[
Bokulich, N. A., Chung, J., Battaglia, T., Henderson, N., Jay, M., Li, H., Lieber, A. D., Wu, F., Perez-Perez, G. I., Chen, Y., et al. (2016). Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci. Transl. Med., 8 (343), 343ra82. https://doi.org/10.1126/scitranslmed.aad7121.
]Search in Google Scholar
[
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnol., 37 (8), 852–857. 10.1038/s41587-019-0209-9). Author Correction in Nature Biotechnol., 37 (9). https://doi.org/10.1038/s41587-019-0252-6.
]Search in Google Scholar
[
Bourke, C. D., Gough, E. K., Pimundu, G., Shonhai, A., Berejena, C., Terry, L., Baumard, L., Choudhry, N., Karmali, Y., Bwakura-Dangarembizi, M., et al. (2019). Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation. Sci. Transl. Med., 11 (486), eaav0537. https://doi.org/10.1126/scitranslmed.aav0537.
]Search in Google Scholar
[
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Meth., 13 (7). https://doi.org/10.1038/nmeth.3869.
]Search in Google Scholar
[
Chen, S., Zhou, Y., Chen, Y., Gu, J. (2018). Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34 (17). https://doi.org/10.1093/bioinformatics/bty560.
]Search in Google Scholar
[
Elvers, K. T., Wilson, V. J., Hammond, A., Duncan, L., Huntley, A. L., Hay, A. D., van der Werf, E. T. (2020). Antibiotic-induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: A systematic review. BMJ Open, 10 (9). https://doi.org/10.1136/bmjopen-2019-035677.
]Search in Google Scholar
[
Glöckner, F. O., Yilmaz, P., Quast, C., Gerken, J., Beccati, A., Ciuprina, A., Bruns, G., Yarza, P., Peplies, J., Westram, R., Ludwig, W. (2017). 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol., 261, 169–176. https://doi.org/10.1016/j.jbiotec.2017.06.1198.
]Search in Google Scholar
[
Gudra, D., Pupola, D., Skenders, G., Leja, M., Radovica-Spalvina, I., Gorskis, H., Vangravs, R., Fridmanis, D. (2020). Lack of significant differences between gastrointestinal tract microbial population structure of Helicobacter pylori-infected subjects before and 2 years after a single eradication event. Helicobacter, 25 (5), e12748. https://doi.org/10.1111/hel.12748.
]Search in Google Scholar
[
Katoh, K., Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evolut., 30 (4), 772–780. https://doi.org/10.1093/molbev/mst010.
]Search in Google Scholar
[
Korpela, K., de Vos, W. M. (2018). Early life colonization of the human gut: Microbes matter everywhere. Curr. Opin. Microbiol., 44, 70–78. https://doi.org/10.1016/j.mib.2018.06.003.
]Search in Google Scholar
[
Luo, Y., Li, M., Luo, D., Tang, B. (2025). Gut microbiota: An important participant in childhood obesity. Adv. Nutr., 16 (2), 100362. https://doi.org/10.1016/j.advnut.2024.100362.
]Search in Google Scholar
[
McMurdie, P. J., Holmes, S. (2013). Phyloseq: An R ]ackage for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE, 8 (4), e61217. https://doi.org/10.1371/journal.pone.0061217.
]Search in Google Scholar
[
Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, T., Hansen, T. H., Liang, S., Feng, Q., Zhang, C., et al. (2018). Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat. Microbiol., 3 (11), 1255–1265. https://doi.org/10.1038/s41564-018-0257-9.
]Search in Google Scholar
[
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B. (2011). Scikit-learn: Machine learning in Python. J. Machine Learn. Res., 12, 2825–2830. https://dl.acm.org/doi/10.5555/1953048.2078195.
]Search in Google Scholar
[
Price, M. N., Dehal, P. S., Arkin, A. P. (2010). FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS ONE, 5 (3), 9490. https://doi.org/10.1371/journal.pone.0009490
]Search in Google Scholar
[
Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F. (2016). VSEARCH: A versatile open source tool for metagenomics. Peer J., 4, e2584. https://doi.org/10.7717/peerj.2584.
]Search in Google Scholar
[
Ssekagiri, A. (2023). microbiomeSeq: Microbial community analysis in an environmental context. GitHub. http://www.github.com/umerijaz/microbiomeseq.
]Search in Google Scholar
[
Vangay, P., Ward, T., Gerber, J. S., Knights, D. (2015). Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe, 17 (5), 553-564. https://doi.org/10.1016/j.chom.2015.04.006
]Search in Google Scholar
[
Wurm, J., Curtis, N., Zimmermann, P. (2024). The effect of antibiotics on the intestinal microbiota in children: A systematic review. Frontiers Allergy, 5. https://doi.org/10.3389/falgy.2024.1458688.
]Search in Google Scholar
[
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A. M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., Lander, E. S., Knip, M., Xavier, R. J. (2016). Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl. Med., 8 (343), 343ra81. https://doi.org/10.1126/scitranslmed.aad0917.
]Search in Google Scholar
[
Zimmermann, P., Curtis, N. (2019). The effect of antibiotics on the composition of the intestinal microbiota: a systematic review. J. Infect., 79 (6), 471-489. https://doi.org/10.1016/j.jinf.2019.10.008.
]Search in Google Scholar
[
Zuo, W., Wang, B., Bai, X., Luan, Y., Fan, Y., Michail, S., Sun, F. (2022). 16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis. Sci. Rep., 12 (1)., 6421. https://doi.org/10.1038/s41598-022-07995-7.
]Search in Google Scholar