GTX-GUT: A Standardized Metagenomic Workflow for Gut Microbiome Profiling and Clinical Associations

Robust taxonomic classification in gut and vaginal microbiomes demonstrated through benchmarking with age-specific synthetic communities

Multi-layer gut microbiome variation in type 2 diabetes despite preserved higher-order community structure

These findings provide a multi-layer description of T2D-associated gut microbiome variation within this cohort, consistent with preserved higher-order community organization accompanied by finer-scale differences in species composition, functional potential, community-state occupancy, statistical co-occurrence, and wit...

Bioinformatic tools for microbiome analysis: from raw sequences to biological insights

This review presents a practical, workflow-oriented guide to microbiome data analysis, from raw DNA sequence processing to statistical interpretation and biological insight, and highlights emerging technologies, including machine learning methods that are beginning to reshape the field.

MGM2 as a Unified Foundation Model for Microbiome World Exploration

MGM2 provides a sequence-aware and interpretable representation layer for microbiome classification, paired-community prediction, forecasting and feature discovery and a 4,096-feature sparse autoencoder atlas resolves taxonomic, abundance, ecological and technical signals.

HuMMANet: A Harmonized Cross-Study Resource for Integrative Analysis of Human Gut Microbiome–Metabolome Associations

HuMMANet provides a standardized framework for reproducible microbiome–metabolome integration, enabling cross-study discovery and translational prioritization of conserved microbiome-derived metabolic signatures across human populations and disease states.

Metagenomic analysis of tongue samples from healthy subjects identifies distinct microbiome orotypes

The findings identify distinct tongue microbiome orotypes with conserved core functions, divergent taxonomic and metabolic profiles, and provide new insights into the tongue phageome, establishing a foundation for investigating their roles in health.