M. Dueholm

发表

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

M. Nierychlo, M. Peces, Chenjing Jiang, 2020, bioRxiv.

Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)

S. McIlroy, P. Nielsen, E. Yashiro, 2020, mBio.

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)

M. Nierychlo, S. McIlroy, P. Nielsen, 2020 .

Survival and activity of individual bioaugmentation strains.

J. Nielsen, P. Nielsen, M. Dueholm, 2015, Bioresource Technology.

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

M. Nierychlo, S. McIlroy, P. Nielsen, 2016, The ISME Journal.

A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis

S. Matthews, C. Robinson, H. Bayley, 2017, Nature Communications.

Functional Amyloids Keep Quorum-sensing Molecules in Check*

D. Otzen, P. Nielsen, Liang Yang, 2015, The Journal of Biological Chemistry.

Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

Liping Hao, P. Nielsen, R. Kirkegaard, 2020, The ISME Journal.

In situ Sub-Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy.

D. Otzen, T. Knowles, M. Dueholm, 2021, Small methods.

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

M. Nierychlo, S. McIlroy, P. Nielsen, 2017, bioRxiv.

The Sheaths of Methanospirillum Are Made of a New Type of Amyloid Protein

D. Otzen, K. Finster, P. Nielsen, 2018, Front. Microbiol..

The fungal community changes over time in developing wheat heads.

T. Sondergaard, M. Dueholm, J. L. Sørensen, 2016, International journal of food microbiology.

Novel prosthecate bacteria from the candidate phylum Acetothermia

Liping Hao, S. McIlroy, P. Nielsen, 2017, bioRxiv.

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

S. McIlroy, P. Nielsen, Eustace Y. Fernando, 2017, Front. Microbiol..

Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)

S. McIlroy, P. Nielsen, E. Yashiro, 2019, mBio.

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

M. Nierychlo, P. Nielsen, K. S. Andersen, 2019, bioRxiv.

Aalborg Universitet Novel prosthecate bacteria from the candidate phylum

Liping Hao, S. McIlroy, P. Nielsen, 2018 .

High-Quality Draft Genome Sequence of Sphaerisporangium cinnabarinum ATCC 31213

D. Otzen, M. Dueholm, Line Friis Bakmann Christensen, 2018, Genome Announcements.

Detection of Pathogenic Biofilms with Bacterial Amyloid Targeting Fluorescent Probe, CDy11.

D. Otzen, Young‐Tae Chang, P. Nielsen, 2016, Journal of the American Chemical Society.

Species-level diversity of the filamentous Candidatus Microthrix in Danish full-scale WWTPs and their influence on sludge settling properties

M. Nierychlo, P. Nielsen, K. S. Andersen, 2019 .

Controlling the degree of esterification in lipase catalysed synthesis of xylitol fatty acid esters

S. B. Nielsen, M. Dueholm, R. Wimmer, 2007 .

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge.

M. Nierychlo, Chenjing Jiang, P. Nielsen, 2020, Water research.

Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems

M. Nierychlo, S. McIlroy, P. Nielsen, 2018, Front. Microbiol..

Extracellular polymeric substances of biofilms: Suffering from an identity crisis.

M. V. van Loosdrecht, Hanqing Yu, H. Horn, 2019, Water research.

Biophysical Characterization of Naturally Occurring Bacterial Amyloids

M. Dueholm, 2009 .

Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420

P. Nielsen, M. Dueholm, V. Cattoir, 2014, Genome Announcements.

Complete Genome Sequences of Pseudomonas monteilii SB3078 and SB3101, Two Benzene-, Toluene-, and Ethylbenzene-Degrading Bacteria Used for Bioaugmentation

J. Nielsen, P. Nielsen, M. Dueholm, 2014, Genome Announcements.

Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria

J. Enghild, P. Højrup, D. Otzen, 2009, Applied and Environmental Microbiology.

Functional amyloid in Pseudomonas

J. Enghild, D. Otzen, J. Nielsen, 2010, Molecular microbiology.

Ecology and Biogenesis of Functional Amyloids in Pseudomonas

S. Matthews, S. Rouse, M. Dueholm, 2018, Journal of molecular biology.

Epigallocatechin Gallate Remodels Overexpressed Functional Amyloids in Pseudomonas aeruginosa and Increases Biofilm Susceptibility to Antibiotic Treatment*

D. Otzen, P. Nielsen, R. Meyer, 2016, The Journal of Biological Chemistry.

Expression of Fap amyloids in Pseudomonas aeruginosa, P. fluorescens, and P. putida results in aggregation and increased biofilm formation

D. Otzen, M. Overgaard, A. Stensballe, 2013, MicrobiologyOpen.

Amyloid adhesins are abundant in natural biofilms.

D. Otzen, J. Nielsen, R. Wetzel, 2007, Environmental microbiology.

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

T. Zhang, M. V. van Loosdrecht, T. Leiknes, 2021, Nature Communications.

Evolutionary Insight into the Functional Amyloids of the Pseudomonads

D. Otzen, P. Nielsen, M. Dueholm, 2013, PloS one.

Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild‐type rats

D. Otzen, M. Dueholm, Florian-Alexander Herbst, 2021, Protein science : a publication of the Protein Society.

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

D. Otzen, M. Dueholm, Florian-Alexander Herbst, 2021, bioRxiv.

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

Per Halkjær Nielsen, Simon Jon McIlroy, Rasmus Hansen Kirkegaard, 2016, The ISME Journal.

Curli Functional Amyloid Systems Are Phylogenetically Widespread and Display Large Diversity in Operon and Protein Structure

D. Otzen, P. Nielsen, M. Dueholm, 2012, PloS one.

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

Mads Albertsen, Simon J McIlroy, S. McIlroy, 2018, Nature Biotechnology.

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

P. Nielsen, R. Kirkegaard, M. Dueholm, 2021, Nature Communications.

Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

Liping Hao, P. Nielsen, R. Kirkegaard, 2020, The ISME Journal.

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

Mads Albertsen, P. Nielsen, Martin H Andersen, 2020, bioRxiv.

Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology

M. Nierychlo, S. McIlroy, P. Nielsen, 2019 .

Label‐free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase

P. Nielsen, M. Dueholm, Florian-Alexander Herbst, 2015, Proteomics.

“Candidatus Galacturonibacter soehngenii” Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex

J. Pronk, M. V. van Loosdrecht, M. Diender, 2020, Frontiers in Microbiology.

Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry

A. Stensballe, P. Nielsen, M. Dueholm, 2017, Biomolecules.

The Tubular Sheaths Encasing Methanosaeta thermophila Filaments Are Functional Amyloids*

D. Otzen, K. Finster, P. Nielsen, 2015, The Journal of Biological Chemistry.

The Proteome of Tetrasphaera elongata is adapted to Changing Conditions in Wastewater Treatment Plants

M. Dueholm, Florian-Alexander Herbst, Per Halkjær Nielsen, 2019, bioRxiv.

Novel prosthecate bacteria from the candidate phylum Acetothermia

Liping Hao, S. McIlroy, P. Nielsen, 2017, bioRxiv.

Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1

S. McIlroy, P. Nielsen, M. Dueholm, 2015, Genome Announcements.

Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs

M. Nierychlo, M. Peces, P. Nielsen, 2021, Frontiers in Microbiology.

The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide

M. Nierychlo, M. Peces, P. Nielsen, 2022, The ISME Journal.

Functional Amyloids in Bacteria

D. Otzen, M. Chapman, P. Nielsen, 2013 .

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

M. Nierychlo, M. Peces, Chenjing Jiang, 2021, Water research.

Fibrillation of the major curli subunit CsgA under a wide range of conditions implies a robust design of aggregation.

D. Otzen, P. Nissen, P. Nielsen, 2011, Biochemistry.

Functional Bacterial Amyloids in Biofilms

D. Otzen, J. Nielsen, P. Nielsen, 2011 .

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

S. McIlroy, P. Nielsen, R. Kirkegaard, 2016, bioRxiv.

On the evolution and physiology of cable bacteria

M. Wagner, M. Nierychlo, P. Nielsen, 2019, Proceedings of the National Academy of Sciences.

The impact of immigration on microbial community composition in full-scale anaerobic digesters

M. Nierychlo, S. McIlroy, P. Nielsen, 2017, Scientific Reports.

Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness

D. Otzen, P. Nielsen, T. Tolker-Nielsen, 2015, Front. Microbiol..

Amyloids – a neglected child of the slime

P. Nielsen, M. Dueholm, 2016 .

Major proteomic changes associated with amyloid-induced biofilm formation in Pseudomonas aeruginosa PAO1.

A. Stensballe, P. Nielsen, M. Dueholm, 2015, Journal of proteome research.

Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation