Johan Bengtsson Palme

2024

Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice

2024

Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity

2024

Metagenomic assemblies tend to break around antibiotic resistance genes

2024

Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization

Ceftazidime-avibactam tolerance and persistence among difficult-to-treat KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections

2023

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

2023

Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments

2023

A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments

2023

Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomes

2022

Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities

2019

Mumame: A software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

2019

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

2019

Introducing ribosomal tandem repeat barcoding for fungi

2018

Environmental factors influencing the development and spread of antibiotic resistance

Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms

2018

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

2017

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Using metagenomics to investigate human and environmental resistomes

2017

Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data

Does antifouling paint select for antibiotic resistance?

In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Strategies to improve usability and preserve accuracy in biological sequence databases

2016

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

2016

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms

2016

The structure and diversity of human, animal and environmental resistomes

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

The human gut microbiome as a transporter of antibiotic resistance genes between continents

2015

A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts

2015

Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities

2015

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

2014

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

2014

BacMet: antibacterial biocide and metal resistance genes database

Improving ITS sequence data for identification of plant pathogenic fungi

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Metaxa, overview