Author

Anthony A. Fodor

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Open access Oct 2026

Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes

Accurate species-level profiling of shotgun metagenomes becomes difficult when an organism is represented by only sparse sequence coverage. Per-read k-mer classifiers can retain sensitivity under these conditions, but short reads from conserved or shared genomic regions can generate false-positive calls among closely r...

Shan Sun, Anthony A. Fodor · bioRxiv · 0 citations

Open access Aug 2026

Defined human Clostridia consortia reverse colitis via dual effects of tryptophan metabolites on microbiota and immunity

SUMMARY Microbial dysbiosis and disrupted mucosal immune homeostasis are integrally involved in the pathogenesis of inflammatory bowel diseases (IBD). Live biotherapeutic products (LBPs) offer a potential therapeutic strategy to restore beneficial microbes and mitigate disease. We investigated the therapeutic efficacy...

A. Oka, G. Bongers, Y. Mishima et al. · Cell Host and Microbe · 0 citations

Open access Aug 2026

Circulating Microbial DNA as a Potential Cancer Biomarker: Technical Challenges and Controlled Evaluation

Much of the apparent cmDNA structure, including its agreement with a published cancer-microbiome catalog, is explained by base composition and reference-database architecture rather than authentic biology, and short-read k-mer pipelines cannot separate the two on their own.

Daisy Fry Brumit, Daniel Bsteh, Shan Sun et al. · bioRxiv · 0 citations