Dennis Sandris Nielsen

This paper introduces a high-throughput sequencing method using Oxford Nanopore Technologies to sequence over 1,200 gut microbiome samples with near-full-length 16S rRNA gene amplicons, achieving high accuracy and scalability.

This study examines how stool timing, sleep, and feeding affect the gut microbiome composition in infants, finding associations between longer intervals since last defecation and increased microbial diversity.

The paper introduces LACA, a de novo clustering workflow for long-read amplicons that improves phylogenetic analysis and phenotype characterization in microbiome data.

This study isolates and characterizes virulent bacteriophages targeting Enterobacteriaceae from preterm piglets with NEC-like inflammation, showing their potential for phage therapy.

This study shows that active donor virome in fecal filtrate transfer reduces NEC severity in preterm piglets, while inactivated virome abolishes these protective effects.

This study shows that gut microbiota influences liver pathology caused by Schistosoma mansoni infection in mice, but not ileum inflammation.

This study examines the relationship between gut microbiota rhythmicity and sleep-wake pattern maturation in infants, finding associations between microbial oscillations and circadian development.

This study investigates how protein fermentation metabolites affect cytokine production in dendritic cells, finding that short-chain fatty acids have distinct immune-modulating effects compared to butyrate.

This study shows that chemostat culturing reduces eukaryotic virus load in fecal viromes and delays diarrhea in preterm piglets, but does not prevent NEC and reduces microbiome effects.

This paper introduces a single-stranded library preparation method for virome characterization, showing improved accuracy and reduced bias compared to existing methods.

This study shows that polyphenol intake interacts with parasitic whipworm infection in mice, altering immune responses and gut microbial metabolism.

The paper investigates how the choice of ultrafilter affects the recovery of bacteriophages from clinical samples, finding that pore size influences recovery strain- and sample-dependently.

The paper links gut microbiome composition and its metabolic traits to lipoprotein distribution profiles in healthy individuals.

The paper develops PHAMB, a method to bin viral genomes from bulk metagenomics data, and applies it to the HMP2 cohort to recover viral genomes and explore viral-host interactions.

The paper develops partial least squares regression models to predict human blood lipoprotein subfractions from 1H NMR spectra, achieving high accuracy in independent cohorts.