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van Beek et al. Microbiome Res Rep 2025;4:13 https://dx.doi.org/10.20517/mrr.2024.45 Page 17 of 19

6. 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. DOI PubMed
7. Yu JC, Khodadadi H, Malik A, et al. Innate immunity of neonates and infants. Front Immunol 2018;9:1759. DOI PubMed PMC
8. Liu W, Hu D, Huo H, et al. Intestinal alkaline phosphatase regulates tight junction protein levels. J Am Coll Surg 2016;222:1009-17.
DOI PubMed PMC
9. Jokela R, Ponsero AJ, Dikareva E, et al. Sources of gut microbiota variation in a large longitudinal Finnish infant cohort.
EBioMedicine 2023;94:104695. DOI PubMed PMC
10. Korpela K, Hurley S, Ford SA, et al; CORAL Study Group. Association between gut microbiota development and allergy in infants
born during pandemic-related social distancing restrictions. Allergy 2024;79:1938-51. DOI PubMed
11. Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A. Challenges and future directions for studying effects of host genetics on
the gut microbiome. Nat Genet 2022;54:100-6. DOI PubMed
12. Jian C, Luukkonen P, Yki-Järvinen H, Salonen A, Korpela K. Quantitative PCR provides a simple and accessible method for
quantitative microbiota profiling. PLoS One 2020;15:e0227285. DOI PubMed PMC
13. Jian C, Salonen A, Korpela K. Commentary: how to count our microbes? The effect of different quantitative microbiome profiling
approaches. Front Cell Infect Microbiol 2021;11:627910. DOI PubMed PMC
14. Pang T, Leach ST, Katz T, Day AS, Ooi CY. Fecal biomarkers of intestinal health and disease in children. Front Pediatr 2014;2:6.
DOI PubMed PMC
15. Singh SB, Lin HC. Role of intestinal alkaline phosphatase in innate immunity. Biomolecules 2021;11:1784. DOI PubMed PMC
16. Theprungsirikul J, Skopelja-Gardner S, Rigby WFC. Killing three birds with one BPI: bactericidal, opsonic, and anti-inflammatory
functions. J Transl Autoimmun 2021;4:100105. DOI PubMed PMC
17. Bevins CL, Salzman NH. Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nat Rev Microbiol
2011;9:356-68. DOI PubMed
18. Topic RZ, Dodig S. Eosinophil cationic protein--current concepts and controversies. Biochem Med 2011;21:111-21. DOI PubMed
19. Damo SM, Kehl-Fie TE, Sugitani N, et al. Molecular basis for manganese sequestration by calprotectin and roles in the innate immune
response to invading bacterial pathogens. Proc Natl Acad Sci U S A 2013;110:3841-6. DOI PubMed PMC
20. Kell DB, Heyden EL, Pretorius E. The biology of lactoferrin, an iron-binding protein that can help defend against viruses and bacteria.
Front Immunol 2020;11:1221. DOI PubMed PMC
21. Takeuchi T, Ohno H. IgA in human health and diseases: potential regulator of commensal microbiota. Front Immunol
2022;13:1024330. DOI PubMed PMC
22. metagenome data. Microbiome 2021;9:165. DOI PubMed PMC
Johansson MEV, Holmén Larsson JM, Hansson GC. The two mucus layers of colon are organized by the MUC2 mucin, whereas the
outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci U S A 2011;108 Suppl 1:4659-65. DOI PubMed PMC
23. Wang L, Llorente C, Hartmann P, Yang AM, Chen P, Schnabl B. Methods to determine intestinal permeability and bacterial
translocation during liver disease. J Immunol Methods 2015;421:44-53. DOI PubMed PMC
24. Korpela K, Dikareva E, Hanski E, Kolho KL, de Vos WM, Salonen A. Cohort profile: Finnish Health and Early Life Microbiota
(HELMi) longitudinal birth cohort. BMJ Open 2019;9:e028500. DOI PubMed PMC
25. Salonen A, Nikkilä J, Jalanka-Tuovinen J, et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray:
effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 2010;81:127-34. DOI
26. Dubois L, Valles-Colomer M, Ponsero A, et al. Paternal and induced gut microbiota seeding complement mother-to-infant
transmission. Cell Host Microbe 2024;32:1011-24.e4. DOI
27. Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta 2023;2:e107. DOI
PubMed PMC
28. Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience 2021;10:giab008. DOI PubMed PMC
29. Hiseni P, Rudi K, Wilson RC, Hegge FT, Snipen L. HumGut: a comprehensive human gut prokaryotic genomes collection filtered by

30. Katrikorpela. mare. 2016. Available from: https://zenodo.org/records/50310. [Last accessed on 25 Dec 2024].
31. Wickham H. Reshaping data with the reshape package. J Stat Soft 2007;21:1-20. DOI
32. nlme: linear and nonlinear mixed effects models. Version 3.1-166. 2024. DOI
33. gplots: various r programming tools for plotting data. Version 3.1.3.1. 2024. DOI
34. Van den Abbeele P, Deyaert S, Thabuis C, et al. Bridging preclinical and clinical gut microbiota research using the ex vivo SIFR®
technology. Front Microbiol 2023;14:1131662. DOI PubMed PMC
35. Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci
2018;75:149-60. DOI PubMed PMC
36. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech
2015;8:1-16. DOI PubMed PMC
37. Ballard O, Morrow AL. Human milk composition: nutrients and bioactive factors. Pediatr Clin North Am 2013;60:49-74. DOI
PubMed PMC
38. Henrick BM, Hutton AA, Palumbo MC, et al. Elevated fecal pH indicates a profound change in the breastfed infant gut microbiome
due to reduction of Bifidobacterium over the past century. mSphere 2018;3:e00041-18. DOI PubMed PMC
39. Yamamura R, Inoue KY, Nishino K, Yamasaki S. Intestinal and fecal pH in human health. Front Microbiomes 2023;2:1192316. DOI