REFERENCES

1. Rodríguez JM, Murphy K, Stanton C, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis 2015;26:26050.

2. Galazzo G, van Best N, Bervoets L, et al; GI-MDH consortium. Development of the microbiota and associations with birth mode, diet, and atopic disorders in a longitudinal analysis of stool samples, collected from infancy through early childhood. Gastroenterology 2020;158:1584-96.

3. de Koff EM, van Baarle D, van Houten MA, et al. Mode of delivery modulates the intestinal microbiota and impacts the response to vaccination. Nat Commun 2022;13:6638.

4. Ahmadizar F, Vijverberg SJH, Arets HGM, et al. Early-life antibiotic exposure increases the risk of developing allergic symptoms later in life: a meta-analysis. Allergy 2018;73:971-86.

5. Habicht JP. Expert consultation on the optimal duration of exclusive breastfeeding. In: Pickering LK, Morrow AL, Ruiz-palacios GM, Schanler RJ, editors. Protecting infants through human milk. Boston: Springer US; 2004. pp. 79-87.

6. Ojo-Okunola A, Nicol M, du Toit E. Human breast milk bacteriome in health and disease. Nutrients 2018;10:1643.

7. Cortes-Macías E, Selma-Royo M, García-Mantrana I, et al. Maternal diet shapes the breast milk microbiota composition and diversity: impact of mode of delivery and antibiotic exposure. J Nutr 2021;151:330-40.

8. Xiao L, Wang J, Zheng J, Li X, Zhao F. Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. Genome Biol 2021;22:243.

9. Ding M, Zheng Y, Liu F, et al. Lactation time influences the composition of Bifidobacterium and Lactobacillus at species level in human breast milk. Benef Microbes 2022;13:319-30.

10. Edwards CA, Van Loo-Bouwman CA, Van Diepen JA, et al. A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut. Benef Microbes 2022;13:365-82.

11. Braegger C, Chmielewska A, Decsi T, et al; ESPGHAN Committee on Nutrition. Supplementation of infant formula with probiotics and/or prebiotics: a systematic review and comment by the ESPGHAN committee on nutrition. J Pediatr Gastroenterol Nutr 2011;52:238-50.

12. Halken S, Muraro A, de Silva D, et al; European Academy of Allergy and Clinical Immunology Food Allergy and Anaphylaxis Guidelines Group. EAACI guideline: preventing the development of food allergy in infants and young children (2020 update). Pediatr Allergy Immunol 2021;32:843-58.

13. He X, Parenti M, Grip T, et al. Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial. Sci Rep 2019;9:11589.

14. Zhao J, Yi W, Liu B, et al. MFGM components promote gut Bifidobacterium growth in infant and in vitro. Eur J Nutr 2022;61:277-88.

15. Lemaire M, Le Huërou-Luron I, Blat S. Effects of infant formula composition on long-term metabolic health. J Dev Orig Health Dis 2018;9:573-89.

16. Graversen KB, Larsen JM, Pedersen SS, et al. Partially hydrolysed whey has superior allergy preventive capacity compared to intact whey regardless of amoxicillin administration in brown norway rats. Front Immunol 2021;12:705543.

17. Freidl R, Garib V, Linhart B, et al. Extensively hydrolyzed hypoallergenic infant formula with retained T cell reactivity. Nutrients 2022;15:111.

18. De Weirdt R, Possemiers S, Vermeulen G, et al. Human faecal microbiota display variable patterns of glycerol metabolism. FEMS Microbiol Ecol 2010;74:601-11.

19. Van de Wiele T, Van den Abbeele P, Ossieur W, Possemiers S, Marzorati M. The simulator of the human intestinal microbial ecosystem (SHIME^®). In: Verhoeckx K, Cotter P, López-Expósito I, Kleiveland C, Lea T, Mackie A, Requena T, Swiatecka D, Wichers H, editors. The impact of food bioactives on health. Springer, Cham; 2015. pp. 305-17.

20. Molly K, Vande Woestyne M, Verstraete W. Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem. Appl Microbiol Biotechnol 1993;39:254-8.

21. Possemiers S, Verthé K, Uyttendaele S, Verstraete W. PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 2004;49:495-507.

22. Marsaux B, Van den Abbeele P, Ghyselinck J, Prioult G, Marzorati M, Bogićević B. Synbiotic effect of Bifidobacterium lactis CNCM I-3446 and bovine milk-derived oligosaccharides on infant gut microbiota. Nutrients 2020;12:2268.

23. Calatayud M, Van den Abbeele P, Ghyselinck J, Marzorati M, Rohs E, Birkett A. Comparative effect of 22 dietary sources of fiber on gut microbiota of healthy humans in vitro. Front Nutr 2021;8:700571.

24. Hoefman S, Pommerening-Röser A, Samyn E, De Vos P, Heylen K. Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria for the scientific community. Res Microbiol 2013;164:288-92.

25. Duysburgh C, Van den Abbeele P, Krishnan K, Bayne TF, Marzorati M. A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro. Int J Pharm X 2019;1:100021.

26. Boon N, Top EM, Verstraete W, Siciliano SD. Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load. Appl Environ Microbiol 2003;69:1511-20.

27. Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019;20:257.

28. O’Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016;44:D733-45.

29. Sayers EW, Cavanaugh M, Clark K, Ostell J, Pruitt KD, Karsch-Mizrachi I. GenBank. Nucleic Acids Res 2019;47:D94-9.

30. Harrison PW, Ahamed A, Aslam R, et al. The European nucleotide archive in 2020. Nucleic Acids Res 2021;49:D82-5.

31. Ogasawara O, Kodama Y, Mashima J, Kosuge T, Fujisawa T. DDBJ Database updates and computational infrastructure enhancement. Nucleic Acids Res 2020;48:D45-50.

32. Almeida A, Nayfach S, Boland M, et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat Biotechnol 2021;39:105-14.

33. Hoffmann C, Dollive S, Grunberg S, et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 2013;8:e66019.

34. Wampach L, Heintz-Buschart A, Hogan A, et al. Colonization and succession within the human gut microbiome by archaea, bacteria, and microeukaryotes during the first year of life. Front Microbiol 2017;8:738.

35. Arrieta MC, Arévalo A, Stiemsma L, et al. Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting. J Allergy Clin Immunol 2018;142:424-34.e10.

36. Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 2017;3:e104.

37. Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol 2017;35:316-9.

38. Oksanen J, Simpson GL, Blanchet FG, et al. vegan: Community ecology package. Available from: https://cran.r-project.org/web/packages/vegan/index.html. [Last accessed on 27 Jun 2024].

39. Wichham H. ggplot2: elegant graphics for data analysis. 2nd edition. New York: Springer Cham. 2016.

40. Casaburi G, Frese SA. Colonization of breastfed infants by Bifidobacterium longum subsp. infantis EVC001 reduces virulence gene abundance. Hum Microbiome J 2018;9:7-10.

41. Alba C, Carrera M, Álvarez-Calatayud G, Arroyo R, Fernández L, Rodríguez JM. Evaluation of safety and beneficial health effects of the human-milk strain Bifidobacterium breve DSM32583: an infant pilot trial. Nutrients 2024;16:1134.

42. Rodríguez-Sojo MJ, Ruiz-Malagón AJ, Rodríguez-Cabezas ME, Gálvez J, Rodríguez-Nogales A. Limosilactobacillus fermentum CECT5716: mechanisms and therapeutic insights. Nutrients 2021;13:1016.

43. Lagkouvardos I, Intze E, Schaubeck M, et al. Early life gut microbiota profiles linked to synbiotic formula effects: a randomized clinical trial in European infants. Am J Clin Nutr 2023;117:326-39.

44. Piloquet H, Vrignaud B, Gillaizeau F, et al; GOLF III Study Group. Efficacy and safety of a synbiotic infant formula for the prevention of respiratory and gastrointestinal infections: a randomized controlled trial. Am J Clin Nutr 2024;119:1259-69.

45. Maldonado J, Gil-Campos M, Maldonado-Lobón JA, et al. Evaluation of the safety, tolerance and efficacy of 1-year consumption of infant formula supplemented with Lactobacillus fermentum CECT5716 Lc40 or Bifidobacterium breve CECT7263: a randomized controlled trial. BMC Pediatr 2019;19:361.

46. Rycroft CE, Jones MR, Gibson GR, Rastall RA. Fermentation properties of gentio-oligosaccharides. Lett Appl Microbiol 2001;32:156-61.

47. Yu X, Gurry T, Nguyen LTT, Richardson HS, Alm EJ. Prebiotics and community composition influence gas production of the human gut microbiota. mBio 2020;11:e00217-20.

48. Roager HM, Stanton C, Hall LJ. Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life. Gut Microbes 2023;15:2192151.

49. Pham VT, Lacroix C, Braegger CP, Chassard C. Early colonization of functional groups of microbes in the infant gut. Environ Microbiol 2016;18:2246-58.

50. Asnicar F, Manara S, Zolfo M, et al. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling. mSystems 2017;2:e00164-16.

51. Campana R, van Hemert S, Baffone W. Strain-specific probiotic properties of lactic acid bacteria and their interference with human intestinal pathogens invasion. Gut Pathog 2017;9:12.

52. Vatanen T, Plichta DR, Somani J, et al. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol 2019;4:470-9.

53. Goussarov G, Claesen J, Mysara M, et al. Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics. Environ Microbiome 2022;17:9.

54. Chan YH, Shek LPC, Aw M, Quak SH, Lee BW. Use of hypoallergenic formula in the prevention of atopic disease among Asian children. J Paediatr Child Health 2002;38:84-8.

55. Nentwich I, Pazdírková A, Lokaj J, Szepfalusi Z, Hrstková H. [Early feeding in infancy and atopic dermatitis - a prospective observational study]. Klin Padiatr 2009;221:78-82.

56. Vandenplas Y, Latiff AHA, Fleischer DM, et al. Partially hydrolyzed formula in non-exclusively breastfed infants: a systematic review and expert consensus. Nutrition 2019;57:268-74.

57. Kok CR, Brabec B, Chichlowski M, et al. Stool microbiome, pH and short/branched chain fatty acids in infants receiving extensively hydrolyzed formula, amino acid formula, or human milk through two months of age. BMC Microbiol 2020;20:337.

58. von Wright A. Regulating the safety of probiotics - the European approach. Curr Pharm Des 2005;11:17-23.

59. Salminen S, Stahl B, Vinderola G, Szajewska H. Infant formula supplemented with biotics: current knowledge and future perspectives. Nutrients 2020;12:1952.

60. Almeida CC, Mendonça Pereira BF, Leandro KC, Costa MP, Spisso BF, Conte-Junior CA. Bioactive compounds in infant formula and their effects on infant nutrition and health: a systematic literature review. Int J Food Sci 2021;2021:8850080.

61. Heppner N, Reitmeier S, Heddes M, et al. Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula. bioRxiv. [Preprint] Oct 19, 2023. [accessed on 2024 Jun 26]. Available from: https://www.biorxiv.org/content/10.1101/2023.10.19.563092v1.