In Silico Technologies Advancing Microbial Science: A Visionary Review
Received: 02 Dec 2025 | Accepted: 16 Dec 2025 | Published: 05 Jan 2026
Woo, P.C.Y. Rigorous Analysis of Microbes and Infectious Diseases Using an Expanding Range of Robust in Silico Technologies. eMicrobe 2025, 1, 1. https://doi.org/10.53941/emicrobe.2025.100001.
Saenz, C.; Nigro, E.; Gunalan, V.; et al. MIntO: A Modular and Scalable Pipeline for Microbiome Metagenomic and Metatranscriptomic Data Integration. Front. Bioinform. 2022, 2, 846922. https://doi.org/10.3389/fbinf.2022.846922.
Peng, Y.; Liu, Y.; Liu, Y.; et al. Comprehensive Data Optimisation and Risk Prediction Framework: Machine Learning Methods for Inflammatory Bowel Disease Prediction Based on the Human Gut Microbiome Data. Front. Microbiol. 2024, 15, 1483084. https://doi.org/10.3389/fmicb.2024.1483084.
Gao, Y.; Liu, M. Application of Machine Learning Based Genome Sequence Analysis in Pathogen Identification. Front. Microbiol. 2024, 15, 1474078. https://doi.org/10.3389/fmicb.2024.1474078.
Dakal, T.C.; Xu, C.; Kumar, A. Advanced Computational Tools, Artificial Intelligence and Machine Learning Approaches in Gut Microbiota and Biomarker Identification. Front. Med. Technol. 2025, 6, 1434799. https://doi.org/10.3389/fmedt.2024.1434799.
Liu, Y.Y. Deep Learning for Microbiome-Informed Precision Nutrition. Natl. Sci. Rev. 2025, 12, nwaf148. https://doi.org/10.1093/nsr/nwaf148.
Nahar, L. Gut Feeling: What Gut Microbes Do and Why They Matter. J. Med. Nat. Prod. 2025, 2, 100022. https://doi.org/10.53941/jmnp.2025.100022.
Michel, C.; Martin, C.; Smeesters, P.; et al. Next‑Generation Sequencing: What Are the Needs in Routine Clinical Microbiology? A Survey Among Clinicians Involved in Infectious‑Diseases Practice. Front. Med. 2023, 10, 1225408. https://doi.org/10.3389/fmed.2023.1225408.
Elbehiry, A.; Abalkhail, A. Metagenomic Next‑Generation Sequencing in Infectious Diseases: Clinical Applications, Translational Challenges, and Future Directions. Diagnostics 2025, 15, 1991. https://doi.org/10.3390/diagnostics15161991.
Huttenhower, C.; Finn, R.D.; McHardy, A.C. Challenges and Opportunities in Sharing Microbiome Data and Analyses. Nat. Microbiol. 2023, 8, 1960–1970. https://doi.org/10.1038/s41564-023-01484-x.
Fahmi, A.; Palin, V.; Zhong, X.; et al. Evaluation of the Impact of COVID‑19 Pandemic on Hospital Admission Related to Common Infections: Risk Prediction Models to Tackle Antimicrobial Resistance in Primary Care. PLoS One 2025, 20, e0321408. https://doi.org/10.1371/journal.pone.0321408.
Newton, C.R. Research and Open Access from Low‑ and Middle‑Income Countries. Dev. Med. Child Neurol. 2020, 62, 537. https://doi.org/10.1111/dmcn.14513.

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