Alan J. Wolfe

This study uses long-read shotgun metagenomics to identify distinct urogenital microbial community states in pregnant women, linking them to functional potential and UTI risk.

This study compares five methods for detecting the urobiome in urine samples, finding that shotgun metagenomic sequencing provides the broadest species-level view, while culture methods have specific strengths.

This paper introduces an expanded urine culturing workflow to recover diverse urobiome isolates from postmenopausal women, enabling better characterization of previously underrepresented taxa.

The paper analyzes cross-study metagenomics data to identify microbial signatures associated with urinary tract infections and their genomic variation.

The paper identifies carbamylation as a regulatory modification in β-cell metabolism and insulin processing in T1D by analyzing proteomic changes in NOD and MIN6 cells.

PTMOverlay visualizes post-translational modifications across species by aligning PTM sites to protein sequences, revealing conserved modifications in bacterial central carbon metabolism.

The paper introduces SimUrine, a fully defined synthetic urine medium that supports diverse urinary microbiome growth and reveals novel microbial interactions and antimicrobial susceptibility patterns.

This study examines how Enterococcus faecalis affects the transcriptome and metabolism of Escherichia coli in co-culture, revealing strain-specific responses and nutrient cross-feeding.

The paper investigates the presence of an indigenous urobiome in female mice by analyzing urine samples using different extraction methods and sequencing techniques.

This study uses genomic analysis of environmental samples to identify and assign lineages of Bacillus anthracis in Pakistan, providing new reference genomes and identifying a minor sublineage.

This study investigates urinary free oligosaccharides and microbial gene capacity for glycan digestion in women with and without overactive bladder syndrome.

The paper assesses how common storage conditions and additives affect urinary metabolite profiles, finding minimal impact from storage but significant changes from a DNA-stabilizer.

The paper identifies conserved bacterial protein methylation, showing ribosomal protein L11 methylation regulates stringent response signaling and ribosomal homeostasis.

This study shows species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing by optimizing reference databases and variable regions.

This study evaluates two computational methods for removing contaminants in low biomass 16S rRNA gene sequencing, finding that Decontam consistently outperforms SourceTracker in contaminant removal.