Topic: Tools and Resources for Microbiome Research

Rapid advances in microbiome science increasingly rely on powerful computational tools, comprehensive databases, and high-quality datasets to support robust analysis, interpretation, and integration of complex microbial community data. Together, these tools and resources are expected to enable deeper functional interpretation of microbiome composition, facilitate the discovery of microbe–microbe and microbe–host interactions, and accelerate mechanistic insights into microbiome-associated health and disease.

This Special Issue, entitled “Tools and Resources for Microbiome Research,” invites contributions that present innovative methods, platforms, benchmarks, and data resources addressing key challenges in microbiome science—from data generation and processing to analysis, interpretation, and application. We particularly welcome submissions that strengthen the computational and data infrastructure of microbiome research, support open and FAIR (Findable, Accessible, Interoperable, and Reusable) data practices, and catalyze broad adoption by the international research community.

● We encourage submissions on, but not limited to, the following themes:

● Original tools and software developed for microbiome data processing, analysis, visualization, or interpretation [e.g., pipelines, packages, workflows, and application programming interfaces (APIs)];

● Tool updates and enhancements that provide significant improvements over existing methods in terms of accuracy, scalability, usability, or interoperability;

● Benchmark studies comparing methods for key microbiome analysis tasks, such as taxonomic profiling, functional prediction, genome assembly, binning, strain-level resolution, and statistical modeling;

● Databases and repositories that curate microbiome-relevant data (e.g., gut microbiome-human disease associations, environmental microbiomes, and host-associated microbiomes) with rich metadata and standardized formats;

● Novel datasets and genomic resources, including high-quality metagenome-assembled genomes (MAGs), viral genomes, reference collections, mock communities, and multi-omics datasets that can serve as community standards;

● Standards, data formats, and ontologies that advance FAIR principles for microbiome data and tools.

Microbiome bioinformatics, computational tools, benchmarking and method evaluation; microbiome databases, metagenomic resources, metagenome-assembled genomes (MAGs) , data resources and repositories, fair data and reproducibility, microbiome analytics, open-source software