REFERENCES
1. Wirbel J, Pyl PT, Kartal E, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. 2019;25:679-89.
2. Clarke G, O’Mahony SM, Dinan TG, Cryan JF. Priming for health: gut microbiota acquired in early life regulates physiology, brain and behaviour. Acta Paediatr. 2014;103:812-9.
3. Vemuri R, Herath MP. Beyond the gut, emerging microbiome areas of research: a focus on early-life microbial colonization. Microorganisms. 2023;11:239.
4. 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.
5. Fundora JB, Guha P, Shores DR, Pammi M, Maheshwari A. Intestinal dysbiosis and necrotizing enterocolitis: assessment for causality using Bradford Hill criteria. Pediatr Res. 2020;87:235-48.
6. Kennedy KM, de Goffau MC, Perez-Muñoz ME, et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 2023;613:639-49.
7. Bolte EE, Moorshead D, Aagaard KM. Maternal and early life exposures and their potential to influence development of the microbiome. Genome Med. 2022;14:4.
8. Hornef MW, Torow N. ‘Layered immunity’ and the ‘neonatal window of opportunity’ - timed succession of non-redundant phases to establish mucosal host-microbial homeostasis after birth. Immunology. 2020;159:15-25.
9. Torow N, Marsland BJ, Hornef MW, Gollwitzer ES. Neonatal mucosal immunology. Mucosal Immunol. 2017;10:5-17.
10. Yassour M, Jason E, Hogstrom LJ, et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe. 2018;24:146-54.e4.
11. Wampach L, Heintz-Buschart A, Fritz JV, et al. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nat Commun. 2018;9:5091.
12. Ferretti P, Pasolli E, Tett A, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133-45.e5.
13. Browne HP, Shao Y, Lawley TD. Mother-infant transmission of human microbiota. Curr Opin Microbiol. 2022;69:102173.
14. Wang S, Ryan CA, Boyaval P, Dempsey EM, Ross RP, Stanton C. Maternal vertical transmission affecting early-life microbiota development. Trends Microbiol. 2020;28:28-45.
15. Wang S, Egan M, Ryan CA, et al. A good start in life is important - perinatal factors dictate early microbiota development and longer term maturation. FEMS Microbiol Rev. 2020;44:763-81.
17. Warda AK, Dempsey EM, Forssten SD, et al. Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery. BMJ Open. 2022;12:e064398.
18. Hurley E, Mullins D, Barrett MP, et al. The microbiota of the mother at birth and its influence on the emerging infant oral microbiota from birth to 1 year of age: a cohort study. J Oral Microbiol. 2019;11:1599652.
19. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107:11971-5.
20. Yu Z, Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 2004;36:808-12.
21. Fouhy F, Deane J, Rea MC, et al. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One. 2015;10:e0119355.
22. Parnell LA, Briggs CM, Cao B, Delannoy-Bruno O, Schrieffer AE, Mysorekar IU. Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles. Sci Rep. 2017;7:11200.
23. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10.
24. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581-3.
25. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590-6.
26. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
27. Turunen J, Tejesvi MV, Paalanne N, et al. Presence of distinctive microbiome in the first-pass meconium of newborn infants. Sci Rep. 2021;11:19449.
28. Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6:226.
30. Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. F1000Res. 2016;5:1492.
31. Douglas GM, Maffei VJ, Zaneveld JR, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38:685-8.
32. Markowitz VM, Chen IM, Palaniappan K, et al. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115-22.
33. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109-14.
34. Neu AT, Allen EE, Roy K. Defining and quantifying the core microbiome: challenges and prospects. Proc Natl Acad Sci U S A. 2021;118:e2104429118.
35. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000;7:203-14.
36. Hsieh TC, Ma KH, Chao A, Mcinerny G. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol Evol. 2016;7:1451-6.
37. Lubbe S, Filzmoser P, Templ M. Comparison of zero replacement strategies for compositional data with large numbers of zeros. Chemom Intell Lab Syst. 2021;210:104248.
38. Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11:3514.
39. Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123-4.
40. Kennedy KM, Gerlach MJ, Adam T, et al. Fetal meconium does not have a detectable microbiota before birth. Nat Microbiol. 2021;6:865-73.
41. Briana DD, Papaevangelou V, Malamitsi-Puchner A. The jury is still out on the existence of a placental microbiome. Acta Paediatr. 2021;110:2958-63.
42. Blaser MJ, Devkota S, McCoy KD, Relman DA, Yassour M, Young VB. Lessons learned from the prenatal microbiome controversy. Microbiome. 2021;9:8.
43. de Goffau MC, Lager S, Salter SJ, et al. Recognizing the reagent microbiome. Nat Microbiol. 2018;3:851-3.
44. Heida FH, Kooi EMW, Wagner J, et al. Weight shapes the intestinal microbiome in preterm infants: results of a prospective observational study. BMC Microbiol. 2021;21:219.
45. Altuntas EG. Isolation, identification and characterization of Staphylococcus epidermidis in human milk. LWT Food Sci Technol. 2015;60:36-41.
46. Moles L, Gómez M, Heilig H, et al. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS One. 2013;8:e66986.
47. Jiménez E, Delgado S, Maldonado A, et al. Staphylococcus epidermidis: a differential trait of the fecal microbiota of breast-fed infants. BMC Microbiol. 2008;8:143.
48. Klopp J, Ferretti P, Meyer CU, et al; the PRIMAL Consortium. Meconium microbiome of very preterm infants across Germany. mSphere. 2022;7:e0080821.
49. Kang HM, Kim S, Hwang-Bo S, et al. Compositional differences of meconium microbiomes of preterm and term infants, and infants that developed necrotizing enterocolitis or feeding intolerance. Pathogens. 2022;12:55.
50. Rocha-Viggiano AK, Aranda-Romo S, Salgado-Bustamante M, Ovando-Vázquez C, Wu J. Meconium microbiota composition and association with birth delivery mode. Adv Gut Microbiome Res. 2022;2022:1-18.
51. Panzer JJ, Romero R, Greenberg JM, et al. Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets. BMC Microbiol. 2023;23:76.
52. Sterpu I, Fransson E, Hugerth LW, et al. No evidence for a placental microbiome in human pregnancies at term. Am J Obstet Gynecol. 2021;224:296.e1-23.
53. Leiby JS, McCormick K, Sherrill-Mix S, et al. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome. 2018;6:196.
54. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
55. Tanner MA, Goebel BM, Dojka MA, Pace NR. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl Environ Microbiol. 1998;64:3110-3.
56. Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, et al. The oral metagenome in health and disease. ISME J. 2012;6:46-56.
57. Mason MR, Chambers S, Dabdoub SM, Thikkurissy S, Kumar PS. Characterizing oral microbial communities across dentition states and colonization niches. Microbiome. 2018;6:67.
58. Dzidic M, Collado MC, Abrahamsson T, et al. Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay. ISME J. 2018;12:2292-306.
59. Xiao J, Fiscella KA, Gill SR. Oral microbiome: possible harbinger for children’s health. Int J Oral Sci. 2020;12:12.
60. La X, Jiang H, Chen A, et al. Profile of the oral microbiota from preconception to the third trimester of pregnancy and its association with oral hygiene practices. J Oral Microbiol. 2022;14:2053389.
61. Jang H, Patoine A, Wu TT, Castillo DA, Xiao J. Oral microflora and pregnancy: a systematic review and meta-analysis. Sci Rep. 2021;11:16870.
62. DiGiulio DB, Callahan BJ, McMurdie PJ, et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci U S A. 2015;112:11060-5.
63. Jo R, Yama K, Aita Y, et al. Comparison of oral microbiome profiles in 18-month-old infants and their parents. Sci Rep. 2021;11:861.
64. Dashper SG, Mitchell HL, Lê Cao KA, et al. Temporal development of the oral microbiome and prediction of early childhood caries. Sci Rep. 2019;9:19732.
65. Lif Holgerson P, Esberg A, Sjödin A, West CE, Johansson I. A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents. Sci Rep. 2020;10:9629.
66. Gajer P, Brotman RM, Bai G, et al. Temporal dynamics of the human vaginal microbiota. Sci Transl Med. 2012;4:132ra52.
67. Shipitsyna E, Roos A, Datcu R, et al. Composition of the vaginal microbiota in women of reproductive age - sensitive and specific molecular diagnosis of bacterial vaginosis is possible? PLoS One. 2013;8:e60670.
68. Ceccarani C, Foschi C, Parolin C, et al. Diversity of vaginal microbiome and metabolome during genital infections. Sci Rep. 2019;9:14095.
69. Liu F, Zhou Y, Zhu L, et al. Comparative metagenomic analysis of the vaginal microbiome in healthy women. Synth Syst Biotechnol. 2021;6:77-84.
70. 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.
71. Kageyama S, Furuta M, Takeshita T, Ma J, Asakawa M, Yamashita Y. High-level acquisition of maternal oral bacteria in formula-fed infant oral microbiota. mBio. 2022;13:e0345221.
72. Marsh PD, Martin MV, Lewis MAO, Williams D. Oral microbiology. 5th edition. Elsevier Health Sciences; 2009. Available from: https://shop.elsevier.com/books/oral-microbiology/marsh/978-0-443-10144-1. [Last accessed on 29 May 2025].
73. Cephas KD, Kim J, Mathai RA, et al. Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing. PLoS One. 2011;6:e23503.
75. Yang NY, Zhang Q, Li JL, Yang SH, Shi Q. Progression of periodontal inflammation in adolescents is associated with increased number of Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis, and Fusobacterium nucleatum. Int J Paediatr Dent. 2014;24:226-33.
76. Yu JC, Khodadadi H, Salles ÉL, et al. Oral microbiome and innate immunity in health and disease: building a predictive, preventive and personalized therapeutic approach. In: Boyko N, Golubnitschaja O, editors. Microbiome in 3P medicine strategies. Cham: Springer International Publishing; 2023. pp. 391-409.
77. Gomez-Arango LF, Barrett HL, McIntyre HD, Callaway LK, Morrison M, Dekker Nitert M. Antibiotic treatment at delivery shapes the initial oral microbiome in neonates. Sci Rep. 2017;7:43481.
78. Li H, Wang J, Wu L, et al. The impacts of delivery mode on infant’s oral microflora. Sci Rep. 2018;8:11938.
79. Bartlett A, Padfield D, Lear L, Bendall R, Vos M. A comprehensive list of bacterial pathogens infecting humans. Microbiology. 2022;168:1269.
80. Rigauts C, Aizawa J, Taylor SL, et al. R othia mucilaginosa is an anti-inflammatory bacterium in the respiratory tract of patients with chronic lung disease. Eur Respir J. 2022;59:2101293.
81. Zhang C, Yu Z, Zhao J, Zhang H, Zhai Q, Chen W. Colonization and probiotic function of Bifidobacterium longum. J Funct Foods. 2019;53:157-65.
82. Turroni F, Peano C, Pass DA, et al. Diversity of bifidobacteria within the infant gut microbiota. PLoS One. 2012;7:e36957.
83. Mills S, Yang B, Smith GJ, Stanton C, Ross RP. Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond. Gut Microbes. 2023;15:2186098.
84. Choby JE, Skaar EP. Heme synthesis and acquisition in bacterial pathogens. J Mol Biol. 2016;428:3408-28.
85. Palmer LD, Skaar EP. Transition metals and virulence in bacteria. Annu Rev Genet. 2016;50:67-91.
86. Costalonga M, Herzberg MC. The oral microbiome and the immunobiology of periodontal disease and caries. Immunol Lett. 2014;162:22-38.
87. Shabayek S, Abdellah AM, Salah M, Ramadan M, Fahmy N. Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester. BMC Microbiol. 2022;22:313.
88. Piot P, Van Dyck E, Godts P, Vanderheyden J. The vaginal microbial flora in non-specific vaginitis. Eur J Clin Microbiol. 1982;1:301-6.
89. Ison CA, Easmon CS, Dawson SG, Southerton G, Harris JW. Non-volatile fatty acids in the diagnosis of non-specific vaginitis. J Clin Pathol. 1983;36:1367-70.
90. Donders GG, Vereecken A, Bosmans E, Dekeersmaecker A, Salembier G, Spitz B. Definition of a type of abnormal vaginal flora that is distinct from bacterial vaginosis: aerobic vaginitis. BJOG. 2002;109:34-43.
91. Liu Y, Qin S, Song Y, et al. The perturbation of infant gut microbiota caused by cesarean delivery is partially restored by exclusive breastfeeding. Front Microbiol. 2019;10:598.
92. Louis P, Duncan SH, Sheridan PO, Walker AW, Flint HJ. Microbial lactate utilisation and the stability of the gut microbiome. Gut Microbiome. 2022;3:e3.
93. Papapanou PN, Park H, Cheng B, et al. Subgingival microbiome and clinical periodontal status in an elderly cohort: the WHICAP ancillary study of oral health. J Periodontol. 2020;91 Suppl 1:S56-67.
94. Colombo AP, Boches SK, Cotton SL, et al. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol. 2009;80:1421-32.
95. Liu B, Faller LL, Klitgord N, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012;7:e37919.
96. Griffen AL, Beall CJ, Campbell JH, et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012;6:1176-85.
97. Pace RM, Williams JE, Robertson B, et al. Variation in human milk composition is related to differences in milk and infant fecal microbial communities. Microorganisms. 2021;9:1153.
98. Marcobal A, Barboza M, Froehlich JW, et al. Consumption of human milk oligosaccharides by gut-related microbes. J Agric Food Chem. 2010;58:5334-40.
99. Robertson RC, Manges AR, Finlay BB, Prendergast AJ. The human microbiome and child growth - first 1000 days and beyond. Trends Microbiol. 2019;27:131-47.
100. Mach N, Clark A. Micronutrient deficiencies and the human gut microbiota. Trends Microbiol. 2017;25:607-10.
101. Kozyrskyj AL, Kalu R, Koleva PT, Bridgman SL. Fetal programming of overweight through the microbiome: boys are disproportionately affected. J Dev Orig Health Dis. 2016;7:25-34.
102. Gomez A, Luckey D, Taneja V. The gut microbiome in autoimmunity: sex matters. Clin Immunol. 2015;159:154-62.
103. Liu L, Chen J, Chen Y, et al. Characterization of vaginal microbiota in third trimester premature rupture of membranes patients through 16S rDNA sequencing. Pathogens. 2022;11:847.
104. Hezel MP, Weitzberg E. The oral microbiome and nitric oxide homoeostasis. Oral Dis. 2015;21:7-16.
105. Moraes DV, Queiroz DB, Eleutério J Junior. Vaginal probiotics on the outcomes of premature rupture of membranes: a pilot randomised clinical trial. J Obstet Gynaecol. 2022;42:3527-30.
106. Bokulich NA, Chung J, Battaglia T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8:343ra82.
107. Coker MO, Laue HE, Hoen AG, et al. Infant feeding alters the longitudinal impact of birth mode on the development of the gut microbiota in the first year of life. Front Microbiol. 2021;12:642197.
108. Health Research and Information Division. Perinatal Statistics Report 2019. 2021. Available from: https://www.hpo.ie/latest_hipe_nprs_reports/NPRS_2019/Perinatal_Statistics_Report_2019.pdf. [Last accessed on 29 May 2025].
109. Health Service Executive. Irish Maternity Indicator System National Report 2023. 2024. Available from: https://www.hse.ie/eng/about/who/acute-hospitals-division/woman-infants/national-reports-on-womens-health/irish-maternity-indicator-system-national-report-2023.pdf. [Last accessed on 29 May 2025].