Johan Bengtsson-Palme
Om Johan Bengtsson-Palme
Min forskning handlar om mikrobiologi och mikrobiell ekologi, med särskild inrikting på antibiotikaresistens hos bakteriesamhällen. För att undersöka detta använder vi bioinformatik och metagenomik, dvs storskalig sekvensering av DNA från alla bakterier i ett prov.
Jag har tidigare jobbat med toxikologiska frågeställningar, framför allt i marina bakteriesamhällen, med samma metodik som vi ni använder för att undersöka antibiotikaresistens. Jag har också ett intresse för mikrobiell taxonomi och utveckling av metoder för bättre taxonomiska bestämningar utifrån sekvensdata. Besök gärna min hemsida http://microbiology.se för mer information!
-
Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm
delivery.
Tove Wikström, Sanna Abrahamsson, Johan Bengtsson-Palme, C. Joakim Ek, Pihla Kuusela, Elham Rekabdar, Peter Lindgren, Ulla-Britt Wennerholm, Bo Jacobsson, Lil Valentin, Henrik Hagberg
Clinical and translational medicine - 2022 -
Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across
environments
Anna Abramova, Thomas U. Berendonk, Johan Bengtsson-Palme
bioRXIV - 2022 -
The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome
Analysis
Dylan Sonnet, Tanya Brown, Johan Bengtsson-Palme, Jacqueline L Padilla-Gamiño, Jesse R Zaneveld
bioRxiv - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 4: β-Lactams: amoxicillin and penicillin
V
Konstantinos Koutso111umanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides:
lincomycin
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and
tylvalosin
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and
thiamphenicol
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and
valnemulin
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins:
colistin
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic
acid
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11:
Sulfonamides
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and
doxycycline
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines:
trimethoprim
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3:
Amprolium
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling
Approach
Johan Bengtsson-Palme, Viktor Jonsson, Stefanie Heß
Environmental Science and Technology - 2021 -
Microbial retention and resistances in stormwater quality improvement devices treating road
runoff
Renato Liguori, Steffen H Rommel, Johan Bengtsson-Palme, Brigitte Helmreich, Christian Wurzbacher
FEMS Microbes - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and
uncertainties
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and
spectinomycin
Ana Allende, Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordóñez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino López Puente, Marta López-Alonso, Søren Saxmose Nielsen, Alena Pechová, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liébana, Gloria López-Gálvez, Paola Manini, Pietro Stella, Luisa Peixe
EFSA Journal - 2021 -
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing
data
Anna Abramova, Adriana Osinska, Haveela Kunche, Emil Burman, Johan Bengtsson-Palme
Bioinformatics - 2021 -
Microbial Community Interactions Are Sensitive to Small Changes in
Temperature
Emil Burman, Johan Bengtsson-Palme
Frontiers in Microbiology - 2021 -
Microbial model communities: To understand complexity, harness the power of
simplicity
Johan Bengtsson-Palme
Computational and Structural Biotechnology Journal - 2020 -
Strategies to reduce or eliminate resistant pathogens in the
environment
Johan Bengtsson-Palme, Stefanie Hess
Antibiotic Drug Resistance - 2020 -
How next-generation sequencing can address the antimicrobial resistance
challenge
Etienne Ruppé, Johan Bengtsson-Palme, Yannick Charretier, Jacques Schrenzel
AMR Control - 2019 -
Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz,
Bolivia
J. Guzman-Otazo, Lucia Gonzales-Siles, V. Poma, Johan Bengtsson-Palme, Kaisa Thorell, Carl-Fredrik Flach, V. Iniguez, A. Sjoling
PLoS ONE - 2019 -
Mumame: A software tool for quantifying gene-specific point-mutations in shotgun metagenomic
data
Shruthi Magesh, Viktor Jonsson, Johan Bengtsson-Palme
Metabarcoding and Metagenomics - 2019 -
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial
communities
Johan Bengtsson-Palme, M. Milakovic, H. Švecová, M. Ganjto, V. Jonsson, R. Grabic, N. Udikovic-Kolic
Water Research - 2019 -
Introducing ribosomal tandem repeat barcoding for
fungi
Christian Wurzbacher, Ellen Larsson, Johan Bengtsson-Palme, Silke Van den Wyngaert, Sten Svantesson, Erik Kristiansson, Maiko Kagami, R. Henrik Nilsson
Molecular Ecology Resources - 2019 -
Assessment and management of risks associated with antibiotic resistance in the
environment
Johan Bengtsson-Palme
Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment - 2019 -
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic
classifications.
R. Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Johan Bengtsson-Palme, Thomas S Jeppesen, Dmitry Schigel, Peter Kennedy, Kathryn Picard, Frank Oliver Glöckner, Leho Tedersoo, Irja Saar, Urmas Kõljalg, Kessy Abarenkov
Nucleic acids research - 2019 -
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic
marker
Johan Bengtsson-Palme, Rodney T Richardson, Marco Meola, Christian Wurzbacher, Émilie D Tremblay, Kaisa Thorell, Kärt Kanger, Guillaume J Bilodeau, Reed M Johnson, Martin Hartmann, R. Henrik Nilsson
Bioinformatics (Oxford, England) - 2018 -
Strategies for Taxonomic and Functional Annotation of
Metagenomes
Johan Bengtsson-Palme
Metagenomics: Perspectives, Methods, and Applications. Muniyandi Nagarajan (red.) - 2018 -
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen,
UK)
R. Henrik Nilsson, A. F. S. Taylor, R. I. Adams, C. Baschien, Johan Bengtsson-Palme, Patrik Cangren, C. Coleine, H. M. Daniel, S. I. Glassman, Y. Hirooka, L. Irinyi, R. Irsenaite, P. M. Martin-Sanchez, W. Meyer, S. Y. Oh, J. P. Sampaio, K. A. Seifert, F. Sklenar, D. Stubbe, S. O. Suh, R. Summerbell, Sten Svantesson, M. Unterseher, C. M. Visagie, M. Weiss, J. H. C. Woudenberg, Christian Wurzbacher, S. Van den Wyngaert, N. Yilmaz, A. Yurkov, U. Koljalg, K. Abarenkov
Mycokeys - 2018 -
Structure and function of the global topsoil
microbiome
M. Bahram, F. Hildebrand, S. K. Forslund, J. L. Anderson, N. A. Soudzilovskaia, P. M. Bodegom, Johan Bengtsson-Palme, S. Anslan, L. P. Coelho, H. Harend, J. Huerta-Cepas, M. H. Medema, M. R. Maltz, S. Mundra, P. A. Olsson, M. Pent, S. Polme, S. Sunagawa, M. Ryberg, L. Tedersoo, P. Bork
Nature - 2018 -
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing
technologies
A. Angers-Loustau, M. Petrillo, Johan Bengtsson-Palme, T. Berendonk, B. Blais, K. G. Chan, T. M. Coque, P. Hammer, S. Heß, D. M. Kagkli, C. Krumbiegel, V. F. Lanza, J. Y. Madec, T. Naas, J. O'Grady, V. Paracchini, J. W. A. Rossen, E. Ruppé, J. Vamathevan, V. Venturi, G. Van den Eede
F1000Research - 2018 -
The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not
always
Johan Bengtsson-Palme
Microbiome - 2018 -
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic
elements
K Pärnänen, Antti Karkman, Jenni Hultman, C. Lyra, Johan Bengtsson-Palme, D. G. Joakim Larsson, S. Rautava, E. Isolauri, S. Salminen, H. Kumar, R. Satokari, M. Virta
Nature Communications - 2018 -
Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic
resistance
D. G. Joakim Larsson, Antoine Andremont, Johan Bengtsson-Palme, K. K. Brandt, A. M. D. Husman, P. Fagerstedt, J. Fick, Carl-Fredrik Flach, W. H. Gaze, M. Kuroda, Kristian Kvint, R. Laxminarayan, C. M. Manaia, K. M. Nielsen, L. Plant, M. C. Ploy, C. Segovia, P. Simonet, K. Smalla, J. Snape, E. Topp, A. J. van Hengel, D. W. Verner-Jeffreys, M. P. J. Virta, E. M. Wellington, A. S. Wernersson
Environment International - 2018 -
A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding
data
R. T. Richardson, Johan Bengtsson-Palme, M. M. Gardiner, R. M. Johnson
Peerj - 2018 -
Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial
biofilms
Nadine Kraupner, Stefan Ebmeyer, Johan Bengtsson-Palme, J. Fick, Erik Kristiansson, Carl-Fredrik Flach, D. G. Joakim Larsson
Environment International - 2018 -
Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+
site.
Weixiao Yuan Wahlgren, Elin Dunevall, Rachel A North, Aviv Paz, Mariafrancesca Scalise, Paola Bisignano, Johan Bengtsson-Palme, Parveen Goyal, Elin Claesson, Rhawnie Caing Carlsson, Rebecka Andersson, Konstantinos Beis, Ulf J Nilsson, Anne Farewell, Lorena Pochini, Cesare Indiveri, Michael Grabe, Renwick C J Dobson, Jeff Abramson, S Ramaswamy, Rosmarie Friemann
Nature Communications - 2018 -
Environmental factors influencing the development and spread of antibiotic
resistance
Johan Bengtsson-Palme, Erik Kristiansson, D. G. Joakim Larsson
FEMS microbiology reviews - 2018 -
Protection goals must guide risk assessment for
antibiotics
Johan Bengtsson-Palme, D. G. Joakim Larsson
Environment international - 2018 -
Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during
manufacturing?
Johan Bengtsson-Palme, Lina-Maria Gunnarsson, D. G. Joakim Larsson
Journal of Cleaner Production - 2018 -
Does antifouling paint select for antibiotic
resistance?
Carl-Fredrik Flach, Chandan Pal, Carl Johan Svensson, Erik Kristiansson, Marcus Östman, Johan Bengtsson-Palme, Mats Tysklind, D. G. Joakim Larsson
The Science of the total environment - 2017 -
Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic
data
Fanny Berglund, Nachiket Marathe, Tobias Österlund, Johan Bengtsson-Palme, Stathis Kotsakis, Carl-Fredrik Flach, D. G. Joakim Larsson, Erik Kristiansson
Microbiome - 2017 -
Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk
assessment?
Johan Bengtsson-Palme
Current Opinion in Food Science - 2017 -
The relation between Blastocystis and the intestinal microbiota in Swedish
travellers.
Joakim Forsell, Johan Bengtsson-Palme, Martin Angelin, Anders Johansson, Birgitta Evengård, Margareta Granlund
BMC microbiology - 2017 -
In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of
carcinogenesis.
Kaisa Thorell, Johan Bengtsson-Palme, Oscar Hsin-Fu Liu, Reyna Victoria Palacios Gonzales, Intawat Nookaew, Linda Rabeneck, Lawrence Paszat, David Y Graham, Jens Nielsen, Samuel B Lundin, Åsa Sjöling
Infection and immunity - 2017 -
Using metagenomics to investigate human and environmental
resistomes.
Johan Bengtsson-Palme, D. G. Joakim Larsson, Erik Kristiansson
The Journal of antimicrobial chemotherapy - 2017 -
Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data
sets
Fredrik Boulund, Fanny Berglund, Carl-Fredrik Flach, Johan Bengtsson-Palme, Nachiket Marathe, D. G. Joakim Larsson, Erik Kristiansson
BMC Genomics - 2017 -
The complete mitochondrial genome of the copepod Calanus
glacialis
Marvin Choquet, Homére J. Alves Monteiro, Johan Bengtsson-Palme, Galice Hoarau
Mitochondrial DNA Part B - 2017 -
Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Sequence
Data
Rodney T Richardson, Johan Bengtsson-Palme, Reed M Johnson
Molecular Ecology Resources - 2017 -
Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental
regulation
Johan Bengtsson-Palme, D. G. Joakim Larsson
Environment International - 2016 -
FARAO: the flexible all-round annotation
organizer
Rickard Hammarén, Chandan Pal, Johan Bengtsson-Palme
Bioinformatics - 2016 -
Elucidating selection processes for antibiotic resistance in sewage treatment plants using
metagenomics
Johan Bengtsson-Palme, Rickard Hammarén, Chandan Pal, Marcus Östman, Berndt Björlenius, Carl-Fredrik Flach, Jerker Fick, Erik Kristiansson, Mats Tysklind, D. G. Joakim Larsson
Science of the Total Environment - 2016 -
The structure and diversity of human, animal and environmental
resistomes
Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D. G. Joakim Larsson
Microbiome - 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)
Kessy Abarenkov, Rachel I. Adams, Irinyi Laszlo, Ahto Agan, Elia Ambrosio, Alexandre Antonelli, Mohammad Bahram, Johan Bengtsson-Palme, Gunilla Bok, Patrik Cangren, Victor R. M. Coimbra, Claudia Coleine, Claes G. R. Gustafsson, Jinhong He, Tobias Hofmann, Erik Kristiansson, Ellen Larsson, Tomas Larsson, Yingkui Liu, Svante Martinsson, Wieland Meyer, Marina Panova, Nuttapon Pombubpa, Camila Ritter, Martin Ryberg, Sten Svantesson, Ruud Scharn, Ola Svensson, Mats H. Töpel, Martin Unterseher, Cobus Visagie, Christian Wurzbacher, Andy F.S. Taylor, Urmas Kõljalg, Lynn Schriml, R. Henrik Nilsson
MycoKeys - 2016 -
Strategies to improve usability and preserve accuracy in biological sequence
databases
Johan Bengtsson-Palme, Fredrik Boulund, Robert Edström, Amir Feizi, Anna Johnning, Viktor Jonsson, Fredrik H. Karlsson, Chandan Pal, Mariana Buongermino Pereira, Anna Rehammar, José Sánchez, Kemal Sanli, Kaisa Thorell
Proteomics - 2016 -
Why limit antibiotic pollution? The role of environmental selection in antibiotic resistance
development
Johan Bengtsson-Palme, D. G. Joakim Larsson
APUA Newsletter - 2016 -
Minimal selective concentrations of tetracycline in complex aquatic bacterial
biofilms
Sara Lundström, Markus Östman, Johan Bengtsson-Palme, Carolin Rutgersson, Malin Thoudal, Triranta Sircar, Hans Blanck, Karl Martin Eriksson, Mats Tysklind, Carl-Fredrik Flach, D. G. Joakim Larsson
Science of the Total Environment - 2016 -
Antibiotic resistance in the environment: a contribution from metagenomic
studies
-
Time to limit antibiotic
pollution
Johan Bengtsson-Palme, D. G. Joakim Larsson
The Medicine Maker - 2016 -
Metaxa2 Diversity Tools: Easing microbial community analysis with
Metaxa2
Johan Bengtsson-Palme, Kaisa Thorell, Christian Wurzbacher, Åsa Sjöling, R. Henrik Nilsson
Ecological Informatics - 2016 -
Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic
data
Johan Bengtsson-Palme, Martin Hartmann, Karl Martin Eriksson, Chandan Pal, Kaisa Thorell, D. G. Joakim Larsson, R. Henrik Nilsson
Molecular Ecology Resources - 2015 -
Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm
Communities
Kemal Sanli, Johan Bengtsson-Palme, R. Henrik Nilsson, Erik Kristiansson, Magnus Alm Rosenblad, Hans Blanck, Karl Martin Eriksson
Frontiers in Microbiology - 2015 -
The human gut microbiome as a transporter of antibiotic resistance genes between
continents
Johan Bengtsson-Palme, Martin Angelin, Mikael Huss, Sanela Kjellqvist, Erik Kristiansson, Helena Palmgren, D. G. Joakim Larsson, Anders Johansson
Antimicrobial Agents and Chemotherapy - 2015 -
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection
potential
Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D. G. Joakim Larsson
BMC Genomics - 2015 -
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing
efforts
R. Henrik Nilsson, Leho Tedersoo, Martin Ryberg, Erik Kristiansson, Martin Hartmann, Martin Unterseher, Teresita M. Porter, Johan Bengtsson-Palme, Donald M. Walker, Filipe de Sousa, Hannes Andres Gamper, Ellen Larsson, Karl-Henrik Larsson, Urmas Kõljalg, Robert C. Edgar, Kessy Abarenkov
Microbes and Environments - 2015 -
Antibiotic resistance genes in the environment: prioritizing
risks
Johan Bengtsson-Palme, D. G. Joakim Larsson
Nature Reviews Microbiology - 2015 -
The European technical report on aquatic effect-based monitoring tools under the water framework
directive
Ann-Sofie Wernersson, Mario Carere, Chiara Maggi, Petr Tusil, Premysl Soldan, Alice James, Wilfried Sanchez, Valeria Dulio, Katja Broeg, Georg Reifferscheid, Sebastian Buchinger, Hannie Maas, Esther Van Der Grinten, Simon O’Toole, Antonella Ausili, Loredana Manfra, Laura Marziali, Stefano Polesello, Ines Lacchetti, Laura Mancini, Karl Lilja, Maria Linderoth, Tove Lundeberg, Bengt Fjällborg, Tobias Porsbring, D. G. Joakim Larsson, Johan Bengtsson-Palme, Lars Förlin, Cornelia Kienle, Petra Kunz, Etienne Vermeirssen, Inge Werner, Craig D Robinson, Brett Lyons, Ioanna Katsiadaki, Caroline Whalley, Klaas den Haan, Marlies Messiaen, Helen Clayton, Teresa Lettieri, Raquel Negrão Carvalho, Bernd Manfred Gawlik, Henner Hollert, Carolina Di Paolo, Werner Brack, Ulrike Kammann, Robert Kase
Environmental Sciences Europe - 2015 -
ITS1: a DNA barcode better than ITS2 in
eukaryotes?
X-C Wang, C Liu, Liang Huang, Johan Bengtsson-Palme, H Chen, J.H Zhang, D Cai, J-Q Li
Molecular Ecology Resources - 2015 -
BacMet: antibacterial biocide and metal resistance genes
database
Chandan Pal, Johan Bengtsson-Palme, Christopher Rensing, Erik Kristiansson, D. G. Joakim Larsson
Nucleic Acids Research - 2014 -
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in
India
Johan Bengtsson-Palme, Fredrik Boulund, Jerker Fick, Erik Kristiansson, D. G. Joakim Larsson
Frontiers in Microbiology - 2014 -
Improving ITS sequence data for identification of plant pathogenic
fungi
R. Henrik Nilsson, Kevin D. Hyde, Julia Pawłowska, Martin Ryberg, Leho Tedersoo, Anders Bjørnsgard Aas, Siti A. Alias, Artur Alves, Cajsa Lisa Anderson, Alexandre Antonelli, A. Elizabeth Arnold, Barbara Bahnmann, Mohammad Bahram, Johan Bengtsson-Palme, Anna Berlin, Sara Branco, Putarak Chomnunti, Asha Dissanayake, Rein Drenkhan, Hanna Friberg, Tobias Guldberg Frøslev, Bettina Halwachs, Martin Hartmann, Beatrice Henricot, Ruvishika Jayawardena, Ari Jumpponen, Håvard Kauserud, Sonja Koskela, Tomasz Kulik, Kare Liimatainen, Björn Lindahl, Daniel Lindner, Jian-Kui Liu, Sajeewa Maharachchikumbura, Dimuthu Manamgoda, Svante Martinsson, Maria Alice Neves, Tuula Niskanen, Stephan Nylinder, Olinto Liparini Pereira, Danilo Batista Pinho, Teresita M. Porter, Valentin Queloz, Taavi Riit, Marisol Sánchez-García, Filipe de Sousa, Emil Stefańczyk, Mariusz Tadych, Susumu Takamatsu, Qing Tian, Dhanushka Udayanga, Martin Unterseher, Zheng Wang, Saowanee Wikee, Jiye Yan, Ellen Larsson, Karl-Henrik Larsson, Urmas Kõljalg, Kessy Abarenkov
Fungal diversity - 2014 -
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial
communities
Johan Bengtsson-Palme, Magnus Alm Rosenblad, Mikael Molin, Anders Blomberg
BMC Genomics - 2014 -
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing
data
Johan Bengtsson-Palme, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Pierre De Wit, Marisol Sánchez-García, Ingo Ebersberger, Filipe de Sousa, Anthony S. Amend, Ari Jumpponen, Martin Unterseher, Erik Kristiansson, Kessy Abarenkov, Yann Bertrand, Kemal Sanli, Karl Martin Eriksson, Unni Vik, Vilmar Veldre, R. Henrik Nilsson
Methods in Ecology and Evolution - 2013 -
Towards a unified paradigm for sequence-based identification of
fungi.
Urmas Kõljalg, R. Henrik Nilsson, Kessy Abarenkov, Leho Tedersoo, Andy F S Taylor, Mohammad Bahram, Scott T Bates, Thomas D Bruns, Johan Bengtsson-Palme, Tony M Callaghan, Brian Douglas, Tiia Drenkhan, Ursula Eberhardt, Margarita Dueñas, Tine Grebenc, Gareth W Griffith, Martin Hartmann, Paul M Kirk, Petr Kohout, Ellen Larsson, Björn D Lindahl, Robert Lücking, María P Martín, P Brandon Matheny, Nhu H Nguyen, Tuula Niskanen, Jane Oja, Kabir G Peay, Ursula Peintner, Marko Peterson, Kadri Põldmaa, Lauri Saag, Irja Saar, Arthur Schüßler, James A Scott, Carolina Senés, Matthew E Smith, Ave Suija, D Lee Taylor, M Teresa Telleria, Michael Weiss, Karl-Henrik Larsson
Molecular ecology - 2013 -
Metaxa,
overview
Johan Bengtsson-Palme, Martin Hartmann, Karl Martin Eriksson, R. Henrik Nilsson
Encyclopedia of Metagenomics - 2013 -
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS
sequences
R. Henrik Nilsson, Leho Tedersoo, Kessy Abarenkov, Martin Ryberg, Erik Kristiansson, Martin Hartmann, Conrad L. Schoch, Johan A. A. Nylander, Johannes Bergsten, Teresita M. Porter, Ari Jumpponen, Parag Vaishampayan, Otso Ovaskainen, Nils Hallenberg, Johan Bengtsson-Palme, Karl Martin Eriksson, Karl-Henrik Larsson, Ellen Larsson, Urmas Kõljalg
MycoKeys - 2012 -
Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length
metagenomes
Johan Bengtsson-Palme, Martin Hartmann, Martin Unterseher, Parag Vaishampayan, Kessy Abarenkov, Lisa Durso, Elisabeth M. Bik, James R. Garey, Karl Martin Eriksson, R. Henrik Nilsson
Research in Microbiology - 2012 -
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS
sequences
R. Henrik Nilsson, L Tedersoo, K Abarenkov, M Ryberg, Erik Kristiansson, M Hartmann, G Schoch, J Nylander, J Bergsten, T Porter, A Jumpponen, P Vaishampayan , O Ovaskainen, N Hallenberg, Johan Bengtsson-Palme, M Eriksson, K-H Larsson, E Larsson, U Kõljalg
MycoKeys - 2012 -
Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial
Communities
Johan Bengtsson, Fredrik Boulund, Jerker Fick, Erik Kristiansson, D. G. Joakim Larsson
SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012-06-11 - 2012 -
Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial
Communities
Johan Bengtsson, Fredrik Boulund, Jerker Fick, Erik Kristiansson, D. G. Joakim Larsson
ISME14 Conference, Copenhagen, Denmark, 2012-08-20 - 2012 -
Starting to unravel the layer of life on surfaces in the sea: Metagenomics of complex marine biofilm
communities
Karl Martin Eriksson, Kemal Sanli, Johan Bengtsson, R. Henrik Nilsson, Magnus Alm Rosenblad, Hans Blanck
ISME14 Conference, Copenhagen, Denmark, 2012-08-20 - 2012 -
High-Throughput Diversity Analysis and Quality Control of Environmental Data Derived from Next-Generation Sequencing
Studies
Johan Bengtsson, Martin Hartmann, Karl Martin Eriksson, R. Henrik Nilsson
ISME14 Conference, Copenhagen, Denmark, 2012 - 2012 -
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing
datasets
Johan Bengtsson-Palme, Karl Martin Eriksson, Martin Hartmann, Wang Zheng, Belle Damodara Shenoy, Gwen-Aëlle Grelet, Kessy Abarenkov, Anna Petri, Magnus Alm Rosenblad, R. Henrik Nilsson
Antonie van Leeuwenhoek: international journal of general and molecular microbiology - 2011 -
Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and
chloroplasts
Johan Bengtsson, Karl Martin Eriksson, Martin Hartmann, Zheng Wang, Belle D Shenoy, G Grelet, Kessy Abarenkov, Anna Petri, Magnus Alm Rosenblad, R. Henrik Nilsson
SocBiN Bioinformatics Conference, Helsinki, Finland, 2011 - 2011