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Open access Aug 2026

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

Application to a human sample from a patient with type 2 Diabetes Mellitus recovered a dysbiotic signature consistent with the literature, including reduced Firmicutes abundance, elevated Bacteroidetes and Proteobacteria, and a predominance of clinical associations within metabolic and gastrointestinal categories.

Rodrigo Lima Andrade, Tayná da Silva Fiúza, J. Kroll et al. · 0 citations
Open access Sep 2026

Metax enables accurate cross-domain taxonomic profiling of metagenomes.

Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomi...

Zhi-Luo Deng, Nasim Safaei, A. McHardy · 0 citations
Open access Aug 2026

Development and Validation of Mock Communities as Quality Control Materials for Clinical Metagenomic Next-Generation Sequencing.

Background Metagenomic next-generation sequencing (NGS) enables comprehensive detection of a broad spectrum of microorganisms. However, its clinical application faces two major challenges: the development of appropriate microbiome-based biomarkers and the need to ensure the reproducibility and quality of the microbiome...

Dokyun Kim, Songhee Lee, Da-Young Kang et al. · 0 citations
Review Open access Jul 2026

From Scat to Sequencing: Non-Invasive Methods for Wildlife Microbiome Research and Conservation

The gut microbiome, a complex community of microorganisms in the gastrointestinal tract, plays a vital role in host health, nutrition and adaptability. Advances in next-generation sequencing and metagenomics have deepened our understanding of how diet and environmental factors shape microbial diversity. In wild animals...

Pritee Chunarkar, Manoj Malavika, Rahul Gupta et al. · 0 citations
Review Open access Jul 2026

Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems

The recognition of the urinary microbiome (urobiome) has challenged the long-standing paradigm of urinary tract sterility, revealing diverse microbial communities associated with both urinary health and disease. However, the characterization of the urobiome remains highly variable across studies, particularly due to th...

Viviana Méndez-Sacta, Solmayra Agreda Orellana, Luz María Ayavaca-Tapia et al. · 0 citations
Open access Sep 2026

Seven gut microbiome types across two Japanese cohorts defined by co-abundance-based microbial guilds and associated with host physiology

Intensive efforts have been made to capture structural features of the gut microbiome for assessing microbiota status in relation to host health. However, gut microbiome function emerges not only from individual microbial taxa but also from their organization into ecological guilds, complicating microbiome structure-fu...

Jiro Nakayama, Misako Yoden, Ayaka Uchikawa et al. · 0 citations

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