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Ahmed MS, Lauersen KJ, Ikram S, Li C. Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites. ACS Synth Biol 2021; 10:646-669. [PMID: 33751883 DOI: 10.1021/acssynbio.0c00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.
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Affiliation(s)
- Muhammad Saad Ahmed
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, The Mall, Rawalpindi 46000, Pakistan
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Sana Ikram
- Beijing Higher Institution Engineering Research Center for Food Additives and Ingredients, Beijing Technology & Business University (BTBU), Beijing 100048, P. R. China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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Kurata A, Aoki D, Fukuta Y, Kamimura T, Onishi T, Kishimoto N, Uegaki K. Transcriptome analysis of ionic-liquid tolerant Bacillus amyloliquefaciens CMW1 and identification of a novel efflux pump. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1885995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Atsushi Kurata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Daichi Aoki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Yoshihumi Fukuta
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Taichi Kamimura
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Taiki Onishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Noriaki Kishimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
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Lim SK, Kim D, Moon DC, Cho Y, Rho M. Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle. Gigascience 2020; 9:5829833. [PMID: 32369165 PMCID: PMC7317084 DOI: 10.1093/gigascience/giaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. Results In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. Conclusions Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.
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Affiliation(s)
- Suk-Kyung Lim
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Dongjun Kim
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Dong-Chan Moon
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Youna Cho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Mina Rho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering.,Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Biomedical Informatics
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Littlewood S, Tattersall H, Hughes CS, Hussain R, Ma P, Harding SE, Nakayama J, Phillips-Jones MK. The gelatinase biosynthesis-activating pheromone binds and stabilises the FsrB membrane protein in Enterococcus faecalis quorum sensing. FEBS Lett 2019; 594:553-563. [PMID: 31598959 PMCID: PMC7028047 DOI: 10.1002/1873-3468.13634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022]
Abstract
Quorum‐sensing mechanisms regulate gene expression in response to changing cell‐population density detected through pheromones. In Enterococcus faecalis, Fsr quorum sensing produces and responds to the gelatinase biosynthesis‐activating pheromone (GBAP). Here we establish that the enterococcal FsrB membrane protein has a direct role connected with GBAP by showing that GBAP binds to purified FsrB. Far‐UV CD measurements demonstrated a predominantly α‐helical protein exhibiting a small level of conformational flexibility. Fivefold (400 μm) GBAP stabilised FsrB (80 μm) secondary structure. FsrB thermal denaturation in the presence and absence of GBAP revealed melting temperatures of 70.1 and 60.8 °C, respectively, demonstrating GBAP interactions and increased thermal stability conferred by GBAP. Addition of GBAP also resulted in tertiary structural changes, confirming GBAP binding.
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Affiliation(s)
- Sean Littlewood
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - Helena Tattersall
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - Charlotte S Hughes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Pikyee Ma
- Astbury Centre for Structural Molecular Biology, University of Leeds, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, UK
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Abdel-Motaal H, Meng L, Zhang Z, Abdelazez AH, Shao L, Xu T, Meng F, Abozaed S, Zhang R, Jiang J. An Uncharacterized Major Facilitator Superfamily Transporter From Planococcus maritimus Exhibits Dual Functions as a Na +(Li +, K +)/H + Antiporter and a Multidrug Efflux Pump. Front Microbiol 2018; 9:1601. [PMID: 30061877 PMCID: PMC6055358 DOI: 10.3389/fmicb.2018.01601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 02/01/2023] Open
Abstract
Within major facilitator superfamily (MFS), up to 27 unknown major facilitator families and many members of 60 well-characterized families have been functionally unknown as yet, due to their sharing no or significantly low sequence identity with characterized MFS members. Here we present the first report on the characterization of one functionally unknown MFS transporter designated MdrP with the accession version No. ANU18183.1 from the slight halophile Planococcus maritimus DS 17275T. During the screening of Na+/H+ antiporter genes, we found at first that MdrP exhibits Na+(Li+, K+)/H+ antiport activity, and propose that it should represent a novel class of Na+(Li+, K+)/H+ antiporters. However, we speculate that MdrP may possess an additional protein function. The existence of the signature Motif A of drug/H+antiporter (DHA) family members and phylogenetic analysis suggest that MdrP may also function as a drug efflux pump, which was established by minimum inhibitory concentration tests and drug efflux activity assays. Taken together, this novel MFS transporter exhibits dual functions as a Na+(Li+, K+)/H+ antiporter and a multidrug efflux pump, which will be very helpful to not only positively contribute to the function prediction of uncharacterized MFS members especially DHA1 family ones, but also broaden the knowledge of Na+/H+ antiporters.
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Affiliation(s)
- Heba Abdel-Motaal
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China.,Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Lin Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Zhenglai Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Amro H Abdelazez
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Li Shao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Tong Xu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Fankui Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Shaima Abozaed
- Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Rui Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Juquan Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
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Li L, Tetu SG, Paulsen IT, Hassan KA. A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria. Methods Mol Biol 2018; 1700:221-235. [PMID: 29177833 DOI: 10.1007/978-1-4939-7454-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The core genomes of most bacterial species include a large number of genes encoding putative efflux pumps. The functional roles of most of these pumps are unknown, however, they are often under tight regulatory control and expressed in response to their substrates. Therefore, one way to identify pumps that function in antimicrobial resistance is to examine the transcriptional responses of efflux pump genes to antimicrobial shock. By conducting complete transcriptomic experiments following antimicrobial shock treatments, it may be possible to identify novel drug efflux pumps encoded in bacterial genomes. In this chapter we describe a complete workflow for conducting transcriptomic analyses by RNA sequencing, to determine transcriptional changes in bacteria responding to antimicrobials.
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Affiliation(s)
- Liping Li
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.
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Hassan KA, Fagerlund A, Elbourne LDH, Vörös A, Kroeger JK, Simm R, Tourasse NJ, Finke S, Henderson PJF, Økstad OA, Paulsen IT, Kolstø AB. The putative drug efflux systems of the Bacillus cereus group. PLoS One 2017; 12:e0176188. [PMID: 28472044 PMCID: PMC5417439 DOI: 10.1371/journal.pone.0176188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/06/2017] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group of bacteria includes seven closely related species, three of which, B. anthracis, B. cereus and B. thuringiensis, are pathogens of humans, animals and/or insects. Preliminary investigations into the transport capabilities of different bacterial lineages suggested that genes encoding putative efflux systems were unusually abundant in the B. cereus group compared to other bacteria. To explore the drug efflux potential of the B. cereus group all putative efflux systems were identified in the genomes of prototypical strains of B. cereus, B. anthracis and B. thuringiensis using our Transporter Automated Annotation Pipeline. More than 90 putative drug efflux systems were found within each of these strains, accounting for up to 2.7% of their protein coding potential. Comparative analyses demonstrated that the efflux systems are highly conserved between these species; 70-80% of the putative efflux pumps were shared between all three strains studied. Furthermore, 82% of the putative efflux system proteins encoded by the prototypical B. cereus strain ATCC 14579 (type strain) were found to be conserved in at least 80% of 169 B. cereus group strains that have high quality genome sequences available. However, only a handful of these efflux pumps have been functionally characterized. Deletion of individual efflux pump genes from B. cereus typically had little impact to drug resistance phenotypes or the general fitness of the strains, possibly because of the large numbers of alternative efflux systems that may have overlapping substrate specificities. Therefore, to gain insight into the possible transport functions of efflux systems in B. cereus, we undertook large-scale qRT-PCR analyses of efflux pump gene expression following drug shocks and other stress treatments. Clustering of gene expression changes identified several groups of similarly regulated systems that may have overlapping drug resistance functions. In this article we review current knowledge of the small molecule efflux pumps encoded by the B. cereus group and suggest the likely functions of numerous uncharacterised pumps.
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Affiliation(s)
- Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Annette Fagerlund
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Liam D. H. Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Aniko Vörös
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Jasmin K. Kroeger
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Freiburg, Germany
| | - Roger Simm
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Nicolas J. Tourasse
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Sarah Finke
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Peter J. F. Henderson
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (ABK); (ITP)
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- * E-mail: (ABK); (ITP)
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