REFERENCES
1. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015;21:8787-803.
2. Hill CJ, Lynch DB, Murphy K, et al. Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome. 2017;5:4.
3. Vandenplas Y, Carnielli VP, Ksiazyk J, et al. Factors affecting early-life intestinal microbiota development. Nutrition. 2020;78:110812.
4. Rizzo SM, Alessandri G, Lugli GA, et al. Exploring molecular interactions between human milk hormone insulin and bifidobacteria. Microbiol Spectr. 2023;11:e0066523.
5. Korpela K, Blakstad EW, Moltu SJ, et al. Intestinal microbiota development and gestational age in preterm neonates. Sci Rep. 2018;8:2453.
6. Chu DM, Meyer KM, Prince AL, Aagaard KM. Impact of maternal nutrition in pregnancy and lactation on offspring gut microbial composition and function. Gut Microbes. 2016;7:459-70.
7. Davis EC, Castagna VP, Sela DA, et al. Gut microbiome and breast-feeding: implications for early immune development. J Allergy Clin Immunol. 2022;150:523-34.
8. Bäckhed F, Roswall J, Peng Y, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 2015;17:690-703.
9. Chong HY, Tan LT, Law JW, et al. Exploring the potential of human milk and formula milk on infants’ gut and health. Nutrients. 2022;14:3554.
10. Yi DY, Kim SY. Human breast milk composition and function in human health: from nutritional components to microbiome and microRNAs. Nutrients. 2021;13:3094.
11. Turroni F, Rizzo SM, Ventura M, Bernasconi S. Cross-talk between the infant/maternal gut microbiota and the endocrine system: a promising topic of research. Microbiome Res Rep. 2022;1:14.
12. Pannaraj PS, Li F, Cerini C, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171:647-54.
13. Seki D, Errerd T, Hall LJ. The role of human milk fats in shaping neonatal development and the early life gut microbiota. Microbiome Res Rep. 2023;2:8.
14. Andreas NJ, Kampmann B, Mehring Le-Doare K. Human breast milk: a review on its composition and bioactivity. Early Hum Dev. 2015;91:629-35.
15. Lyons KE, Ryan CA, Dempsey EM, Ross RP, Stanton C. Breast milk, a source of beneficial microbes and associated benefits for infant health. Nutrients. 2020;12:1039.
16. Martin AJM, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D. Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium. Microbiome Res Rep. 2023;2:17.
17. 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.
18. Duranti S, Lugli GA, Milani C, et al.
19. O’Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925.
20. Archer D, Perez-Muñoz ME, Tollenaar S, et al. The importance of the timing of microbial signals for perinatal immune system development. Microbiome Res Rep. 2023;2:11.
21. Longhi G, van Sinderen D, Ventura M, Turroni F. Microbiota and cancer: the emerging beneficial role of bifidobacteria in cancer immunotherapy. Front Microbiol. 2020;11:575072.
22. Lugli GA, Duranti S, Milani C, et al. Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers. FEMS Microbiol Ecol. 2020;96:fiaa049.
23. Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M. Glycan utilization and cross-feeding activities by bifidobacteria. Trends Microbiol. 2018;26:339-50.
24. Häusler S, Lanzinger E, Sams E, et al. Melatonin in human breast milk and its potential role in circadian entrainment: a nod towards chrononutrition?. Nutrients. 2024;16:1422.
25. Cohen Engler A, Hadash A, Shehadeh N, Pillar G. Breastfeeding may improve nocturnal sleep and reduce infantile colic: potential role of breast milk melatonin. Eur J Pediatr. 2012;171:729-32.
26. Melatonin. In: Drugs and Lactation Database (LactMed®). Available from: https://www.ncbi.nlm.nih.gov/books/NBK501863/. [Last accessed on 14 May 2025].
27. Acuña-Castroviejo D, Escames G, Venegas C, et al. Extrapineal melatonin: sources, regulation, and potential functions. Cell Mol Life Sci. 2014;71:2997-3025.
28. Caba-Flores MD, Ramos-Ligonio A, Camacho-Morales A, Martínez-Valenzuela C, Viveros-Contreras R, Caba M. Breast milk and the importance of chrononutrition. Front Nutr. 2022;9:867507.
29. Akanalçı C, Bilici S. Biological clock and circadian rhythm of breast milk composition. Chronobiol Int. 2024;41:1226-36.
30. Qin Y, Shi W, Zhuang J, et al. Variations in melatonin levels in preterm and term human breast milk during the first month after delivery. Sci Rep. 2019;9:17984.
31. Wang X, Wang Z, Cao J, Dong Y, Chen Y. Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation. Microbiome. 2023;11:17.
32. Graniczkowska KB, Shaffer CL, Cassone VM. Transcriptional effects of melatonin on the gut commensal bacterium Klebsiella aerogenes. Genomics. 2022;114:110321.
33. Paulose JK, Wright JM, Patel AG, Cassone VM. Human gut bacteria are sensitive to melatonin and express endogenous circadian rhythmicity. PLoS One. 2016;11:e0146643.
34. Yi X, Cai R, Shaoyong W, et al. Melatonin promotes gut anti-oxidative status in perinatal rat by remodeling the gut microbiome. Redox Biol. 2023;65:102829.
35. Argentini C, Lugli GA, Tarracchini C, et al. Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. Front Microbiol. 2024;15:1349391.
36. Alessandri G, Fontana F, Tarracchini C, et al. Identification of a prototype human gut Bifidobacterium longum subsp. longum. ;14:1130592.
37. 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.
38. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 2019;570:462-7.
39. Lugli GA, Mancabelli L, Milani C, et al. Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. NPJ Biofilms Microbiomes. 2023;9:25.
40. Serafini F, Strati F, Ruas-Madiedo P, et al. Evaluation of adhesion properties and antibacterial activities of the infant gut commensal Bifidobacterium bifidum PRL2010. Anaerobe. 2013;21:9-17.
41. Guglielmetti S, Tamagnini I, Mora D, et al. Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells. Appl Environ Microbiol. 2008;74:4695-702.
42. Turroni F, Serafini F, Foroni E, et al. Role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proc Natl Acad Sci U S A. 2013;110:11151-6.
43. Turroni F, Foroni E, O’Connell Motherway M, et al. Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Appl Environ Microbiol. 2010;76:3206-19.
44. Milani C, Lugli GA, Fontana F, et al. METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses. mSystems. 2021;6:e0058321.
45. Langdon WB. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min. 2015;8:1.
46. Anders S, Pyl PT, Huber W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
47. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
48. Fontana F, Alessandri G, Tarracchini C, et al. Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. Environ Microbiol. 2022;24:5825-39.
49. Turroni F, Milani C, Duranti S, et al. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci. 2018;75:103-18.
50. Arnao MB, Hernández-Ruiz J, Cano A, Reiter RJ. Melatonin and carbohydrate metabolism in plant cells. Plants. 2021;10:1917.
51. Huang K, Luo X, Zhong Y, Deng L, Feng J. New insights into the role of melatonin in diabetic cardiomyopathy. Pharmacol Res Perspect. 2022;10:e00904.
52. Turroni F, Foroni E, Montanini B, et al. Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative real-time PCR. Appl Environ Microbiol. 2011;77:8578-87.
53. Wada J, Ando T, Kiyohara M, et al.
54. Speciale I, Verma R, Di Lorenzo F, Molinaro A, Im SH, De Castro C.
55. Verma R, Lee C, Jeun EJ, et al. Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells. Sci Immunol. 2018;3:eaat6975.
56. Oliveira FS, Dieckman K, Mota D, et al. Melatonin in human milk: a scoping review. Biol Res Nurs. 2025;27:142-67.
57. Henrick BM, Rodriguez L, Lakshmikanth T, et al. Bifidobacteria-mediated immune system imprinting early in life. Cell. 2021;184:3884-98.e11.
58. Lordan C, Roche AK, Delsing D, et al. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev. 2024;88:e0009423.
59. Bosheva M, Tokodi I, Krasnow A, et al; 5 HMO Study Investigator Consortium. Infant formula with a specific blend of five human milk oligosaccharides drives the gut microbiota development and improves gut maturation markers: a randomized controlled trial. Front Nutr. 2022;9:920362.
60. Brink LR, Mercer KE, Piccolo BD, et al. Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Am J Clin Nutr. 2020;111:1190-202.
