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Items: 38

1.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia.

Guzman-Otazo J, Gonzales-Siles L, Poma V, Bengtsson-Palme J, Thorell K, Flach CF, Iñiguez V, Sjöling Å.

PLoS One. 2019 Jan 14;14(1):e0210735. doi: 10.1371/journal.pone.0210735. eCollection 2019.

2.

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.

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 JY, Naas T, O'Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G.

Version 2. F1000Res. 2018 Apr 13 [revised 2018 Jan 1];7. pii: ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018.

3.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K.

Nucleic Acids Res. 2019 Jan 8;47(D1):D259-D264. doi: 10.1093/nar/gky1022.

4.

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.

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.

Nat Commun. 2018 Sep 24;9(1):3891. doi: 10.1038/s41467-018-06393-w.

5.

Introducing ribosomal tandem repeat barcoding for fungi.

Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH.

Mol Ecol Resour. 2019 Jan;19(1):118-127. doi: 10.1111/1755-0998.12944. Epub 2018 Oct 24.

PMID:
30240145
6.

Structure and function of the global topsoil microbiome.

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.

Nature. 2018 Aug;560(7717):233-237. doi: 10.1038/s41586-018-0386-6. Epub 2018 Aug 1.

PMID:
30069051
7.
8.

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data.

Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM.

PeerJ. 2018 Jun 26;6:e5126. doi: 10.7717/peerj.5126. eCollection 2018.

9.

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

Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ÉD, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH.

Bioinformatics. 2018 Dec 1;34(23):4027-4033. doi: 10.1093/bioinformatics/bty482.

10.

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.

Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach CF, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Plant L, Ploy MC, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel AJ, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson AS.

Environ Int. 2018 Aug;117:132-138. doi: 10.1016/j.envint.2018.04.041. Epub 2018 May 7.

11.

Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.

Wahlgren WY, Dunevall E, North RA, Paz A, Scalise M, Bisignano P, Bengtsson-Palme J, Goyal P, Claesson E, Caing-Carlsson R, Andersson R, Beis K, Nilsson UJ, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, Friemann R.

Nat Commun. 2018 May 1;9(1):1753. doi: 10.1038/s41467-018-04045-7.

12.

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

Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach CF, Larsson DGJ.

Environ Int. 2018 Jul;116:255-268. doi: 10.1016/j.envint.2018.04.029. Epub 2018 Apr 25.

PMID:
29704804
13.

The relation between Blastocystis and the intestinal microbiota in Swedish travellers.

Forsell J, Bengtsson-Palme J, Angelin M, Johansson A, Evengård B, Granlund M.

BMC Microbiol. 2017 Dec 11;17(1):231. doi: 10.1186/s12866-017-1139-7.

14.

Protection goals must guide risk assessment for antibiotics.

Bengtsson-Palme J, Larsson DGJ.

Environ Int. 2018 Feb;111:352-353. doi: 10.1016/j.envint.2017.10.019. Epub 2017 Oct 31. No abstract available.

PMID:
29097053
15.

Environmental factors influencing the development and spread of antibiotic resistance.

Bengtsson-Palme J, Kristiansson E, Larsson DGJ.

FEMS Microbiol Rev. 2018 Jan 1;42(1). doi: 10.1093/femsre/fux053. Review.

16.

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

Berglund F, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach CF, Larsson DGJ, Kristiansson E.

Microbiome. 2017 Oct 12;5(1):134. doi: 10.1186/s40168-017-0353-8.

17.

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

Boulund F, Berglund F, Flach CF, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E.

BMC Genomics. 2017 Sep 2;18(1):682. doi: 10.1186/s12864-017-4064-0.

18.

In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.

Thorell K, Bengtsson-Palme J, Liu OH, Palacios Gonzales RV, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å.

Infect Immun. 2017 Sep 20;85(10). pii: e00031-17. doi: 10.1128/IAI.00031-17. Print 2017 Oct.

19.

Using metagenomics to investigate human and environmental resistomes.

Bengtsson-Palme J, Larsson DGJ, Kristiansson E.

J Antimicrob Chemother. 2017 Oct 1;72(10):2690-2703. doi: 10.1093/jac/dkx199. Review.

PMID:
28673041
20.

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, Kristiansson E, Östman M, Bengtsson-Palme J, Tysklind M, Larsson DGJ.

Sci Total Environ. 2017 Jul 15;590-591:461-468. doi: 10.1016/j.scitotenv.2017.01.213. Epub 2017 Mar 8.

PMID:
28284638
21.

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data.

Richardson RT, Bengtsson-Palme J, Johnson RM.

Mol Ecol Resour. 2017 Jul;17(4):760-769. doi: 10.1111/1755-0998.12628. Epub 2016 Nov 21.

PMID:
27797448
22.

The structure and diversity of human, animal and environmental resistomes.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG.

Microbiome. 2016 Oct 7;4(1):54.

23.

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

Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach CF, Fick J, Kristiansson E, Tysklind M, Larsson DGJ.

Sci Total Environ. 2016 Dec 1;572:697-712. doi: 10.1016/j.scitotenv.2016.06.228. Epub 2016 Aug 17.

PMID:
27542633
24.

Strategies to improve usability and preserve accuracy in biological sequence databases.

Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sanchez J, Sanli K, Thorell K.

Proteomics. 2016 Sep;16(18):2454-60. doi: 10.1002/pmic.201600034.

PMID:
27528420
25.

FARAO: the flexible all-round annotation organizer.

Hammarén R, Pal C, Bengtsson-Palme J.

Bioinformatics. 2016 Dec 1;32(23):3664-3666. Epub 2016 Aug 4.

PMID:
27493193
26.

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.

Lundström SV, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach CF, Larsson DGJ.

Sci Total Environ. 2016 May 15;553:587-595. doi: 10.1016/j.scitotenv.2016.02.103. Epub 2016 Mar 22.

PMID:
26938321
27.

Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.

Bengtsson-Palme J, Larsson DG.

Environ Int. 2016 Jan;86:140-9. doi: 10.1016/j.envint.2015.10.015. Epub 2015 Nov 17.

28.

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.

Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM.

Front Microbiol. 2015 Oct 30;6:1192. doi: 10.3389/fmicb.2015.01192. eCollection 2015.

29.

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

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG.

BMC Genomics. 2015 Nov 17;16:964. doi: 10.1186/s12864-015-2153-5.

30.

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.

Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DG, Johansson A.

Antimicrob Agents Chemother. 2015 Oct;59(10):6551-60. doi: 10.1128/AAC.00933-15. Epub 2015 Aug 10.

31.

Antibiotic resistance genes in the environment: prioritizing risks.

Bengtsson-Palme J, Larsson DG.

Nat Rev Microbiol. 2015 Jun;13(6):396. doi: 10.1038/nrmicro3399-c1. Epub 2015 Apr 27. No abstract available.

PMID:
25915637
32.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.

Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K.

Microbes Environ. 2015;30(2):145-50. doi: 10.1264/jsme2.ME14121. Epub 2015 Mar 19.

33.

METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.

Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, Nilsson RH.

Mol Ecol Resour. 2015 Nov;15(6):1403-14. doi: 10.1111/1755-0998.12399. Epub 2015 Mar 23.

PMID:
25732605
34.

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

Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DG.

Front Microbiol. 2014 Dec 2;5:648. doi: 10.3389/fmicb.2014.00648. eCollection 2014.

35.

ITS1: a DNA barcode better than ITS2 in eukaryotes?

Wang XC, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang JH, Cai D, Li JQ.

Mol Ecol Resour. 2015 May;15(3):573-86. doi: 10.1111/1755-0998.12325. Epub 2014 Sep 24.

PMID:
25187125
36.

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.

Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A.

BMC Genomics. 2014 Sep 1;15:749. doi: 10.1186/1471-2164-15-749.

37.

BacMet: antibacterial biocide and metal resistance genes database.

Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG.

Nucleic Acids Res. 2014 Jan;42(Database issue):D737-43. doi: 10.1093/nar/gkt1252. Epub 2013 Dec 3.

38.

Towards a unified paradigm for sequence-based identification of fungi.

Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, 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, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH.

Mol Ecol. 2013 Nov;22(21):5271-7. doi: 10.1111/mec.12481. Epub 2013 Sep 24.

PMID:
24112409

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