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View article: Unveiling the global urban virome through wastewater metagenomics
Unveiling the global urban virome through wastewater metagenomics Open
Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and res…
View article: Unveiling the global urban virome: insights from wastewater metagenomics
Unveiling the global urban virome: insights from wastewater metagenomics Open
Understanding global viral dynamics is critical for public health1. Traditional infectious disease surveillance primarily focuses on individual pathogens and relies on the identification and reporting of symptomatic cases, which may not ca…
View article: High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes
High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes Open
Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling …
View article: PanRes - Collection of antimicrobial resistance genes
PanRes - Collection of antimicrobial resistance genes Open
PanRes database of antimicrobial resistance genes Many different collections of antimicrobial resistance genes (ARGs) have been collected and used for various purposes. In order to develop a workflow for mass screening of public metagenome…
View article: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance
Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance Open
Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve …
View article: Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa
Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa Open
Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed…
View article: Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark
Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark Open
We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted c…
View article: Discovery of Vibrio cholerae in urban sewage in Copenhagen, Denmark
Discovery of Vibrio cholerae in urban sewage in Copenhagen, Denmark Open
We report the unexpected discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally tr…
View article: Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome Open
The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is ess…
View article: Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance
Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance Open
Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve …
View article: The European livestock resistome
The European livestock resistome Open
Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total o…
View article: ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets Open
Motivation Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the compa…
View article: MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis Open
Background The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for singl…
View article: Additional file 1 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
Additional file 1 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis Open
Additional file 1. General summary of simulated community 1a. MAGICIAN output summarizing general information on one of the simulation runs for community 1a. BBTools’ stats output is summarized in the “BBstats” sheet, CheckM output is summ…
View article: Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis
Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis Open
Analysis of flanking region sequences can be useful when comparing mobile prokaryotic sequences from different bacterial isolates or metagenomes. Here, we report a new bioinformatics tool, a pipeline called Flankophile, which can analyze f…
View article: PanRes - Collection of antimicrobial resistance genes
PanRes - Collection of antimicrobial resistance genes Open
PanRes database of antimicrobial resistance genes Many different collections of antimicrobial resistance genes (ARGs) have been collected and used for various purposes. In order to develop a workflow for mass screening of public metagenome…
View article: MAGICIAN v1.1.0 example output
MAGICIAN v1.1.0 example output Open
Example output for version 1.1.0 of the MAGICIAN pipeline
View article: MAGICIAN v1.1.0 example output
MAGICIAN v1.1.0 example output Open
Example output for version 1.1.0 of the MAGICIAN pipeline
View article: MAGICIAN: MAG simulation for Investigating Criteria for bioInformatic ANalysis
MAGICIAN: MAG simulation for Investigating Criteria for bioInformatic ANalysis Open
Background The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for singl…
View article: PanRes - Collection of antimicrobial resistance genes
PanRes - Collection of antimicrobial resistance genes Open
PanRes database of antimicrobial resistance genes Many different collections of antimicrobial resistance genes (ARGs) have been collected and used for various purposes. In order to develop a workflow for mass screening of public metagenome…
View article: Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome
Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome Open
Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the com…
View article: Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance Open
In this article, the author name Antoinette Ngandjio was incorrectly written as Antoinette Ngandijo. In this article, the affiliation details for Author Sara Cuadros-Orellana were incorrectly given as ‘Centro de Biotecnologνa de los Recurs…
View article: MetalResistance - Collection of metal resistance genes
MetalResistance - Collection of metal resistance genes Open
MetalResistance database of genes providing resistance towards heavy metals The sequences encoding the proteins in BacMet 1.1 (experimentally confirmed) were supplemented with a number of genes identified through screening of research arti…
View article: MetalResistance - Collection of metal resistance genes
MetalResistance - Collection of metal resistance genes Open
MetalResistance database of genes providing resistance towards heavy metals The sequences encoding the proteins in BacMet 1.1 (experimentally confirmed) were supplemented with a number of genes identified through screening of research arti…