REFERENCES
1. Milani C, Duranti S, Bottacini F, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev 2017;81:e00036-17.
2. Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol 2016;16:341-52.
3. Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res 2020;30:492-506.
4. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. Brit Med J 2018;361:k2179.
5. Dahl WJ, Rivero Mendoza D, Lambert JM. Diet, nutrients and the microbiome. Prog Mol Biol Transl Sci 2020;171:237-63.
6. Fassarella M, Blaak EE, Penders J, Nauta A, Smidt H, Zoetendal EG. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut 2021;70:595-605.
7. Reyman M, van Houten MA, van Baarle D, et al. Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nat Commun 2019;10:4997.
8. Zhang C, Li L, Jin B, et al. The effects of delivery mode on the gut microbiota and health: state of art. Front Microbiol 2021;12:724449.
9. Mancabelli L, Tarracchini C, Milani C, et al. Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs). Comput Struct Biotechnol J 2020;18:2480-93.
10. Ventura M, Milani C, Lugli GA, van Sinderen D. Health benefits conferred by the human gut microbiota during infancy. Microb Biotechnol 2019;12:243-8.
11. Turroni F, Milani C, Ventura M, van Sinderen D. The human gut microbiota during the initial stages of life: insights from bifidobacteria. Curr Opin Biotechnol 2022;73:81-7.
12. Yao Y, Cai X, Ye Y, Wang F, Chen F, Zheng C. The role of microbiota in infant health: from early life to adulthood. Front Immunol 2021;12:708472.
13. Browne HP, Shao Y, Lawley TD. Mother-infant transmission of human microbiota. Curr Opin Microbiol 2022;69:102173.
14. Hoang DM, Levy EI, Vandenplas Y. The impact of caesarean section on the infant gut microbiome. Acta Paediatr 2021;110:60-7.
15. Callaway E. C-section babies are missing key microbes. Nature 2019; doi: 10.1038/d41586-019-02807-x.
16. Gregory KE, Deforge CE, Natale KM, Phillips M, Van Marter LJ. Necrotizing enterocolitis in the premature infant: neonatal nursing assessment, disease pathogenesis, and clinical presentation. Adv Neonatal Care 2011;11:155-64; quiz 165.
17. Baranowski JR, Claud EC. Necrotizing enterocolitis and the preterm infant microbiome. Adv Exp Med Biol 2019;1125:25-36.
18. El Manouni El Hassani S, Niemarkt HJ, Berkhout DJC, et al. Profound pathogen-specific alterations in intestinal microbiota composition precede late-onset sepsis in preterm infants: a longitudinal, multicenter, case-control study. Clin Infect Dis 2021;73:e224-32.
19. Liu Y, Du X, Zhai S, Tang X, Liu C, Li W. Gut microbiota and atopic dermatitis in children: a scoping review. BMC Pediatr 2022;22:323.
20. Yu L, Deng YH, Huang YH, Ke HJ, Guo Y, Wu JL. Comparison of gut microbiota between infants with atopic dermatitis and healthy controls in Guangzhou, China. J Asthma Allergy 2021;14:493-500.
21. Reddel S, Del Chierico F, Quagliariello A, et al. Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture. Sci Rep 2019;9:4996.
22. Cong X, Judge M, Xu W, et al. Influence of feeding type on gut microbiome development in hospitalized preterm infants. Nurs Res 2017;66:123-33.
23. Parra-Llorca A, Gormaz M, Alcántara C, et al. Preterm gut microbiome depending on feeding type: significance of donor human milk. Front Microbiol 2018;9:1376.
24. Guaraldi F, Salvatori G. Effect of breast and formula feeding on gut microbiota shaping in newborns. Front Cell Infect Microbiol 2012;2:94.
25. Unger S, Stintzi A, Shah P, Mack D, O’Connor DL. Gut microbiota of the very-low-birth-weight infant. Pediatr Res 2015;77:205-13.
26. Alderete TL, Jones RB, Shaffer JP, et al. Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. Gut Microbes 2021;13:1961203.
27. Luoto R, Kalliomäki M, Laitinen K, Isolauri E. The impact of perinatal probiotic intervention on the development of overweight and obesity: follow-up study from birth to 10 years. Int J Obes 2010;34:1531-7.
28. Chouraqui JP, Grathwohl D, Labaune JM, et al. Assessment of the safety, tolerance, and protective effect against diarrhea of infant formulas containing mixtures of probiotics or probiotics and prebiotics in a randomized controlled trial. Am J Clin Nutr 2008;87:1365-73.
29. Soderborg TK, Clark SE, Mulligan CE, et al. The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD. Nat Commun 2018;9:4462.
30. Koleva PT, Bridgman SL, Kozyrskyj AL. The infant gut microbiome: evidence for obesity risk and dietary intervention. Nutrients 2015;7:2237-60.
31. Roggero P, Giannì ML, Amato O, et al. Evaluation of air-displacement plethysmography for body composition assessment in preterm infants. Pediatr Res 2012;72:316-20.
32. Mancabelli L, Milani C, Fontana F, et al. Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection. Environ Microbiol 2022;24:6453-62.
33. Milani C, Hevia A, Foroni E, et al. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One 2013;8:e68739.
34. Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019;37:852-7.
35. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-6.
36. Milani C, Casey E, Lugli GA, et al. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. Microbiome 2018;6:145.
37. Milani C, Lugli GA, Fontana F, et al. METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses. mSystems 2021;6:e0058321.
39. Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics 2019;35:421-32.
40. Chen Y, Ye W, Zhang Y, Xu Y. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res 2015;43:7762-8.
41. Caspi R, Billington R, Ferrer L, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2016;44:D471-80.
42. Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 2012;28:125-6.
43. Ye Y, Choi JH, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 2011;12:159.
45. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001;125:279-84.
46. Rutayisire E, Huang K, Liu Y, Tao F. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol 2016;16:86.
47. Alessandri G, Fontana F, Mancabelli L, et al. Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. NPJ Biofilms Microbiomes 2022;8:88.
48. Matharu D, Ponsero AJ, Dikareva E, et al.
49. Mitchell CM, Mazzoni C, Hogstrom L, et al. Delivery mode affects stability of early infant gut microbiota. Cell Rep Med 2020;1:100156.
50. Gao X, Zhang M, Xue J, et al. Body mass index differences in the gut microbiota are gender specific. Front Microbiol 2018;9:1250.
51. Lv Y, Qin X, Jia H, Chen S, Sun W, Wang X. The association between gut microbiota composition and BMI in Chinese male college students, as analysed by next-generation sequencing. Br J Nutr 2019;122:986-95.
52. Kim MH, Yun KE, Kim J, et al. Gut microbiota and metabolic health among overweight and obese individuals. Sci Rep 2020;10:19417.
53. Palmas V, Pisanu S, Madau V, et al. Gut microbiota markers associated with obesity and overweight in Italian adults. Sci Rep 2021;11:5532.
54. Ignacio A, Fernandes MR, Rodrigues VA, et al. Correlation between body mass index and faecal microbiota from children. Clin Microbiol Infect 2016;22:258.e1-8.
55. Greathouse KL, White JR, Padgett RN, et al. Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC. BMJ Open Gastroenterol 2019;6:e000247.
56. Barratt MJ, Nuzhat S, Ahsan K, et al.
57. Michael DR, Jack AA, Masetti G, et al. A randomised controlled study shows supplementation of overweight and obese adults with lactobacilli and bifidobacteria reduces bodyweight and improves well-being. Sci Rep 2020;10:4183.
58. Alessandri G, Lugli GA, Tarracchini C, et al. Disclosing the genomic diversity among members of the
59. Turroni F, Milani C, Duranti S, et al. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr 2020;46:16.
60. Tanaka M, Nakayama J. Development of the gut microbiota in infancy and its impact on health in later life. Allergol Int 2017;66:515-22.
61. van Beijsterveldt IALP, de Fluiter KS, Breij LM, van der Steen M, Hokken-Koelega ACS. Fat mass and fat-free mass track from infancy to childhood: new insights in body composition programming in early life. Obesity 2021;29:1899-906.
62. Leunissen RW, Kerkhof GF, Stijnen T, Hokken-Koelega A. Timing and tempo of first-year rapid growth in relation to cardiovascular and metabolic risk profile in early adulthood. J Am Med Assoc 2009;301:2234-42.