Knut Rudi

This study benchmarks 16S rRNA gene analysis pipelines in high-diversity datasets, revealing trade-offs between clustering accuracy, species recovery, and abundance reconstruction.

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

The paper develops a targeted reference database, AQUAeD-DB, to improve taxonomic accuracy of 16S rRNA sequencing data from seafloor sediments using Oxford Nanopore Technologies.

This study compares Illumina and Nanopore 16S rRNA sequencing for predicting seafloor ecological state using machine learning and feature selection, showing comparable performance with Nanopore as a viable alternative.

The paper examines the relationship between microbial sulfur and ammonium oxidizers and macrofaunal state in coastal seafloor samples, finding distinct microbial networks linked to macrofauna loss or preservation.

The paper traces streptococcal strains from infant stool to other body sites, showing gut-specific strains are linked to adhesin gene differences.

This study examines how dietary chitin affects chitinase activity, gene expression, and gut microbial composition in Atlantic salmon.

The paper presents the Salmon Microbial Genome Atlas, a collection of bacterial genomes from Atlantic salmon, and functionally characterizes key gut microbiota populations involved in nutrient processing and health.

This study examines the relationship between gut microbiota and metabolism in Atlantic salmon, finding significant associations between specific microbial OTUs and metabolic phenotypes.

The paper uses reduced metagenome sequencing to analyze genetic diversity and mother-child sharing of gut microbiota in 17 pairs, finding significant sequence overlap and transmission of specific bacteria.