The paper develops a tool to analyze tetranucleotide frequencies in metagenomes, revealing environmental-specific microbial community patterns and metabolic trends across 12,000 samples.

mSystems · Jul 8, 2025Peer-reviewedEcology

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle:High-Resolution Sampling Every 4 Hours Over 22 Days

Brook L. Nunn, Emma Timmins‐Schiffman, Miranda C. Mudge, Deanna L. Plubell, Gabriella Chebli, Julia Kubanek, Michael E. Riffle, William Stafford Noble, Elizabeth L. Harvey, Tasman A. Nunn, Tatiana Rynearson, Marcel Huntemann, Kurt LaButti, Brian Foster, Bryce Foster, , Emiley A. Eloe‐Fadrosh

The paper describes a high-resolution microbial metagenome dataset collected over 22 days during a phytoplankton bloom cycle, including gene abundances and time-matched environmental data.

Scientific Data · Nov 22, 2024Peer-reviewedEcology

Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot

Antônio Pedro Camargo, Rafael Soares Correa de Souza, Juliana José, Isabel Rodrigues Gerhardt, Ricardo Augusto Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo Falsarella Carazzolle, Paulo Arruda

The paper investigates how plant-associated microbiomes in nutrient-poor Brazilian campos rupestres substrates contribute to nutrient cycling, revealing novel microbial populations and mechanisms for phosphorus and nitrogen turnover.

The ISME Journal · Dec 19, 2022Peer-reviewedGenomics

The DOE JGI Metagenome Workflow

Alicia Clum, Marcel Huntemann, Brian Bushnell, Brian Foster, Bryce Foster, Simon Roux, Patrick P. Hajek, Neha Jacob Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris G. Daum, Yuko Yoshinaga, Ronan C. O’Malley, R. Seshadri, Nikos C. Kyrpides, , Natalia Ivanova

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.

mSystems · May 17, 2021Peer-reviewedBioinformatics