Raphael Eisenhofer

The paper introduces SMF, an algorithm to estimate bacterial and archaeal DNA prevalence in metagenomes, revealing biome-specific patterns and highlighting issues with human host DNA in public repositories.

This study compares 16S amplicon sequencing and genome-resolved metagenomics for analyzing bat gut microbiomes, finding significant differences in diversity and functional profiles between methods.

This study examines changes in the echidna pseudo-pouch microbiome during lactation, finding a reduction in potentially pathogenic bacteria, and compares wild and zoo-managed animals.

This paper reviews 243 insect microbiota studies and finds that two-thirds lack negative controls, highlighting a major gap in contamination control practices.

This study examines how gut microbiota changes in domestic and feral cats worldwide, finding functional differences linked to feral lifestyle adaptations.

This study uses paleogenomic and paleoclimatic data to reconstruct historical changes in coral holobiont composition linked to anthropogenic disturbances in a Caribbean reef.

The paper compares short-read, HiFi long-read, and hybrid sequencing strategies for genome-resolved metagenomics, finding each excels in different metrics like assembly quality, bin refinement, and mapping rate.

The paper quantifies eukaryotic DNA in metagenomes and shows it biases microbial trait estimation, finding that correcting this improves the relationship between genome size and soil pH.