This paper compares metagenomic sequencing with traditional culture methods for diagnosing companion animal skin infections, showing that metagenomics identifies pathogens and antibiotic resistance genes as effectively as culture-based methods and provides additional insights into microbiome composition.

bioRxiv · Sep 26, 2025 · PreprintMicrobiology

DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle

Daniel Cook, Brandon Kocurek, Clinton A. Stonecipher, Kevin D. Welch, Dale R. Gardner, Mark K. Mammel, Elizabeth A. Reed, Padmini Ramachandran, David L. Erickson, Seth Commichaux, Andrea Ottesen

The paper uses DNA data and chemical analysis to identify toxic plants in contaminated forage linked to cattle poisoning.

Toxicon · Feb 5, 2025Peer-reviewedGenomics

Paired metagenomic and chemical evaluation of an aflatoxin contaminated dog kibble

Andrea Ottesen, Brandon Kocurek, Elizabeth A. Reed, Seth Commichaux, Mark K. Mammel, Padmini Ramachandran, Patrick F. McDermott, Brenna M. Flannery, Errol A. Strain

The paper evaluates aflatoxin-contaminated dog kibble using paired metagenomic and chemical data to correlate fungal DNA abundance with toxin levels.

Frontiers in Veterinary Science · Apr 11, 2024Peer-reviewedMicrobiology

bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Kranti Konganti, Elizabeth A. Reed, Mark K. Mammel, Tunc Kayikcioglu, Rachel Binet, Karen G. Jarvis, Christina M. Ferreira, Rebecca L. Bell, Jie Zheng, Amanda Windsor, Andrea Ottesen, Christopher J. Grim, Padmini Ramachandran

bettercallsal identifies multiple Salmonella serotypes from enrichment cultures using shotgun metagenomics, outperforming existing tools in accuracy and throughput for outbreak analysis.

Frontiers in Microbiology · Aug 2, 2023Peer-reviewedGenomics