J. L. Mark Welch

Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

This study identifies phages as significant contributors to the strain-level diversity and ecology of Porphyromonas gingivalis, revealing their role in shaping bacterial physiology and interactions.

Spatial organization of the kelp microbiome at micron scales

The paper characterizes the spatial organization of microbial communities on kelp blades, revealing dense, spatially differentiated biofilms and their association with kelp health.

Site-specificity of streptococci in the oral microbiome

The paper investigates site-specificity of Streptococcus species in the human oral microbiome using genomic and metagenomic data, finding that closely related species occupy distinct niches despite similar environmental conditions.

Mechanisms underlying proximity between oral commensal bacteria

The paper investigates interactions between Haemophilus parainfluenzae and Streptococcus mitis in the oral microbiome, revealing density-dependent co-occurrence and metabolic dependencies.

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

The paper uses metapangenomics to analyze oral microbiome diversity, revealing habitat-specific genomic groups and highlighting limitations in cultivated organisms' representation.

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

The paper analyzes oral microbiome metagenomes to identify niche partitioning among TM7 taxa, revealing distinct ecological and genetic patterns between plaque and tongue-associated TM7.

Preservation of three-dimensional spatial structure in the gut microbiome

This study evaluates embedding methods for preserving three-dimensional spatial structure in mouse gut tissue for fluorescence imaging, finding that Technovit H8100 better preserves spatial organization than common media.