M. S. Dueholm

The predicted secreted proteome of activated sludge microorganisms indicate distinct nutrient niches

The paper predicts secreted proteomes of activated sludge microorganisms to identify nutrient niches, finding distinct enzyme profiles among microbial taxa.

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

This study characterizes Chloroflexota in wastewater treatment plants globally, identifying novel taxa and their ecological roles in carbon and nutrient cycling.

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

The paper constructs MiDAS 4, a comprehensive 16S rRNA gene reference database for wastewater treatment plants, improving classification accuracy and revealing microbial community patterns globally.

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers

This study characterizes the microbial communities in 46 anaerobic digesters over six years, identifying key drivers shaping microbiome structure and highlighting the role of immigration in bacterial diversity.

Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing

The paper uses long-read sequencing to recover over 1000 high-quality MAGs from wastewater treatment plants, enabling linkage of microbial community structure to function.

Functional amyloids in the microbiomes of a rat Parkinson's disease model and wild-type rats

The paper identifies functional amyloid proteins in the microbiomes of Parkinson's disease and wild-type rats, showing they form stable amyloid structures but do not promote SN aggregation.

Generation of comprehensive ecosystems-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax)

The paper generates ecosystem-specific 16S rRNA gene reference databases with high-identity sequences and introduces AutoTax for automated taxonomy assignment, improving classification accuracy for microbial communities.

Species-level microbiome composition of activated sludge - introducing the MiDAS 3 ecosystem-specific reference database and taxonomy

The paper introduces MiDAS 3, a 16S rRNA gene reference database for activated sludge and anaerobic digesters, and updates the MiDAS Field Guide with species-level taxonomy and functional information.

The proteome of Tetrasphaera elongata is adapted to changing conditions in wastewater treatment plants

This study investigates how Tetrasphaera elongata adapts to aerobic-anoxic shifts in wastewater treatment plants using proteomics and metabolomics, revealing efficient substrate utilization and pre-existing anaerobic pathways.

Novel prosthecate bacteria from the candidate phylum Acetothermia revealed by culture-independent genomics and advanced microscopy

The paper identifies a novel Acetothermia bacterium from anaerobic digesters, characterizes its genome and metabolism, and proposes a role for its unique prosthecae in nutrient uptake.

Identifying the abundant and active microorganisms common to full scale anaerobic digesters

The paper identifies abundant and active microorganisms in full-scale anaerobic digesters by analyzing microbial communities over six years using 16S rRNA sequencing.