinal microbiota in pathogen protection. Clin Transl Immunol. 2017;6(2):e128. https://doi.org/10.1038/cti.2017.2

Article  CAS  Google Scholar 

Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, et al. Environmental factors shaping the gut microbiome in a Dutch population. Nature. 2022;604(7907):732–9. https://doi.org/10.1038/s41586-022-04567-7

Article  CAS  PubMed  Google Scholar 

Ahn J, Hayes RB. Environmental influences on the human microbiome and implications for noncommunicable disease. Annu Rev Public Health. 2021;42:277–92. https://doi.org/10.1146/annurev-publhealth-012420-105020

Article  PubMed  PubMed Central  Google Scholar 

Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet. 2021;53(2):156–65. https://doi.org/10.1038/s41588-020-00763-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao J-z, et al. Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 2016;16(1):90. https://doi.org/10.1186/s12866-016-0708-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Derrien M, Alvarez A-S, de Vos WM. The gut microbiota in the first decade of life. Trends Microbiol. 2019;27(12):997–1010. https://doi.org/10.1016/j.tim.2019.08.001

Article  CAS  PubMed  Google Scholar 

Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26:26050. https://doi.org/10.3402/mehd.v26.26050

Article  PubMed  Google Scholar 

Jeffery IB, Lynch DB, O’Toole PW. Composition and temporal stability of the gut microbiota in older persons. ISME J. 2016;10(1):170–82. https://doi.org/10.1038/ismej.2015.88

Article  CAS  PubMed  Google Scholar 

de Vos WM, de Vos EA. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr Rev. 2012;70(Suppl 1):S45–56. https://doi.org/10.1111/j.1753-4887.2012.00505.x

Article  PubMed  Google Scholar 

de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut. 2022;71(5):1020–32. https://doi.org/10.1136/gutjnl-2021-326789

Article  CAS  PubMed  Google Scholar 

van der Meulen TA, Harmsen H, Bootsma H, Spijkervet F, Kroese F, Vissink A. The microbiome-systemic diseases connection. Oral Dis. 2016;22(8):719–34. https://doi.org/10.1111/odi.12472

Article  PubMed  Google Scholar 

Sorbara MT, Pamer EG. Microbiome-based therapeutics. Nat Rev Microbiol. 2022;20(6):365–80. https://doi.org/10.1038/s41579-021-00667-9

Article  CAS  PubMed  Google Scholar 

O’Toole PW, Marchesi JR, Hill C. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nat Microbiol. 2017;2:17057. https://doi.org/10.1038/nmicrobiol.2017.57

Article  CAS  PubMed  Google Scholar 

Cani PD, de Vos WM. Next-generation beneficial microbes: the case of Akkermansia muciniphila. Front Microbiol. 2017;8:1765. https://doi.org/10.3389/fmicb.2017.01765

Article  PubMed  PubMed Central  Google Scholar 

Douillard FP, de Vos WM. Biotechnology of health-promoting bacteria. Biotechnol Adv. 2019;37(6):107369. https://doi.org/10.1016/j.biotechadv.2019.03.008

Article  CAS  PubMed  Google Scholar 

Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635–8. https://doi.org/10.1126/science.1110591

Article  PubMed  PubMed Central  Google Scholar 

Rajilić-Stojanović M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol. 2007;9(9):2125–36. https://doi.org/10.1111/j.1462-2920.2007.01369.x

Article  PubMed  Google Scholar 

Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, et al. Diversity of bifidobacteria within the infant gut microbiota. PLoS ONE. 2012;7(5):e36957. https://doi.org/10.1371/journal.pone.0036957

Article  CAS  PubMed  PubMed Central  Google Scholar 

Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118(2):511–21. https://doi.org/10.1542/peds.2005-2824

Article  PubMed  Google Scholar 

Korpela K, de Vos WM. Early life colonization of the human gut: microbes matter everywhere. Curr Opin Microbiol. 2018;44:70–8. https://doi.org/10.1016/j.mib.2018.06.003

Article  PubMed  Google Scholar 

Lebeaux RM, Madan JC, Nguyen QP, Coker MO, Dade EF, Moroishi Y, et al. Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Pediatr Res. 2022. https://doi.org/10.1038/s41390-022-02104-w

Article  PubMed  PubMed Central  Google Scholar 

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, et al. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat Commun. 2016;7:10410. https://doi.org/10.1038/ncomms10410

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hopkins MJ, Macfarlane GT, Furrie E, Fite A, Macfarlane S. Characterisation of intestinal bacteria in infant stools using real-time PCR and northern hybridisation analyses. FEMS Microbiol Ecol. 2005;54(1):77–85. https://doi.org/10.1016/j.femsec.2005.03.001

Article  CAS  PubMed  Google Scholar 

Long SS. Infant botulism. Pediatr Infect Dis J. 2001;20(7):707–9. https://doi.org/10.1097/00006454-200107000-00013

Article  CAS  PubMed  Google Scholar 

Arnon SS. Infant Botulism. Ann Rev Med. 1980;31(1):541–60. https://doi.org/10.1146/annurev.me.31.020180.002545

Article  CAS  PubMed  Google Scholar 

Huhtanen CM. Bile acid inhibition of Clostridium botulinum. Appl Environ Microbiol. 1979;38(2):216–8. https://doi.org/10.1128/aem.38.2.216-218.1979

Article