Page 53 - Read Online

Kreuze et al. Microbiome Res Rep 2025;4:7 https://dx.doi.org/10.20517/mrr.2024.51 Page 11 of 14

diversity in the infant gut. BMC Genomics 2023;24:295. DOI PubMed PMC
17. Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The gut virome database reveals age-dependent patterns of
virome diversity in the human gut. Cell Host Microbe 2020;28:724-40.e8. DOI PubMed PMC
18. Yu MK, Fogarty EC, Eren AM. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and
MobMess. Nat Microbiol 2024;9:830-47. DOI PubMed PMC
19. Vatanen T, Jabbar KS, Ruohtula T, et al. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly
and metabolism. Cell 2022;185:4921-36.e15. DOI PubMed PMC
20. Shah SA, Deng L, Thorsen J, et al. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023;8:986-98. DOI
PubMed PMC
21. He W, Russel J, Klincke F, Nesme J, Sørensen SJ. Insights into the ecology of the infant gut plasmidome. Nat Commun
2024;15:6924. DOI PubMed PMC
22. Hall JPJ, Harrison E, Baltrus DA. Introduction: the secret lives of microbial mobile genetic elements. Philos Trans R Soc Lond B Biol
Sci 2022;377:20200460. DOI PubMed PMC
23. Bittinger K, Zhao C, Li Y, et al. Bacterial colonization reprograms the neonatal gut metabolome. Nat Microbiol 2020;5:838-47. DOI
PubMed PMC
24. Vatanen T, Ang QY, Siegwald L, et al. A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during
weaning. Cell 2022;185:4280-97.e12. DOI PubMed
25. Liang G, Zhao C, Zhang H, et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 2020;581:470-
4. DOI PubMed PMC
26. Bethke JH, Ma HR, Tsoi R, Cheng L, Xiao M, You L. Vertical and horizontal gene transfer tradeoffs direct plasmid fitness. Mol Syst
Biol 2023;19:e11300. DOI PubMed PMC
27. Ewald PW. Transmission modes and evolution of the parasitism-mutualism continuum. Ann N Y Acad Sci 1987;503:295-306. DOI
PubMed
28. Turner PE, Cooper VS, Lenski RE. Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution
1998;52:315-29. DOI PubMed
29. Rankin DJ, Rocha EP, Brown SP. What traits are carried on mobile genetic elements, and why? Heredity 2011;106:1-10. DOI
PubMed PMC
30. Niu J, Xu L, Qian Y, et al. Evolution of the gut microbiome in early childhood: a cross-sectional study of Chinese children. Front
Microbiol 2020;11:439. DOI PubMed PMC
Mäntynen S, Laanto E, Oksanen HM, Poranen MM, Díaz-Muñoz SL. Black box of phage-bacterium interactions: exploring
31. kingdom marker gene analysis. bioRxiv 2023. DOI PubMed PMC
alternative phage infection strategies. Open Biol 2021;11:210188. DOI PubMed PMC
32. Davray D, Deo D, Kulkarni R. Plasmids encode niche-specific traits in Lactobacillaceae. Microb Genom 2021;7:mgen000472. DOI
PubMed PMC
33. LeGault KN, Hays SG, Angermeyer A, et al. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts.
Science 2021;373:eabg2166. DOI PubMed PMC
34. Dragoš A, Andersen AJC, Lozano-Andrade CN, Kempen PJ, Kovács ÁT, Strube ML. Phages carry interbacterial weapons encoded
by biosynthetic gene clusters. Curr Biol 2021;31:3479-89.e5. DOI PubMed
35. Dineen RL, Bottacini F, O’Connell-Motherway M, van Sinderen D. Transcriptional landscape of the pMP7017 megaplasmid and its
impact on the Bifidobacterium breve UCC2003 transcriptome. Microb Biotechnol 2024;17:e14405. DOI PubMed PMC
36. Martínez Arbas S, Narayanasamy S, Herold M, et al. Roles of bacteriophages, plasmids and CRISPR immunity in microbial
community dynamics revealed using time-series integrated meta-omics. Nat Microbiol 2021;6:123-35. DOI PubMed PMC
37. Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. Bacteriophage 2011;1:31-45. DOI PubMed PMC
38. Tisza M, Lloyd R, Hoffman K, et al; TEDDY Study Group. Phage-bacteria dynamics during the first years of life revealed by trans-

39. Lou YC, Chen L, Borges AL, et al. Infant gut DNA bacteriophage strain persistence during the first 3 years of life. Cell Host Microbe
2024;32:35-47.e6. DOI PubMed PMC
40. Maqsood R, Rodgers R, Rodriguez C, et al. Discordant transmission of bacteria and viruses from mothers to babies at birth.
Microbiome 2019;7:156. DOI PubMed PMC
41. Garmaeva S, Sinha T, Gulyaeva A, et al; Lifelines NEXT cohort study. Transmission and dynamics of mother-infant gut viruses
during pregnancy and early life. Nat Commun 2024;15:1945. DOI PubMed PMC
42. Mathieu A, Dion M, Deng L, et al. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than
temperate coliphages. Nat Commun 2020;11:378. DOI PubMed PMC
43. Redgwell TA, Thorsen J, Petit MA, et al. Prophages in the infant gut are largely induced, and may be functionally relevant to their
hosts. Available from: https://www.biorxiv.org/content/10.1101/2021.06.25.449885v1. [Last accessed on 8 Nov 2024].
44. Beller L, Deboutte W, Vieira-Silva S, et al. The virota and its transkingdom interactions in the healthy infant gut. Proc Natl Acad Sci
U S A 2022;119:e2114619119. DOI PubMed PMC
45. Zeng S, Almeida A, Li S, et al. A metagenomic catalog of the early-life human gut virome. Nat Commun 2024;15:1864. DOI
PubMed PMC
46. Humphrey S, Fillol-Salom A, Quiles-Puchalt N, et al. Bacterial chromosomal mobility via lateral transduction exceeds that of