REFERENCES
1. Milani C, Mancabelli L, Lugli GA, et al. Exploring vertical transmission of bifidobacteria from mother to child. Appl Environ Microbiol. 2015;81:7078-87.
2. Longhi G, Lugli G, Bianchi M, et al. Highly conserved bifidobacteria in the human gut: Bifidobacterium longum subsp. longum as a potential modulator of elderly innate immunity. Benef. Microbes. 2024;15:241-58.
3. 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.
4. Feehily C, O’neill IJ, Walsh CJ, et al. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nat Commun. 2023;14:3015.
5. Duval A, Opatowski L, Brisse S. Defining genomic epidemiology thresholds for common-source bacterial outbreaks: a modelling study. The Lancet Microbe. 2023;4:e349-57.
6. Coll F, Raven KE, Knight GM, et al. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. The Lancet Microbe. 2020;1:e328-35.
7. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
8. Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10:giab008.
9. Lugli GA, Fontana F, Tarracchini C, et al. MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes. Microbiome Res Rep. 2023;2:15.
10. Hernández-Salmerón JE, Moreno-Hagelsieb G. FastANI, Mash and dashing equally differentiate between Klebsiella species. PeerJ. 2022;10:e13784.
11. Shaw J, Yu YW. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat Methods. 2023;20:1661-5.
12. Viver T, Conrad RE, Rodriguez-r LM, et al. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun. 2024;15:544.
13. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 2009;106:19126-31.
14. Salamzade R, Kottapalli A, Kalan LR. skDER and CiDDER: two scalable approaches for microbial genome dereplication. Microbial Genomics. 2025;11:001438.
15. Castillo-Ramírez S. On the road to genomically defining bacterial intra-species units. mSystems. 2024;9:e00584-24.
16. Rodriguez-R LM, Conrad RE, Viver T, et al. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio. 2024;15:e02696-23.
