M. Shaffer

Time resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation

This study uses multi-omics to analyze Salmonella's metabolic strategies in mice on different diets over time, identifying phase-specific gene expression linked to infection stages and therapeutic targets.

Heat Inactivation of Aqueous Viable Norovirus and MS2 Bacteriophage

This study compares heat inactivation kinetics of viable human norovirus and MS2 bacteriophage using human intestinal enteroids, finding significant differences in decay rates and showing RNA titers do not reflect viable virus persistence.

Environmental Persistence and Disinfection of Lassa Virus

This study examines the environmental persistence of Lassa virus strains on surfaces and their inactivation by sodium hypochlorite.

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

The paper analyzes spatial and temporal metagenomic data from a wastewater-impacted river to reveal viral and microbial community dynamics and their potential roles in biogeochemical cycles.

Human-gut phages harbor sporulation genes

The paper identifies sporulation genes in human gut phages that may influence bacterial spore formation and host microbiome health.

Exposing New Taxonomic Variation with Inflammation-A Murine Model-Specific Genome Database for Gut Microbiome Researchers

The paper presents a genomic catalog of the CBA/J murine gut microbiome, revealing taxonomic and functional changes during Salmonella-induced inflammation.

Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments

The paper integrates metagenomic, metaproteomic, and metabolomic data from river sediments to uncover microbial and viral roles in carbon and nitrogen cycling, creating a genomic resource called HUM-V.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

DRAM automates microbiome function curation by translating genomic data into microbial traits, accurately assigning metabolic roles in soil and gut communities.

AMON: Annotation of metabolite origins via networks to better integrate microbiome and metabolome data

AMON identifies the origin of metabolites as host, microbial, or environmental to improve integration of microbiome and metabolome data.

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

The paper examines microbiome differences in HIV-infected and uninfected men who have sex with men, identifying lifestyle, ART, and HIV-related factors influencing gut microbiota composition.