Nature Search

Assessing antimicrobial resistance connectivity across One Health sectors

Antimicrobial resistance has evolved over decades due to widespread antimicrobial use, with resistance genes now circulating across humans, animals and the environment, creating complex cross-sector connectivity challenges. This Perspective advocates for genomics-based studies of AMR connectivity to enable coordinated global action and investment under the One Health framework.

Liguan Li
Bing Li
Tong Zhang
Reviews29 Sept 2025
Nature Water

P: 1-14
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats

Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Mantas Sereika
Aaron James Mussig
Mads Albertsen
ResearchOpen Access24 Jul 2025
Nature Microbiology

Volume: 10, P: 2018-2030
Author Correction: MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Morten Kam Dahl Dueholm
Marta Nierychlo
Per Halkjær Nielsen
Amendments and CorrectionsOpen Access11 Jul 2022
Nature Communications

Volume: 13, P: 1-2
Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

Simon Jon McIlroy
Rikke Kristiansen
Per Halkjær Nielsen
Research28 Feb 2013
The ISME Journal

Volume: 7, P: 1161-1172
MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.

Morten Kam Dahl Dueholm
Marta Nierychlo
Per Halkjær Nielsen
ResearchOpen Access07 Apr 2022
Nature Communications

Volume: 13, P: 1-15
MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digesters play an important role in biodegradation. In the MiDAS 5 project, the authors use global 16S rRNA sequencing to expand the microbial reference database, improving taxonomic classification and revealing how environmental factors and geography shape microbial communities in anaerobic digesters.

Morten Kam Dahl Dueholm
Kasper Skytte Andersen
Per Halkjær Nielsen
ResearchOpen Access25 Jun 2024
Nature Communications

Volume: 15, P: 1-16
A country-wide survey into the composition and transformation of short-chain organic acids in anaerobic sludge digesters at wastewater treatment plants in Denmark

Zijun Li
Morten Kam Dahl Dueholm
Liping Hao
ResearchOpen Access11 Jul 2025
Scientific Reports

Volume: 15, P: 1-12
Limited dissemination of the wastewater treatment plant core resistome

Wastewater treatment plants (WWTPs) are thought to play a central role in the dissemination of antibiotic resistance genes. Here, the authors identify novel antibiotic resistance genes in WWTPs and show that only a few of the most abundant resistance genes are found outside the WWTP environment.

Christian Munck
Mads Albertsen
Morten O. A. Sommer
ResearchOpen Access30 Sept 2015
Nature Communications

Volume: 6, P: 1-10
MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data

Kang Soo Lee
Zachary Landry
Roman Stocker
Correspondence07 May 2024
Nature Microbiology

Volume: 9, P: 1152-1156
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

Simon Jon McIlroy
Søren Michael Karst
Per Halkjær Nielsen
Research23 Feb 2016
The ISME Journal

Volume: 10, P: 2223-2234
A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

Mads Albertsen
Lea Benedicte Skov Hansen
Kåre Lehmann Nielsen
Research15 Dec 2011
The ISME Journal

Volume: 6, P: 1094-1106
Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

Maria Mooshammer
Katharina Kitzinger
Michael Wagner
ResearchOpen Access02 Sept 2020
The ISME Journal

Volume: 15, P: 348-353
Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman–FISH

Eustace Y. Fernando
Simon Jon McIlroy
Per Halkjær Nielsen
ResearchOpen Access20 Mar 2019
The ISME Journal

Volume: 13, P: 1933-1946
In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina

Lars Behrendt
Jean-Baptiste Raina
Michael Kühl
Research31 Oct 2017
The ISME Journal

Volume: 12, P: 556-567
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

Rasmus Hansen Kirkegaard
Morten Simonsen Dueholm
Per Halkjær Nielsen
ResearchOpen Access08 Apr 2016
The ISME Journal

Volume: 10, P: 2352-2364
A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

Rikke Kristiansen
Hien Thi Thu Nguyen
Per Halkjær Nielsen
Research22 Nov 2012
The ISME Journal

Volume: 7, P: 543-554
Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Mantas Sereika
Francesca Petriglieri
Mads Albertsen
ResearchOpen Access25 Jan 2023
The ISME Journal

Volume: 17, P: 561-569
Microbial communities across activated sludge plants show recurring species-level seasonal patterns

Miriam Peces
Giulia Dottorini
Per Halkjær Nielsen
ResearchOpen Access18 Feb 2022
ISME Communications

Volume: 2, P: 1-11
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

Liping Hao
Thomas Yssing Michaelsen
Morten Simonsen Dueholm
ResearchOpen Access02 Jan 2020
The ISME Journal

Volume: 14, P: 906-918
Novel prosthecate bacteria from the candidate phylum Acetothermia

Liping Hao
Simon Jon McIlroy
Morten Simonsen Dueholm
ResearchOpen Access08 Jun 2018
The ISME Journal

Volume: 12, P: 2225-2237
Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

Yingyu Law
Rasmus Hansen Kirkegaard
Rohan B. H. Williams
ResearchOpen Access19 May 2016
Scientific Reports

Volume: 6, P: 1-15
Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge

Martin Hesselsoe
Stephanie Füreder
Alexander Loy
Research02 Jul 2009
The ISME Journal

Volume: 3, P: 1349-1364

Search

Assessing antimicrobial resistance connectivity across One Health sectors

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats

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

Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

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

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

A country-wide survey into the composition and transformation of short-chain organic acids in anaerobic sludge digesters at wastewater treatment plants in Denmark

Limited dissemination of the wastewater treatment plant core resistome

MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data

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

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman–FISH

In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina

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

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Microbial communities across activated sludge plants show recurring species-level seasonal patterns

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

Novel prosthecate bacteria from the candidate phylum Acetothermia

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge

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