Publications

Peer-reviewed journal papers
° indicates equal contributions

— 2024 —
  1. Abichabki N, Gaspar GG, Bortolato LR, Lima DAFS, Silva LN, Pocente RHC, Ferreira JC, Ogasawara TC, Pereira D, Guerra RR, Wilhelm C, Barth P, Martins AF, Barth A, Braga GUL, De Martinis ECP, Bengtsson-Palme J, Bellissimo-Rodrigues F, Bollela VR, Darini ALC, Andrade LN: Ceftazidime-avibactam tolerance and persistence among KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections. European Journal of Clinical Microbiology & Infectious Diseases, Early view (2024). doi: 10.1007/s10096-024-05005-4 [Paper link]
  2. Abramova A, Karkman A, Bengtsson-Palme J: Metagenomic assemblies tend to break around antibiotic resistance genes. BMC Genomics, 25, 959 (2024). doi: 10.1186/s12864-024-10876-0 [Paper link]
  3. Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR: The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses. ISME Communications, ycae114 (2024). doi: 10.1093/ismeco/ycae114 [Paper link]
  4. Erb IK, Suarez C, Frank EM, Bengtsson-Palme J, Lindberg E, Paul CJ: Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance and antibiotic resistance to infer contamination or naturalisation. FEMS Microbes (advance article) xtae024 (2024). doi: 10.1093/femsmc/xtae024 [Paper link].
  5. Jarquín-Díaz VH, Ferreira SCM, Balard A, Ďureje Ľ, Macholán M, Piálek J, Bengtsson-Palme J, Kramer-Schadt S, Forslund-Startceva SK, Heitlinger E: Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice. ISME Communications, ycae053 (2024). doi: 10.1093/ismeco/ycae053 [Paper link]
  6. Moraes Zenker M, Pineda Portella T, Costa Pessoa FA, Bengtsson-Palme J, Galetti PM: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity. Scientific Reports, 14, 7432 (2024). doi: 10.1038/s41598-024-58071-1 [Paper link]
— 2023 —
  1. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 178, 108089 (2023). doi: 10.1016/j.envint.2023.108089 [Paper link]
  2. Abramova A, Berendonk TU, Bengtsson-Palme J: A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments. Environment International, 178, 108084 (2023). doi: 10.1016/j.envint.2023.108084 [Paper link]
  3. Bargheet A, Klingenberg C, Esaiassen E, Hjerde E, Cavanagh JP, Bengtsson-Palme J, Pettersen VK: Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments. eBio Medicine, 92, 104613 (2023). doi: 10.1016/j.ebiom.2023.104613 [Paper link]
  4. Inda-Díaz JS, Lund D, Parras-Moltó M, Johnning A, Bengtsson-Palme J, Kristiansson E: Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. Microbiome, 11, 44 (2023). doi: 10.1186/s40168-023-01479-0 [Paper link]
— 2022 —
  1. Wikström T, Abrahamsson S, Bengtsson-Palme J, Ek CJ, Kuusela P, Rekabdar E, Lindgren P, Wennerholm UB, Jacobsson B, Valentin L, Hagberg H: Microbial and human transcriptome in vaginal fluid at midgestation: association with spontaneous preterm delivery. Clinical and Translational Medicine, 12, 9, e1023 (2022). doi: 10.1002/ctm2.1023 [Paper link]
— 2021 —
  1. Bengtsson-Palme J, Jonsson V, Heß S: What is the role of the environment in the emergence of novel antibiotic resistance genes? A modelling approach. Environmental Science & Technology, 55, 23, 15734–15743 (2021). doi: 10.1021/acs.est.1c02977 [Paper link]
  2. EFSA Panel on Biological Hazards (BIOHAZ), Allende A, Koutsoumanis K, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson-Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López-Alonso M, Saxmose Nielsen S, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Lorenzo Innocenti M, Liébana E, López-Gálvez G, Manini P, Stella P, Peixe L: Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. EFSA Journal, 19, 10 (2021). doi: 10.2903/j.efsa.2021.6852 [Paper link]
  3. Ligouri R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C: Microbial retention and resistances in stormwater quality improvement devices treating road runoff. FEMS Microbes, 2 (2021). doi: 10.1093/femsmc/xtab008 [Paper link]
  4. Burman E, Bengtsson-Palme J: Microbial community interactions are sensitive to small differences in temperature. Frontiers in Microbiology, 12, 672910 (2021). doi: 10.3389/fmicb.2021.672910 [Paper link]
  5. Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J: CAFE: A software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics, 37, 1, 121–122 (2021). doi: 10.1093/bioinformatics/btaa1086 [Paper link]
— 2020 —
  1. Bengtsson-Palme J: Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal, 18, 3987-4001 (2020). doi: 10.1016/j.csbj.2020.11.043 [Paper link]
— 2019 —
  1. Brown P, RELISH Consortium, Zhou Y: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database, 2019: 1–66 (2019). doi: 10.1093/database/baz085 [Paper link]
  2. Magesh S, Jonsson V, Bengtsson-Palme J: Mumame: A software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics, 3: 59–67 (2019). doi: 10.3897/mbmg.3.36236 [Paper link]
  3. Bengtsson-Palme J, Milakovic M, Švecová H, Ganjto M, Jonsson V, Grabic R, Udiković Kolić N: Pharmaceutical wastewater treatment plant enriches resistance genes and alter the structure of microbial communities. Water Research, 162, 437-445 (2019). doi: 10.1016/j.watres.2019.06.073 [Paper link]
  4. Guzman-Otazo J, Gonzales-Siles L, Poma V, Bengtsson-Palme J, Thorell K, Flach C-F, Iñiguez V, Sjöling Å: Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia. PLoS ONE, 14, 1, e0210735 (2019). doi: 10.1371/journal.pone.0210735 [Paper link]
— 2018 —
  1. Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.2 [Paper link]
  2. Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K: The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47, D1, D259–D264 (2019). doi: 10.1093/nar/gky1022 [Paper link]
  3. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Isolauri E, Salminen S, Kumar H, Satokari R, Virta M: Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature Communications, 9, 3891 (2018). doi: 10.1038/s41467-018-06393-w [Paper link]
  4. Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH: Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources, 19, 1, 118–127 (2019). doi: 10.1111/1755-0998.12944 [Paper link]
  5. Bahram M°, Hildebrand F°, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P: Structure and function of the global topsoil microbiome. Nature, 560, 7717, 233–237 (2018). doi: 10.1038/s41586-018-0386-6 [Paper link]
  6. Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. Microbiome, 6, 125 (2018). doi: 10.1186/s40168-018-0508-2 [Paper link]
  7. Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data. PeerJ, 6, e5126 (2018). doi: 10.7717/peerj.5126 [Paper link]
  8. Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Metaxa2 Database Builder: Enabling taxonomic identification from metagenomic and metabarcoding data using any genetic marker. Bioinformatics, 34, 23, 4027–4033 (2018). doi: 10.1093/bioinformatics/bty482 [Paper link]
  9. Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018). doi: 10.1016/j.envint.2018.04.041 [Paper link]
  10. Wahlgren WY°, North RA°, Dunevall E°, Paz A, Scalise M, Bisognano P, Bengtsson-Palme J, Goyal P, Claesson E, Caing-Carlsson R, Andersson R, Beis K, Nilsson U, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, Friemann R: Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a novel Na+ site. Nature Communications, 9, 1753 (2018). doi: 10.1038/s41467-018-04045-7 [Paper link]
  11. Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ: Selective concentration for ciprofloxacin in Escherichia coli grown in complex aquatic bacterial biofilms. Environment International, 116, 255–268 (2018). doi: 10.1016/j.envint.2018.04.029 [Paper link]
  12. Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršenaite R, Martin-Sánchez PM, Meyer W, Oh S-O, Sampaio JP, Seifert KA, Sklenár F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg J, Wurzbacher C, Van den Wyngaert S, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K: Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys, 28, 65–82 (2018). doi: 10.3897/mycokeys.28.20887 [Paper link]
— 2017 —
  1. Forsell J, Bengtsson-Palme J, Angelin M, Johansson A, Evengård B, Granlund M: The relation between Blastocystis and the intestinal microbiota in Swedish travellers. BMC Microbiology, 17, 231 (2017). doi: 10.1186/s12866-017-1139-7 [Paper link]
  2. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053 [Paper link] (Editor’s choice)
  3. Berglund F, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach C-F, Larsson DGJ, Kristiansson E: Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome, 5, 134 (2017). doi: 10.1186/s40168-017-0353-8 [Paper link]
  4. Bengtsson-Palme J°, Gunnarsson L°, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? Journal of Cleaner Production, 171, 137–146 (2018). doi: 10.1016/j.jclepro.2017.09.247 [Paper link]
  5. Boulund F, Berglund F, Flach C-F, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E: Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics, 18, 682 (2017). doi: 10.1186/s12864-017-4064-0 [Paper link]
  6. Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G: The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2, 2, 506–507 (2017). doi: 10.1080/23802359.2017.1361357 [Paper link]
  7. Thorell K, Bengtsson-Palme J, Liu OH, Gonzales RVP, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å: In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis. Infection and Immunity, 85, 10, e00031-17 (2017). doi: 10.1128/IAI.00031-17 [Paper link]
  8. Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. Journal of Antimicrobial Chemotherapy, 72, 2690–2703 (2017). doi: 10.1093/jac/dkx199 [Paper link]
  9. Flach C-F, Pal C, Svensson CJ, Kristiansson E, Östman M, Bengtsson-Palme J, Tysklind M, Larsson DGJ: Does antifouling paint select for antibiotic resistance? Science of the Total Environment, 590–591, 461–468 (2017). doi: 10.1016/j.scitotenv.2017.01.213 [Paper link]
— 2016 —
  1. Richardson RT, Bengtsson-Palme J, Johnson RM: Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Sequence Data. Molecular Ecology Resources, 17, 4, 760–769 (2017). doi: 10.1111/1755-0998.12628 [Paper link]
  2. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: The structure and diversity of human, animal and environmental resistomes. Microbiome, 4, 54 (2016). doi: 10.1186/s40168-016-0199-5 [Paper link] (Cited more than 100 times)
  3. Abarenkov K, Adams RI, Laszlo I, Agan A, Ambrioso E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Untersehrer M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH: 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). MycoKeys, 16, 1–15 (2016). doi: 10.3897/mycokeys.16.10000 [Paper link]
  4. Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach C-F, Kristiansson E, Fick J, Tysklind M, Larsson DGJ: Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Science of the Total Environment, 572, 697–712 (2016). doi: 10.1016/j.scitotenv.2016.06.228 [Paper link]
  5. Hammarén R, Pal C, Bengtsson-Palme J: FARAO: The Flexible All-Round Annotation Organizer. Bioinformatics, 32, 23, 3664-3666 (2016). doi: 10.1093/bioinformatics/btw499 [Paper link]
  6. Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH: Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2. Ecological Informatics, 33, 45–50 (2016). doi: 10.1016/j.ecoinf.2016.04.004 [Paper link]
  7. Lundström S, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Science of the Total Environment, 553, 587–595 (2016). doi: 10.1016/j.scitotenv.2016.02.103 [Paper link]
— 2015 —
  1. Bengtsson-Palme J, Larsson DGJ: Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation. Environment International, 86, 140–149 (2016). doi: 10.1016/j.envint.2015.10.015 [Paper link] (Cited more than 100 times)
  2. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics, 16, 964 (2015). doi: 10.1186/s12864-015-2153-5 [Paper link] (Cited more than 100 times)
  3. Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM: Metagenomic sequencing of marine periphyton: Taxonomic and functional insights into biofilm communities. Frontiers in Microbiology, 6, 1192 (2015). doi: 10.3389/fmicb.2015.01192 [Paper link]
  4. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551–6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]
  5. Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker D, de Sousa F, Gamper HA, Larsson E, Larsson K-H, Kõljalg U, Edgar R, Abarenkov K: A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30, 2, 145–150 (2015). doi: 10.1264/jsme2.ME14121 [Paper link]
  6. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Dulio V, Broeg K, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, O’Toole S, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Hollert H, Di Paolo C, Brack W. Kammann U, Kase R: The European technical report on aquatic effect-based monitoring tools under the water framework directive. Environmental Sciences Europe, 27, 7 (2015). doi: 10.1186/s12302-015-0039-4 [Paper link] (Cited more than 100 times)
  7. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]
— 2014 —
  1. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648 [Paper link] (Cited more than 100 times)
  2. Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q: ITS1: A DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources, 15, 3, 573–586 (2015). doi: 10.1111/1755-0998.12325 [Paper link]
  3. Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics, 15, 749 (2014). doi: 10.1186/1471-2164-15-749 [Paper link]
  4. Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F, Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson K-H, Kõljalg U, Abarenkov K: Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67, 1, 11–19 (2014). doi: 10.1007/s13225-014-0291-8 [Paper link]
— 2013 —
  1. Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DGJ: BacMet: Antibacterial biocide and metal resistance genes database. Nucleic Acids Research, 42, D1, D737–D743 (2014). doi: 10.1093/nar/gkt1252 [Paper link] (Cited more than 100 times)
  2. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M, Larsson KH: Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22, 21, 5271–5277 (2013). doi: 10.1111/mec.12481 [Paper link] (Cited more than 1100 times)
  3. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Souza F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4, 10, 914–919 (2013). doi: 10.1111/2041-210X.12073 [Paper link] (Cited more than 300 times)
— 2012 —
  1. Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E, Kõljalg U: Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys, 4, 37–63 (2012). doi: 10.3897/mycokeys.4.3606 [Paper link]
  2. Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH: 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. Research in Microbiology, 163, 6–7, 407–412 (2012). doi: 10.1016/j.resmic.2012.07.001. [Paper link]
— 2011 —
  1. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: 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. Antonie van Leeuwenhoek, 100, 3, 471–475 (2011). doi:10.1007/s10482-011-9598-6. [Paper link]

Opinion papers

  1. Bengtsson-Palme J: Surveillance of antimicrobial resistance – flying blind or flying behind? The Swedish Pathogens Portal, Editorial (2024). doi: 10.17044/scilifelab.27045433 [Link]
  2. Ruppé E, Bengtsson-Palme J, Charretier Y, Schrenzel J: How next-generation sequencing can address the antimicrobial resistance challenge. AMR Control, 2019-20, 60-65 (2019). [Paper link]
  3. Bengtsson-Palme J, Larsson DGJ: Protection goals must guide risk assessment for antibiotics. Environment International, 111, 352–353 (2018). doi: 10.1016/j.envint.2017.10.019 [Paper link]
  4. Bengtsson-Palme J: Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Current Opinion in Food Science, 14, 66–71 (2017). doi: 10.1016/j.cofs.2017.01.010 [Paper link]
  5. Bengtsson-Palme J, Larsson DGJ: Why limit antibiotic pollution? The role of environmental selection in antibiotic resistance development. APUA Newsletter, 34, 2, 6-9 (2016). [Paper link]
  6. Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sánchez J, Sanli K, Thorell K: Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics, 16, 18, 2454–2460 (2016). doi: 10.1002/pmic.201600034 [Paper link]
  7. Bengtsson-Palme J, Larsson DGJ: Time to limit antibiotic pollution. The Medicine Maker, 0416, 302, 17–18 (2016). [Paper link]
  8. Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nature Reviews Microbiology, 13, 369 (2015). doi: 10.1038/nrmicro3399-c1 [Paper link]

Preprints

  1. Tskhay F, Köbsch C, Elena AX, Bengtsson-Palme J, Berendonk TU, Klümper U: Fish are poor sentinels for surveillance of riverine AMR. bioRxiv 2024.10.22.619632 (2024). doi: 10.1101/2024.10.22.619632 [Link]
  2. Teichmann L, Wenne M, Luitwieler S, Dugar S, Bengtsson-Palme J, ter Kuile B: Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE. bioRxiv 2024.10.05.616818 (2024). doi: 10.1101/2024.10.05.616818 [Link]
  3. Teichmann L, Luitwieler S, Bengtsson-Palme J, ter Kuile B: Fluoroquinolone-Specific Resistance Trajectories in E. coli and their Dependence on the SOS-Response. bioRxiv 2024.06.06.597756 (2024). doi: 10.1101/2024.06.06.597756 [Link]
  4. Abramova A, Karkman A, Bengtsson-Palme J: Metagenomic assemblies tend to break around antibiotic resistance genes. bioRxiv 2023.12.13.571436 (2023). doi: 10.1101/2023.12.13.571436 [Link]
  5. Heß S, Bengtsson-Palme J: A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants. SSRN Preprint (2023). doi: 10.2139/ssrn.4615467 [Link]
  6. Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño J, Zaneveld JR: The Organelle in the Ointment: cryptic mitochondria account for many unknown sequences in cross-species microbiome comparisons. bioRxiv, 431501v2 (2023). doi: 10.1101/2021.02.23.431501 [Link]
  7. Bargheet A, Klingenberg C, Esaiassen E, Hjerde E, Cavanagh JP, Bengtsson-Palme J, Pettersen VK: Development of Early Life Gut Resistome and Mobilome Across Gestational Ages and Microbiota-Modifying Treatments. SSRN Preprint (2023). doi: 10.2139/ssrn.4325239 [Link]
  8. Kampouris ID, Berendonk TU, Bengtsson-Palme J, Klümper U: The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomes. bioRxiv, 516424 (2022). doi: 10.1101/2022.11.14.516424 [Link]
  9. Abramova A, Berendonk TU, Bengtsson-Palme J: Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments. bioRxiv, 478248 (2022). doi: 10.1101/2022.01.29.478248 [Link]
  10. Bengtsson-Palme J, Jonsson V, Heß S: What is the role of the environment in the emergence of novel antibiotic resistance genes? – A modelling approach. bioRxiv, 438392 (2021). doi: 10.1101/2021.04.04.438392 [Link]
  11. Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño J, Zaneveld JR: The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis. bioRxiv, 431501 (2021). doi: 10.1101/2021.02.23.431501 [Link]
  12. Ligouri R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C: Microbial retention and resistances in stormwater quality improvement devices treating road runoff. bioRxiv, 426166 (2021). doi: 10.1101/2021.01.12.426166 [Link]
  13. Magesh S, Jonsson V, Bengtsson-Palme J: Quantifying point-mutations in metagenomic data. bioRxiv, 438572 (2018). doi: 10.1101/438572 [Link]
  14. Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH: Introducing ribosomal tandem repeat barcoding for fungi. bioRxiv, 310540 (2018). doi: 10.1101/310540 [Link]
  15. Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.1 [Link]
  16. Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data. PeerJ Preprints, 6, e26662v1 (2018). doi: 10.7287/peerj.preprints.26662v1 [Link]
  17. Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Taxonomic identification from metagenomic or metabarcoding data using any genetic marker. bioRxiv 253377 (2018). doi: 10.1101/253377 [Link]

Books, Book chapters and Theses

  1. Abramova A, Bengtsson-Palme J: Strategies for Taxonomic and Functional Annotation of Metagenomes. In: Nagarajan M (Ed.) Metagenomics: Perspectives, Methods, and Applications, 2nd edition, 57–81. Academic Press, Elsevier, USA (2025). doi: 10.1016/B978-0-323-91631-8.00002-0 [Link]
  2. Bengtsson-Palme J, Heß S: Strategies to reduce or eliminate resistant pathogens in the environment. In: Capelo Martinez JL, Igrejas G (Eds.) Antibiotic Drug Resistance, 637–673. Wiley, NJ, USA (2020). doi: 10.1002/9781119282549.ch24 [Link]
  3. Bengtsson-Palme J: Assessment and management of risks associated with antibiotic resistance in the environment. In: Roig B, Weiss K, Thoreau V (Eds.) Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment, 243–263. Elsevier, UK (2019). doi: 10.1016/B978-0-12-813290-6.00010-X [Paper link]
  4. Bengtsson-Palme J: Strategies for Taxonomic and Functional Annotation of Metagenomes. In: Nagarajan M (Ed.) Metagenomics: Perspectives, Methods, and Applications, 55–79. Academic Press, Elsevier, USA (2018). doi: 10.1016/B978-0-08-102268-9.00003-3 [Link]
  5. Bengtsson-Palme J: Antibiotic resistance in the environment: a contribution from metagenomic studies. Doctoral thesis (medicine), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 2016. [Link]
  6. Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: Metaxa, overview. In:Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg (2013). doi: 10.1007/978-1-4614-6418-1_239-6 [Link]
  7. Bengtsson J: Metagenomic Analysis of Marine Periphyton Communities: Taxonomic and Functional Perspectives on Natural Biofilm-forming Communities. Degree project for Master of Science in Systems Biology, Department of Cell and Molecular Biology, and Department of Plant and Environmental Sciences, University of Gothenburg, 2011.
  8. Bengtsson J: Finding Genes Related to Detoxification in Metagenomic Data. Degree project for Bachelor of Science in Cell Biology, Department of Cell and Molecular Biology University of Gothenburg, 2009.

Signatory to Scientific or Opinion Papers

  1. Moberg C, et al.: De unga gör helt rätt när de stämmer staten. Aftonbladet, 2022-12-07 (2022). [Article link]
  2. Gerhardt K, et al.: Nog nu, politiker – ta klimatkrisen på allvar. Aftonbladet, 2022-08-26 (2022). [Article link]
  3. Ripple WJ, Wolf C, Newsome TM, Barnard P, Moomaw WR: World Scientists’ Warning of a Climate Emergency. BioScience, 70, 1, 8–12 (2020). doi: 10.1093/biosci/biz088 [Paper link]

Contributions to official reports

  1. United Nations Environment Programme: Bracing for Superbugs: Strengthening environmental action in the One Health response to antimicrobial resistance. UNEP, Geneva (2023). [Link]
  2. Joint Programming Initiative on Antimicrobial Resistance: JPIAMR Workshop on Environmental Dimensions of AMR: Summary and recommendations. JPIAMR (2017). [Link]
  3. Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099 [Link]
  4. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Broeg K, Kammann U, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kase R, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Dulio V, Hollert H, Di Paolo C, Brack W (2014). Technical Report on Aquatic Effect-Based Monitoring Tools. European Commission. Technical Report 2014-077, Office for Official Publications of European Communities, ISBN: 978-92-79-35787-9. doi:10.2779/7260 [Link]
  5. Länsstyrelsen i Västra Götalands län. (2012). Swedish monitoring of hazardous substances in the aquatic environment (No. 2012:23). In:Wernersson A-S (Ed.) Current vs required monitoring and potential developments. Länsstyrelsen i Västra Götalands län, vattenvårdsenheten. [Link]

Posters

  1. Varga V, Hugerth LW, Bengtsson-Palme J: Identification of biosynthetic gene clusters from the vaginal microbiome. SymbNET International Conference on Host-Microbe Symbiosis, Olhão, Portugal, 2024.
  2. Mamani Jarro J, Wenne M, Abramova A, Burman E, Vass M, Ottoson J, Bengtsson-Palme J: Antibiotic resistome in young children: A pilot study of Swedish cohort. SymbNET International Conference on Host-Microbe Symbiosis, Olhão, Portugal, 2024.
  3. Abichabki N, Gaspar G, Bortolato L, Lima D, Pocente R, Ferreira J, Ogasawara T, Braga G, De Martinis E, Bellissimo-Rodrigues F, Bengtsson-Palme J, Bollela V, Darini AL, Andrade L: Ceftazidime-avibactam tolerance and resistance among difficult-to-treat Klebsiella pneumoniae clinical isolates from bloodstream infections. 32° Congresso Brasileiro de Microbiologia, Foz do Iguaçu, Brazil, 2023.
  4. Dannborg M, Thorell K, Bengtsson-Palme J: A microbial model community representing the gastric microbiome. 32° Congresso Brasileiro de Microbiologia, Foz do Iguaçu, Brazil, 2023.
  5. Varga V, Bengtsson-Palme J: Benchmarking orthologous clustering programs for proteins – a case study in Pseudomonas aeruginosa. DDLS Annual Meeting 2023, Stockholm, Sweden, 2023.
  6. Wenne M, Bengtsson-Palme J: Navigating the Toolbox: a Comparative Analysis of Metagenomic Tools for Taxonomic and ARG identification. DDLS Annual Meeting 2023, Stockholm, Sweden, 2023.
  7. Lovmar T, Bengtsson-Palme J, Wenne M: Exuberanter: A Versatile Python Tool for Literature Data Extraction. The 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology, Lyon, France, 2023.
  8. Burman E, Bengtsson-Palme J: O-antigen serotype determines selective antagonism by P. aeruginosa in microbial model communites. Cell Symposia: Infection biology in the age of the microbiome, Paris, France, 2023.
  9. Dannborg M, Thorell K, Bengtsson-Palme J: A microbial model community representing the gastric microbiome. Cell Symposia: Infection biology in the age of the microbiome, Paris, France, 2023.
  10. Bengtsson-Palme J, Dannborg M, Burman E: Using microbial model communities to decipher genetic mechanisms behind microbial
interactions in microbiomes. Cell Symposia: Infection biology in the age of the microbiome, Paris, France, 2023.
  11. Baragheet A, Klingenberg C, Esaiassen E, Hjerde E, Cavanagh JP, Bengtsson-Palme J, Pettersen V: Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments. Cell Symposia: Infection biology in the age of the microbiome, Paris, France, 2023.
  12. Abramova A, Bengtsson-Palme J: Recovering Antibiotic Resistance Genes Located in Multiple Genomic Contexts from Metagenomic Data. Swedish Bioinformatics Workshop 2022, Umeå, Sweden, 2022.
  13. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Gschwind R, 
Jarquin Diaz VH, Klümper U, Löber U, Ugarcina Perovic S, Zahra R: Towards Standardized Global Monitoring of Antibiotic Resistance in the Environment:
The EMBARK Program 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  14. Inda-Díaz JS, Lund D, Johnning A, Parras-Moltó M, Bengtsson-Palme J, Kristiansson E: Characterization of the Latent Resistome in External and Host-associated Environments. 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  15. Abramova A, Bengtsson-Palme J: Recovering Antibiotic Resistance Genes Located in Multiple Genomic Contexts from Metagenomic Data. 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  16. Wenne M, Abramova A, Bengtsson-Palme J: Limited Selection for Antibiotic Resistance in Soil Contaminated with Antibiotics. 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  17. Burman E, Bengtsson-Palme J: Large-scale Investigation of Antibiotic Tolerance Determinants in Pseudomonas aeruginosa. 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  18. Dannborg M, Hulterström T, Burman E, Thorell K, Bengtsson-Palme J: Minimum inhibitory concentrations for commonly used antibiotics in gastric bacteria. ISME18 Conference, Lausanne, Switzerland, 2022.
  19. Abramova A, Bengtsson-Palme J: Recovering antibiotic resistance genes located in multiple genomic contexts from metagenomic data. ISME18 Conference, Lausanne, Switzerland, 2022.
  20. Burman E, Bengtsson-Palme J: Microbial model community interactions are sensitive to small changes in temperature. ISME18 Conference, Lausanne, Switzerland, 2022.
  21. Teichmann L, Luitwieler S, Bengtsson-Palme J, der Kuile B: The impact of the SOS response in the development of antimicrobial resistance in Escherichia coli. ISME18 Conference, Lausanne, Switzerland, 2022.
  22. Wenne M, Abramova A, Bengtsson-Palme J: The effects of antibiotic exposure on a soil microbial communities. ISME18 Conference, Lausanne, Switzerland, 2022.
  23. Bengtsson-Palme J, Burman E, Abramova A, Osinska A, Lubna Akter M, Hurley A, Lozano Betancourt GL, Handelsman J: Disentangling Interactions in Disturbed Microbial Communities. World Microbe Forum, Virtual meeting, 2021.
  24. Wettersten S, Bengtsson-Palme J, Wurzbacher C, Eriksson KM, Hartmann M, Nilsson RH: MetaxaQR: High-Quality Taxonomic Classification of Metagenomes and Amplicon Sequencing Data. World Microbe Forum, Virtual meeting, 2021.
  25. Wenne M, Abramova A, Bengtsson-Palme J: Short Duration Exposure of Microbial Communities to Tetracycline or Ciprofloxacin in a Soil Microcosm. World Microbe Forum, Virtual meeting, 2021.
  26. Abramova A, Berendonk TU, Bengtsson-Palme J: The Global Picture of Antibiotic Resistance Gene Prevalence Across Environments. World Microbe Forum, Virtual meeting, 2021.
  27. Abramova A, Bengtsson-Palme J: Recovering antibiotic resistance genes located in multiple genomic contexts from metagenomic data. Applied Bioinformatics and Public Health Microbiology, Virtual meeting, 2021.
  28. Burman E, Bengtsson-Palme J: Microbial model community interactions are sensitive to small changes in temperature. 7th Microbiome and Probiotics R&D Business Collaboration Forum, Virtual meeting, 2020.
  29. Abramova A, EMBARK Consortium, Bengtsson-Palme J: EMBARK: Next-generation monitoring of existing and emerging antibiotic resistance in the environment. 7th Microbiome and Probiotics R&D Business Collaboration Forum, Virtual meeting, 2020.
  30. Bengtsson-Palme J, Garavito MF, Osińska A, Hurley A, Rajendhran J, Burman E, Kristiansson E, Lozano GL, Handelsman J:  Large-scale identification of genes important for bacterial community invasion. Swedish Bioinformatics Workshop, Göteborg, Sweden, 2019.
  31. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Isolauri E, Salminen S, Kumar H, Satokari R, Virta M: Maternal gut and breast milk microbiota affect the infant gut antibiotic resistome and mobilome. ISME16 Conference, Leipzig, Germany, 2018.
  32. Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. WID Symposium, Madison, WI, USA, 2018.
  33. Garavito MF, Hurley A, Li C, Bengtsson-Palme J, Juang DC, Heinritz JR, Lozano GL, Jona O, Meinholz K, Beebe D, Handelsman J: Dynamics and interactions within a multi-phylum model biofilm community. Madison Microbiome Meeting, Madison, WI, USA, 2018.
  34. Wahlgren WY, Dunevall E, North RA, Paz A, Scalise M, Bisignano P, Bengtsson-Palme J, Goyal P, Claesson E, Nilsson U, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, Friemann R: Structural Insights into Bacterial Sialic Acid Transport. Annual Meeting of the Society for Glycobiology, Portland, OR, USA, 2017.
  35. Wurzbacher C, Van den Wyngaert S, Bengtsson-Palme J, Kagami M, Nilsson RH: Phylogenetic anchoring of unkown fungal lineages. London Calling 2017, London, UK, 2017.
  36. Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  37. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Using metagenomics to investigate human and environmental resistomes – Methodological considerations. 8th Next Generation Sequencing Congress, London, Great Britain, 2016.
  38. Bengtsson-Palme J, Lundström SV, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibiotics in complex microbial communities. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  39. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals on bacterial chromosomes and plasmids reveals novel insights into their co-selection potential. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  40. Flach C-F, Svensson C-J, Pal C, Bengtsson-Palme J, Östman M, Kristiansson E, Larsson DGJ: Antifouling paint co-selects for antibiotic resistant bacteria in the marine environment. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  41. Razavi M, Marathe NP, Bengtsson-Palme J, Flach C-F, Kristiansson E, Larsson DGJ: Identification of novel antibiotic resistance genes using amplicon sequencing of integrons from polluted environments in India. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  42. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals on bacterial chromosomes and plasmids reveals novel insights into their co-selection potential. ICETAR 2015: International Conference on the Evolution and Transfer of Antibiotic Resistance, Amsterdam, The Netherlands, 2015.
  43. Flach C-F, Svensson C-J, Pal C, Bengtsson-Palme J, Östman M, Kristiansson E, Larsson DGJ: Antifouling paint co-selects for antibiotic resistant bacteria in the marine environment. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  44. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  45. Hammarén R, Bengtsson-Palme J, Pal C, Flach C-F, Kristiansson E, Larsson DGJ: Elucidating co-selection of genes conferring resistance to biocides and metals with antibiotic resistance genes in Swedish wastewater treatment plants. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  46. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. ISME15 Conference, Seoul, South Korea, 2014.
  47. Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F, Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson K-H, Kõljalg U, Abarenkov K: Improving ITS sequence data for identification of plant pathogenic fungi. The 10th International Mycological Congress, Bangkok, Thailand, 2014.
  48. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Metagenomics Unravels the Antibiotic Resistome of Indian Soils. 2nd Thünen Symposium on Soil Metagenomics, Braunschweig, Germany, 2013.
  49. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Sequencing Depth is Central to Capture the Diversity of Antibiotic Resistance Genes in the Environment. 5th Next Generation Sequencing Congress, London, Great Britain, 2013.
  50. Sanli K, Eriksson KM, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H: Metagenomic Analysis of Periphyton: Taxonomic and Functional Insights into Marine Biofilm Communities. Swedish Bioinformatics Workshop, Skövde, Sweden, 2013.
  51. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Using Large-Scale Sequencing Metagenomics to Assess the Antibiotic Resistome. 4th Next Generation Sequencing Congress, London, Great Britain, 2012.
  52. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  53. Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: High-Throughput Diversity Analysis and Quality Control of Environmental Data Derived from Next-Generation Sequencing Studies. ISME14 Conference, Copenhagen, Denmark, 2012.
  54. Eriksson KM, Sanli K, Bengtsson-Palme J, Nilsson RH, Alm Rosenblad M, Blanck H: Starting to unravel the layer of life on surfaces in the sea: Metagenomics of complex marine biofilm communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  55. Bengtsson J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012.
  56. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts. SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
  57. Bengtsson J, Eriksson M, Alm Rosenblad M, Blanck H: Metagenomic Characterisation of Marine Periphyton Communitites. Deep Sequencing Techniques Workshop, Gothenburg, 2010.
  58. Bengtsson J, Alm Rosenblad M, Forlin L, Celander M, Blanck H, Larsson DGJ, Molin M, Blomberg A: Distribution of Detoxification Genes in Marine Environments. Swedish Bioinformatics Workshop, Gothenburg, 2010.

Conference talks

Presenting author indicated by *

  1. Bengtsson-Palme J*: From model systems to global surveillance programs: Predicting and preventing the disease threats of the future. 32° Congresso Brasileiro de Microbiologia, Foz do Iguaçu, Brazil, 2023.
  2. Bengtsson-Palme J*: Tracking AMR in the Environment:
The EMBARK approach. 39th annual meeting of the Nordic Society of Clinical Microbiology and Infectious Diseases (NSCMID), Örebro, Sweden, 2023.
  3. Wenne M*, Abramova A, Bengtsson-Palme J: Limited Selection for Antibiotic Resistance in Soil Contaminated with Antibiotics. Swedish Bioinformatics Workshop, Umeå, Sweden, 2022.
  4. Teichmann L*, Luitwieler S, Bengtsson-Palme J, der Kuile B: The Role Of The SOS Response In The Acquisition Of Antimicrobial Resistance In Escherichia Coli. 6th International symposium on the environmental dimension of antibiotic resistance (EDAR6), Gothenburg, Sweden, 2022.
  5. Bengtsson-Palme J*, Abramova A, Berendonk TU, Coelho LP, Gschwind R, 
Jarquin Diaz VH, Klümper U, Löber U, Ugarcina Perovic S, Zahra R: Towards Standardized Global Monitoring of Antibiotic Resistance in the Environment:
The EMBARK Program ISME18 Conference, Lausanne, Switzerland, 2022.
  6. Bengtsson-Palme J*: Deciphering the genetic mechanisms behind microbial interactions in microbiomes 7th Microbiome and Probiotics R&D Business Collaboration Forum, Virtual meeting, 2020.
  7. Bengtsson-Palme J*: The Effect of Antibiotics on Interactions in Microbial Communities ASM Microbe 2019, San Francisco, CA, USA, 2019.
  8. Bengtsson-Palme J*: The environment and antibiotic resistance development – now and in the future ICOHAR 2019, Utrecht, Netherlands, 2019.
  9. Bengtsson-Palme J*, Gunnarsson L, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  10. Berglund F*, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Larsson DGJ, Kristiansson E: Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  11. Kraupner N*, Ebmeyer S, Bengtsson-Palme J, Fick J, Flach C-F, Larsson DGJ: Minimal selective concentration of ciprofloxacin for Escherichia coli grown in complex aquatic bacterial biofilms. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  12. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Unravelling the structure and diversity of human, animal and environmental resistomes using metagenomics. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  13. Bengtsson-Palme J*, Hammarén R, Pal C, Östman M, Björlenius B, Flach C-F, Kristiansson E, Fick J, Tysklind M, Larsson DGJ: Elucidating biocide and metal co-selection for antibiotic resistance in sewage treatment plants using metagenomics. The role of metals and biocides in the selection of antibiotic resistant bacteria, Stockholm, Sweden, 2016.
  14. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data. Swedish Bioinformatics Workshop, Stockholm, Sweden, 2015.
  15. Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 6th Congress of European Microbiologists (FEMS2015), Maastricht, The Netherlands, 2015.
  16. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into antibiotic resistance of bacterial communities using metagenomic data. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  17. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of antibacterial biocide, metal and antibiotic resistance genes in bacterial genomes and plasmids reveals novel insights in their co-selection potential. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  18. Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  19. Bengtsson-Palme J*, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  20. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Large-scale analysis of bacterial genomes and plasmids for antibiotic, biocide and metal resistance genes and their co-selection potential. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  21. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Depth Matters: Sequencing depth is central to capture the diversity of antibiotic resistance genes in the environment. Swedish Bioinformatics Workshop 2013, Skövde, Sweden, 2013.
  22. Bengtsson-Palme J*, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  23. Bengtsson J*, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Analyzing antibiotic resistance using metagenomics. SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012
  24. Bengtsson J*, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts. SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.

Software packages

  1. Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J: CAFE – Coefficient-based Analysis of Fitness by read Enrichment (2020)
  2. Magesh S, Jonsson V, Bengtsson-Palme J: Mumame – Mutation Mapping in Metagenomes (2018) [Paper link]
  3. Bengtsson-Palme J, Nilsson RH, Wurzbacher C: Consension – Consensus generation of OTU sequences from long-read sequencing amplicons (2018) [Paper link]
  4. Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Metaxa2 Database Builder (2018) (included with Metaxa2 2.2 and later) [Paper link]
  5. Bengtsson-Palme J: COAT – Conservation-Oriented Alignment Tool (2017)
  6. Hammarén R, Pal C, Bengtsson-Palme J: FARAO – The Flexible All-Round Annotation Organizer (2015) [Paper link]
  7. Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH: Metaxa2 Diversity Tools (2015) (included with Metaxa2 2.1 and later) [Paper link]
  8. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2 – Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data (2014) [Paper link]
  9. Bengtsson-Palme J, Pal C: BacMet-Scan – A tool to scan sequence data against the BacMet database (2013) [Paper link]
  10. Bengtsson-Palme J: TriMetAss – Trinity-based Metagenomics Assembler (2013) [Paper link]
  11. Bengtsson-Palme J, Abarenkov K, Nilsson RH: Atosh – Assign to Species Hypothesis (2013) [This script underlies part of the UNITE database] [Paper link]
  12. Bengtsson-Palme J, Veldre V, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, Bertrand Y, De Wit P, Sanchez M, Ebersberger I, Sanli K, de Souza F, Kristiansson E, Abarenkov K, Eriksson KM, Nilsson RH: ITSx – a software for improved detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing (2013) [Paper link]
  13. Bengtsson-Palme J: PETKit – a set of tools to ease the use of sequences from large-scale sequencing projects generating paired-end reads (2012)
  14. Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH: 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 (2012) [Paper link]
  15. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa – a software package for automated identification and classification of small subunit (SSU) rRNA sequences from archaea, bacteria, eukaryotes, chloroplasts and mitochondria in metagenomic and environmental sequencing data sets (2011) [Paper link]
  16. Bengtsson J: Metaorf – a very simple gene finder adapted for the fragmentary nature of metagenomic data (2010)
  17. Bengtsson J: Bloutminer – a script for mining data from BLAST reports (2010)