What we do?

The Bacterial Synthetic Biology Section at the Center for Biosustainability is led by Professor Morten Sommer. We work broadly within microbiology as it applies to human and planetary health. We develop and apply novel technologies within the fields of microbiome synthetic biology and microbial foods. The two main research areas in the lab are:

Advanced microbiome therapeutics
Microbial foods

As researchers we consider it of key importance that our work has the broadest impact possible. Accordingly, we pay close attention to the potential applications of our work and actively seek to commercialize research results or otherwise deploy them for the benefit of society. Over the past decade members of the laboratory have co-founded several companies, which now employs hundreds of people and are bringing new products and services to the market.

Research

Our work is broadly aimed towards understanding how microbial systems establish, organize and evolve and affect their hosts and environment. We study these systems with a goal towards engineering them for applications within human and planetary health. We use cutting edge technology and aim to translate our basic research findings into entities, policies and education that provide long term benefits to society.

Synthetic biology for sustainable food production

Earth’s population could reach 10 B people leading to a 50-80% increase in global demand for food. Current agriculture cannot support this and climate impact of continuing food production as is would be catastrophic as food production already accounts for approximately 1/3 of total greenhouse gas emissions and +49 million square kilometers corresponding to 38% of earth's land mass. To address this global challenge a combination of new food habits and radical innovation in food production must take place. We use the term microbial foods to describe the use of microbiology for food production comprising everything from natural fermentations to microbial biomass and cell factories. Our research is applications oriented with a goal of developing technology that solves some of the pressing needs of our food system.

Human microbiome and engineered microbiome therapeutics

The human microbiome is to an increasing extent being implicated in a wide range of disease and health states. We study the human microbiome during interventions, with a particular focus on antibiotic treatment and resulting microbiome modulation. We design and build new interventions for modulating the microbiome to promote specific community compositions or functionality. We also design and build interventions that can amend the functionality encoded in the gut microbiome.

Collateral Sensitivity

Lejla Imamovic introduces the principle of collateral sensitivity cycling.

Rapid resistome mapping using nanopore sequencing

Eric van der Helm and Lejla Imamovic

Understanding and addressing heterogeneity in large scale fermentations

Industrial-scale biomanufacturing of therapeutics, enzymes, and chemicals relies on cultivating large volumes of engineered cells in fed-batch or continuous bioprocesses. Clonal expansion of high-performing producer cells can favor the emergence of low-producing escape variants that have shed the load from metabolic burden or toxicities imposed by product synthesis or secretion. Eventually, these low- or non-producing variants can reduce product yield and quality, making genetic homogeneity a crucial, yet often overlooked parameter of process scale-up. We are investigating this problem as it applies to industrial biomanufacturing and develop synthetic biology solutions to limit its detrimental effects on scale-up.

Past research area:
Antibiotic resistance and collateral sensitivity

Evolution is rendering our medicines against many infections useless threatening to bring us back to the pre-antibiotic era. In many cases resistance to a particular antibiotic did not evolve within the resistant human pathogen, but rather was acquired by lateral gene transfer from other resistant bacteria. These resistant donor bacteria need not be pathogenic, yet they contribute to the evolution of antibiotic resistance in human pathogens by serving as an accessible reservoir of resistance genes. We used a variety of culture-dependent and culture-independent methods to characterize how these reservoirs are interacting, with the ultimate goal of creating quantitative models for how antibiotic resistance genes arise in human pathogens. We also studied the adaptive mechanisms of drug resistance and collateral sensitivity using a combination of laboratory evolution and sampling of clinical isolates, with the goal of developing novel treatment strategies for countering resistance development.

In future we should be treated with living medicine

Morten Sommer

Understanding and addressing heterogeneity in large scale fermentations

Industrial-scale biomanufacturing of therapeutics, enzymes, and chemicals relies on cultivating large volumes of engineered cells in fed-batch or continuous bioprocesses. Clonal expansion of high-performing producer cells can favor the emergence of low-producing escape variants that have shed the load from metabolic burden or toxicities imposed by product synthesis or secretion. Eventually, these low- or non-producing variants can reduce product yield and quality, making genetic homogeneity a crucial, yet often overlooked parameter of process scale-up. We are investigating this problem as it applies to industrial biomanufacturing and develop synthetic biology solutions to limit its detrimental effects on scale-up.

People

Here you will find current and past members.

Permanent Staff

  • Morten O. A. SommerMorten O. A. Sommer, Professor
  • Gitte MejlhartGitte Mejlhart,
    PA
  • Susanne KammlerSusanne Kammler, PhD

Researcher Tenure Track Staff

  • Leonie Jahn, PhDLeonie Jahn, PhD

    • Post docs

    • Loes van DamLoes van Dam, PhD
    • Tiffany Mak, PhDTiffany Mak, PhD
    • Alex Hedin, PhDAlex Hedin, PhD

      • Resass

      • Frederik NeergaardFrederik Neergaard
      • Veronica Ramos VianaVeronica Ramos Viana

        • PhD students

        • Andreas KoulouktsisAndreas Koulouktsis
        • Arrate Sainz d.l.M. LarreaArrate Sainz d.l.M. Larrea
        • Elemosho RidwanElemosho Ridwan
        • Hitesh GelliHitesh Gelli
        • Troels Holger VaabenTroels Holger Vaaben

        Students

    TEDxCopenhagen - Morten Sommer - What Bacteria means for the Good life

Funding

Resources to hire personal and conduct experiments are a prerequisite for the laboratory to succeed in its endeavors. Accordingly, we greatly acknowledge the research funding and support we have received since the start of the group in 2010. The laboratory has been sponsored by national and international funding agencies as well as private foundations. This funding has been essential in order to advance our research:

Current funders

Novo Nordisk Foundation (2018-2024) - Design and Engineering of Biological Molecules and Systems

Novo Nordisk Foundation (2022-2025) - Advanced microbiome therapeutics for personalized medicine in non-alcoholic fatty liver disease (NAFLD)

Novo Nordisk Foundation (2023-2024) - Advanced Microbial Therapeutic for Bile Acid Sulfation in Obesity Treatment

Novo Nordisk Foundation (2023-2026) - Improving healthspan through next generation probiotics

Novo Nordisk Foundation (2023-2026) - Immunomodulation of the gut-brain axis in Parkinson's disease using engineered bacteria

GUPD (2023-2025) - Test of antimicrobial properties of surfaces for solid-state fermentation

Good Food Institute (2022-2025) - Creation of a seafood alternative based on fungal mycelium

Past funders

Novo Nordisk Foundation (2021-2022) - A novel bacterial platform for in situ engineering of human immune cells

Novo Nordisk Foundation (2022-2023) - Immunomodulation of the tumor microenvironment using tumor-targeting cytokine-secreting bacteria

Novo Nordisk Foundation (2020-2022) - Microbial cell therapies for modulating the gut-brain axis

EU H2020 ITN BestTreat (2018-2021) - Building a Gut Microbiome Engineering Toolbox for In-Situ Therapeutic Treatments for Non-alcohlic Fatty Liver Disease

SIPROS (2016-2020) - Virtual Laboratory Simulations for Increased Productivity and Occupational Standards in the Biotechnology Industry

EU ERC Starting Grant (2015-2020) - Utilizing evolutionary interactions to limit multidrug resistance

DFF Sapere Aude (2014-2020) - Novel treatment strategies for countering durg resistance

EU H2020 ITN MetaRNA (2015-2019) - RNA-based technologies for single-cell metabolite analysis

Novo Nordisk Foundation (2014-2018) - Biosensor-based genome screening platform for the production of Biosynthethic Precursors and coFactorrs in E.coli

Lundbeck Foundation (2013-2017) - Elucidating antibiotic resistance gene exchange network

EU FP7 PROMYS project (2013-2017) - Programming synthetic networks for bio-based production of value chemicals

EU FP7 ITN Bactory (2012-2016) - Bacterial Factories for Sustainable Chemical and Drug Production

Lundbeck Foundation (2011-2014) - <Understanding the evolution and dissemination of antibiotic resistance

FSS (2011-2014) - Complex drug mixtures for fighting MRSA

Højteknologigonden (2012-2015) - Molecular dianostics for infectious disease

EU FP7 Evotar project (2011-2014) - Evolution and Transfer of Antibiotic Resistance

Publications

Full list from pubmed
Full list from Google Scholar
*Denotes equal contribution
# corresponding author

  • >Tueros FG, Ellabaan MMH, Henrichsson M, Uribe RV, Backhed F, Sommer MOA,# 'Challenging the Hypothesis of de novo Biosynthesis of Bile Acids by Marine Bacteria' (2022) Microbiology and Bitechnology Letters - DOI:10.48022/mbl.2111.11010 - Download link
  • >van 't Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA,# 'High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917' (2022) BMC Bioinformatics - DOI:10.1186/s12859-022-05108-9 - Download link
  • >Wismer P, Soares SA, Einarson KA, Sommer MOA,# 'Laboratory performance prediction using virtual reality behaviometrics' (2022) Plos One - DOI:10.1371/journal.pone.0279320 - Download link
  • Vaaben H, Uribe RV, Sommer MOA,# 'Characterization of Eight Bacterial Biosensors for Microbial Diagnostic and Therapeutic Applications' (2022) ACS Synthetic Biology - DOI:10.1021/acssynbio.2c00491 - Download link
  • Gelli HP, Uribe RV, Sommer MOA,# 'Screening for effective cell-penetrating peptides with minimal impact on epithelial cells and gut commensals in vitro' (2022) Frontiers in Pharmacology - DOI:10.3389/fphar.2022.1049324 - Download link
  • Holst AQ, Hois J, Laursen MF, Sommer MOA, Licht TR, Bahl MI# 'Human milk oligosaccharides induce acute yet reversible compositional changes in the gut microbiota of conventional mice linked to a reduction of butyrate levels' (2022) Microlife - DOI:10.1093/femsml/uqac006 - Download link
  • Hedin AK, Rees VE Zhang H, Kruse V, Uribe RV, Sommer MOA# 'Effects of broad-spectrum antibiotics on the colonisation of probiotic yeast Saccharomyces boulardii in the murine gastrointestinal tract' (2022) Science Reports - DOI:10.1038/s41598-022-12806-0 - Download link
  • Malla S, van der Helm E, Darbani, B, Wieschalka S, Förster J, Borodina I, Sommer MOA# 'A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics' (2022) Frontiers in Microbiology - DOI:10.3389/fmicb.2022.855736 - Download link
  • Lee S-W, Tran KT, Uribe RV, Gotfredsen HC, Clausen MH Mendes BL, Montoya Bach A, Sommer MOA# 'Identification and Optimization of Novel Small-Molecule Cas9 Inhibitors by Cell-Based High-Throughput Screening' (2022) ACS Synthetic Biology - DOI:10.1021/acs.jmedchem.1c01834 - Download link
  • Weiss A, Touret F, Baronti C, Gilles M, Hoen B, Nougaiede A, de Lamballerie X, Sommer MOA# 'Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2)' (2022) PLOS One - DOI:10.101371/journal.pone.0260958 - Download link
  • Armetta J, Schantz-Klausen M, Shepelin, Uribe RV, Bahl MI, Laursen MF, Licht TR, Sommer MOA# 'Escherichia coli Promoters with Consistent Expression throughout the Murine Gut' (2022) ACS Synthetic Biology - DOI:10.1021/acssynbio.1c00325 - Download link
  • Lagler H, Bangert C, Auint T, Österreicher Z, Nussbaumer-Pröll A, Eberl S, Weber M, Karer M, Sommer MOA, Zeitlinger M 'Comparison of non-invasive Staphylococcus aureus sampling methods on lesional skin in patients with atopic dermatitis' (2022) European Journal of Clinical Microbiology & Infectious Diseases - DOI:10.1007/s10096-021-04365-5 - Download link
  • Lee S-W, Rugbjerg P, Sommer MOA#, 'Exploring Selective Pressure Trade-Offs for Synthetic Addiction to Extend Metabolite Productive Lifetimes in Yeast' (2021) ACS Synthetic Biology - DOI:10.1021/acssynbio.1c00240 - Download link
  • Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL Kaiser BK, Malik HS 'The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity' (2021) PLoS Biology - DOI:10.1371/journal.phio.3001428 - Download link
  • Uribe MV, Rathmer C, Jahn LJ, Ellabaan MMH, Simone L, Sommer MOA#, 'Bacterial resistance to CRISPR-Cas antimicrobials' (2021) Science Reports - DOI:10.1038/s41598-021-96735-4 - Download link
  • Ni Y, Lohinai Z, Heshiki Y, Dome B, Moldvay J, Dulka E, Galffy G, Berta J, Weiss G, Sommer MOA#, Panagiotou G 'Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients' (2021) ISME - DOI:10.1038/s41396-021-00998-8 - Download link
  • Ellabaan MMH, Munck C, Porse A, Imamovic L, Sommer MOA#, 'Forecasting the dissemination of antibiotic resistance genes across bacterial genomes' (2021) Nature Communication - DOI:10.1038/s41467-021-022757-1 - Download link
  • Rugbjerg P, Dyerberg ASB, Quainoo S, Munck C, Sommer MOA#, 'Short and long-read ultra-deep sequencing profiles emerging heterogeneity across five platform Escherichia coli strains' (2021) Metabolic Engineering - DOI:10.1016/j.ymben.2021.11.006 - Download link
  • Wismer P, Lopez Cordoba A, Baceviciute S, Clauson-Kaas F, Sommer MOA#, 'Immersive virtual reality as a competitive training strategy for the biopharma industry' (2021) Nature Biotechnology - DOI:10.1038/s41587-020-00784-5 - Download link
  • Senne de Oliveira Lino F, Bajic, D, Villa JCC, Sanchez A, Sommer MOA#, 'Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentation' (2021) Nature Communications - DOI:10.1038/s41467-021-21844-7 - Download link
  • Jahn LJ, Simon D, Jensen M, Bradshaw C, Ellabaan MMH, Sommer MOA#, 'Compatibility of evolutionary responses to constituent antibiotics drive resistance evolution to drug pairs' (2021) Molecular Biology and Evolution - DOI:10.1093/molbev/msab006 - Download link
  • Mirhakkak MH, Schäuble S, Klassert TE, Brunke S, Brandt P, Loos D, Uribe RV, Senne de Oliveira Lino F, Ni Y, Vylkova S, Slevogt H, Hube B, Weiss GJ, Sommer MOA#, Panagiotou G,'Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels' (2020) ISME - DOI:10.1038/s41396-020-00848-z - Download link
  • Rugbjerg P, Dyerberg ASB, Quainoo S, Munck C, Sommer MOA#, 'Short and long-read ultra-deep sequencing profiles emerging heterogeneity across five platform Escherichia coli strains' (2020) Metabolic Engineering - DOI:10.1016/j.ymben.202.11.006 - Download link
  • Rodriguez de Evgrafov MC, Faza M, Asimakopoulos K, Sommer MOA#, 'Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens' (2020) Antimicrob Agents Chemother - DOI:10.1128/AAC.01273-20 - Download link
  • Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, Tsang CC, Lam RP, Sridhar S, Kang K, Hube B, Woo PC, Sommer MOA, Panagiotou G#, 'Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria' (2020) Microbiome - DOI:10.1186/s40168-020-00899-6 - Download link
  • D'Ambrosio V, Dore E, Di Blasi R, van den Broek M, Sudarsan S, Horst JT, Ambri F, Sommer MOA, Rugbjerg P, Keasling JD, Mans R, Jensen MK#, 'Regulatory control circuits for stabilizing long-term anabolic product formation in yeast' (2020) Metabolig Engineering - DOI:10.1016/j.ymben.2020.07.006 - Download link
  • Weiss A, Jellingsø M, Sommer MOA#, 'Spatial and temporal dynamics of SARS-CoV-2 in COVID-19 patients: A systematic review and meta-analysis' (2020) EbioMedicine - DOI:10.1016/j.ebiom.2020.102916 - Download link
  • Ahmed MN, Abdelsamad A, Wassermann T, Porse A, Back J, Sommer MOA, Køiby N, Ciofu O#, 'The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance' (2020) NPF Biofilms Microbiomes - DOI:10.1038/s41522-020-00138-8 - Download link
  • Moeller TSJ, Liu G, Hartman HB, Rau MH, Mortensen S, Thamsborg K, Johansen AE, Sommer MOA#, Guardabassi L, Poolman MG,m Olsen JE 'Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli' (2020) Scientific Report - DOI:10.1038/s41598-020-64995-1 - Download link
  • Bali AP, Lennox-Hvenekilde D, Myling-Petersen N, Buerger J, Salomonsen B, Gronenberg LS, Sommer MOA#, Genee HJ 'Improved biotin, thiamine, and lipoic acid biosynthesis by engineering the global regulator IscR' (2020) Metabolic Engineering - DOI:10.1016/j.ymben.2020.03.005 - Download link
  • Bongers M, Perez-Gil J, Hodson MP, Schrübbers L, Wulff F, Sommer MOA#, Nielsen LK, Vickers CE 'Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production' (2020) Elife - DOI:10.7554/eLife.48685.Elife - Download link
  • Porse A, Jahn LJ, Ellabaan MMH, Sommer MOA#, 'Dominant resistance and negative epistasis can limit the co-selection of de novo resistance mutations and antibiotic resistance genes' (2020) Nature Communications - DOI:10.10138/s41467-020-15080-8 - Download link
  • Heshiki Y, Uribe RV, Li J, Ni Y, Quainoo S, Imamovic L, Li J, Sørensen M, Chow BKC, Weiss GJ, Xu A, Sommer MOA#, Panagiotou G 'Predictable modulation of cancer treatment outcomes by the gut microbiota' (2020) Microbiome - DOI:10.1186/s40168-020-00811-2 - Download link
  • Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA, 'Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla' (2019) Cell Host Microbe - DOI:10.1016/j.chom.2019.09.005 - Download link
  • Rugbjerg P, Sommer MOA, 'Overcoming genetic hetorogeneity in industrial fermentations' (2019) Nature Biotechnology - DOI:10.1038/s41587-019-0171-6 - Download link
  • Prodan A, Sommer MOA, Nieuwdrop M 'Rapid diagnosis of lung infections' (2019) Nature Biotechnology - DOI:10.1038/s41587-019-0174-3 - Download link
  • Li J, Rettedal EA, Buerger J, van der Helm E, Ellabaan M, Panagiotou G, Sommer MOA 'Antibiotic Treatment Drives the Diversification of the Human Gut Resistome' (2019) Genomics Proteomics Bioinformatics - DOI:10.1016/j.gpb.2018.12.003 - Download link
  • Buerger J, Gronenberg LS, Genee HJ, Sommer MOA 'Wiring cell growth to product formation' (2019) Current Opion Biotechnology - DOI:10.1016/j.copbio.2019.02.014 - Download link
  • Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Soenderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcateli P 'NetSurfP -2.0: Improv ed prediction of protein structural features by integrated deep learning' (2019) Proteins - DOI:10.1002/prot.25674 - Download link
  • Uribe RV*, van der Helm E*, Misiakou M-A*, Lee S-A, Kol S,Sommer MOA 'Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla' (2019) Cell Host & Microbe - DOI:10.1016/j.chom.2019.01.003 - Download link
  • Rosenkilde CHE, Munck C, Porse A, Linkevicius M, Andersson DI, Sommer MOA 'Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase' (2019) Nature Communications - DOI:10.1038/s41467-019-08529-y - Download link
  • Lino FSdO, Basso TO,Sommer MOA 'A synthetic medium to simulate sugarcane molasses' (2018) Biotechnology for Biofuels - DOI:10.1186/s13068-018-1221-x - Download link
  • Kang K, Ni Y, Li J, Imamovic L, Sarkar C, Kobler MD, Heshiki Y, Zheng T, Kumari S, Wong JCY, Archna A, Wong CWM, Dingle C, Denizen S, Baker DM, Sommer MOA, Webster CJ, Panagiotou G. 'The environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome' (2018) Cell Reports - DOI:10.1016/j.celrep.2018.06.109 - Download link
  • van der Helm, E., Genee, H.J., Sommer MOA 'The evolving interface between synthetic bilogy and functional metagenomics' (2018) Nature Chemical Biology - DOI:10.1038/s41589-018-0100-x - Download link
  • Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G 'Shared strategies for β-lactam catabolism in the soil microbiome' (2018) Nature Chemical Biology - DOI:10.1038/s41589-018-0052-1 - Download link
  • Ahmed MN, Porse A, Sommer MOA, Høiby N, Ciofu O. 'Evolution of Antibiotic Resistance in Biofilm and Planktonic Pseudomonas aeruginosa Populations Exposed to Subinhibitory Levels of Ciprofloxacin' (2018) American Society for Microbiology - DOI:10.1128/AAC.00320-18 - Download link
  • Jahn LJ, Porse A, Munck C, Simon D, Volkova S, Sommer MOA. 'Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages' (2018) Nature Scientific reports - DOI:10.1038/141598-018-25201-5 - Download link
  • Rugbjerg P, Sarup-Lytsen K, Nagy M, Sommer MOA 'Synthetic addiction extends the productive life time of engineered Eschedrichia coli populations' (2018) PNAS - DOI:10.1073/pnas.1718622115 - Download link
  • Bali AP, Genee HJ, Sommer MOA. 'Directed Evolution of Membrane Transport Using Synthetic Selections' (2018) ACS Synthetic Bioloyg - DOI:10.1021/acssynbio.7b00407 - Download link
  • Rugbjerg, P., Myling-Petersen, N., Porse, A., Sarup-Lytzen, K., Sommer MOA 'Diverse genetic error modes constrain large-scale bio-based production' (2018) Nature Communications - DOI:10.1038/s41467-018-03232-w - Download link
  • Porse, A., Schou, T.S., Munck, C., Ellabaan, M.M.H., Sommer MOA 'Biochemical mechanisms determine the functional compatibility of heterologous genes' (2018) Nature Communications - DOI:10.1038/s41467-018-02944-3 - Download link
  • Imamovic, L., Misiakou, M-A., van der Helm, E., Panagiotou, G., Muniesa, M., Sommer MOA 'Complete Genome Sequence of Escherichia coli Strain WG5' (2018) Genome Announcements - DOI:10.1128/genomeA.01403-17 - Download link
  • Imamovic, L., Ellabaan, M.M.H., Dantaas Machado, A.M., Citterio, L., Wulff, T., Molin, S., Johansen, H.K., Sommer MOA 'Drug-driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections' (2018) Cell - DOI:10.1016/j.cell.2017.12.012 - Download link
  • Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sønderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcitili P 'NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning' (2018) bioRxiv - DOI:10.1101/311209 - Download link
  • Klausen MS, Sommer MOA 'Parts Characterization for Tunable Protein Expression' (2017) Methods in Molecular Biology - DOI:10.1007/978-1-14939-7295-1_1 - Download link
  • Lauritsen I, Porse A, Sommer MOA, Noerholm MHH# 'A versatile one-step CRISPR-Cas9 based approach to pladmid-curing' (2017) Microbial Cell Factories - DOI:10.1186/s12934-017-0748-z - Download link
  • Sommer MOA, Munck C, Toft-Kehler RV, Andersson DI 'Prediction of antibiotic resistance: time for a new preclinical paradigm?' (2017) Nature Reviews Microbiology - DOI:10.1038/nrmicro.2017.75 - Download link
  • Gumpert, H, Kubicek-Sutherland, J.Z, Porse, A., Karami, N., Munck, C., Linkevicius, M., Adlerberth, I., Wold, A.E., Andersson, D.I., Sommer, MOA 'Transfer and persistance of a multi-drug resistance plasnud ub situ of the infant gut microbiota in the abscence of antibiotic treatment' (2017) Frontiers in Microbiology - DOI:10.3389/fmicb.2017.01852 - Download link
  • Koplev S, Longden J, Ferkinghoff-Borg J, Bjerregaard MB, Cox TR, Erler JT, Pedersen JP, Voellmy F, Sommer MOA, Linding R 'Dynamic Rearrangement of Cell States Detected by Systematic Screening og Sequential Anticancer Treatments' (2017) Cell Reports - DOI:10.1016/j.celrep.2017.08.095 - Download link
  • Crofts TS, Wang B, Spicak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G 'Draft Genome Sequences of Three Beta-Lactam-Catabolizing soil Proteobacteria' (2017) Genome Announcements - DOI:10.1128/genomeA.00653-17 - Download link
  • Cardinale S, Tueros FGF, Sommer MOA 'Genetic-Metabolic Coupling for Targeted Metabolic Engineering' (2017) Cell reports - DOI:10.1016/j.celrep.2017.07.015 - Download link
  • Lehning CE, Siedler S, Ellabaan MMH and Sommer MOA# 'Assecing glycolytic flux alterations resulting from genetic perturbations in E.coli using a biosensor' (2017) Metabolic engineering - DOI:10.1016/j.ymben.2017.07.002 - Download link
  • Siedler S, Khatri NK, Zsohár A, Kjærbølling I, Vogt M, Hammar P, Nielsen CF, Marienhagen J, Sommer MOA, Joensson HN 'Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production' (2017) ACS Synthetic Biology - DOI:10.1021/acssynbio.7b00009 - Download link
  • Jiang X, Ellabaan MMH, Charusanti P, Munck C, Kai B, Yaojun T, Tilmann W, Sommer MOA and Sang Yup L# 'Dissemination of antibiotic resistance genes from antibiotic producers to pathogens' (2017) Nature Communications - DOI:10.1038/ncomms15784 - Download link
  • Hickman RA, Munck C and Sommer MOA# 'Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs' (2017) Frontiers in Microbiology - DOI:10.3389/fmicb.2017.00893 - Download link
  • Jahn LH Munck C, Ellabaan MMH and Sommer MOA# 'Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Geonotypes' (2017) Frontiers in Microbiology - DOI:10.3389/fmicb.2017.00816 - Download link
  • Porse A, Gumpert H, Kubicek-Sutherland, JZ, Krami N, Adlerberth I, Wold AE, Andersson DI and Sommer MOA# 'Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss and Persistance of Genetic Elements In situ of the Infant Gut' (2017) Frontiers in Cellular and Infection Microbiology - DOI:10.3389/fcimb.2017.00126 - Download link
  • Sommer MOA 'PROMYS - Pogramming synthetic networks for bio-based production of value chemical - FP7 project' (2017) Impact - DOI:10.21820/23987073.2017.3.45 - Download link
  • van der Helm e, Imamovic L, Ellabaan MMH, van Schaik W, Koza A and Sommer MOA# 'Rapid resistome mapping using nanopore sequencing' (2017) Nucleic Acids Research, DOI:10.1093/nar/gkw1328 - Download link
  • Munck, C., Ellabaan, M.M.H., Klausen, M.S., Sommer MOA 'The resistome of important human pathogens' (2017) bioRxiv - DOI:10.1101/140194 - Download link
  • Genee HJ, Bali AP, Petersen SD, Sielder S, Bonde MT, Gronenberg LS, Kristensen M, Harrison SJ, Sommer MOA# 'Functional mining of transporters using synthetic selections' (2016) Nature Chemical Biology - DOI: 10.1038/nchembio.2189 - Download link
  • Moeller TSB, Overgaard M, Nielsen SS, Bortolaia V, Sommer MOA, Guardabassi L, Olsen JE 'Relation between tetR and tetA expression in tetracycline resistant Escherichia coli' (2016) BMC Microbiology - DOI: 10.1186/s12866-016-0649-z - Download link
  • Versluis D, de Evgrafov MCR, Sommer MOA, Sipkema D, Smidt H and van Passe MWS 'Sponge Microbiota Are a Reservoir of Funtional Antibiotic Resistance Genes' (2016) Frontiers in Microbiology, DOI:10.3389/fmicb.2016.01848 - Download link
  • Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AMD, Rodriguez de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O, Metagenomics of the Human Intestinal Tract (MetaHIT), Consortium, Sommer MOA, S. Ehrlich D, Sicheritz-Pontén T, Brunak S* and Nielsen HB* 'Transcriptional interactions suggest niche segregation among microorganisms in the human gut' (2016) Nature Microbiology - article 16152 - DOI:10.1038/nmicrobiol.2016.152 - Download link
  • Elison M, Vigsnaes LK, Krogsgaard LR, Rasmussen J, Sørensen N, McConnell B, Hennet T, Sommer MOA and Bytzer P* 'Oral supplementation of healthy adults with 2'-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota' (2016) British Journal of Nutrition - 116, 1356-1368 - DOI:10.1017/S0007114516003354 - Download link
  • Porse A, Schoenning K, Munck C, Sommer MOA# 'Survival and evolution of a large multidrug reistance plasmid in new clinical bacterial hosts' (2016) Molecular Biology and Evolution - DOI:10.1093/molbev/msw163 - Download link
  • Moeller TSB, Rau MH, Bonde CS, Sommer MOA, Guardabassi L, Olsen JE# 'Adaptive responses to cefotaxime treatment in ESBL-producing Escherichia coli and the possible use of significantly regulated pathways as novel secondary targets' (2016) Journal of Antimicrobial Chemotherapy - 71, 9, p. 2449-2459 11 p - DOI:10.1093/jac/dkw198 - Download link
  • Rugbjerg P, Genee HJ, Jensen K, Sarup-Lytzen K, Sommer MOA# 'Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals' (2016) ACS SyntheticBiology - DOI:10.1021/acssynbio.5b00213 - Download link
  • Sommer MOA, Suess B '(Meta-)genome mining for new ribo-regulators' (2016) Science - 352 P: 144-145 - DOI: 10.1126/science.aaf6189 - Download link
  • Sommer MOA 'Voices of Biotech' (2016) Nature Biotechnology - V. 34, No 3, P: 273 - DOI: 10.1038/nbt.3502 - Download link
  • Bonde MT, Pedersen M, Klausen MS, Jensen SI,Wulff T, Harrison S, Nielsen AT, Herrgaard MJ, Sommer MOA 'Predictable tuning of protein expression in bacteria' (2016) Nature Methods - DOI: 10.1038/NMETH.3727 - Download link
  • Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehar J#, Sommer MOA# 'Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis' (2016) PLoS ONE - DOI: 10.1371/journal.pone.0147651 - Download link
  • Ronda C, Pedersen LE, Sommer MOA, Toftgaard Nielsen A# 'CRMAGE: CRISPR Optimized MAGE Recombineering' (2016) Scientific Reports - DOI: 10.1038/srep19452 - Download link
  • Klausen MS, Sommer MOA 'Principles of Systems Biology, No 2' (2016) Cell Systems - P. 60 - Download link
  • Sommer LM, Imamovic L, Pressler T,Sommer MOA, Molin S, Johansen HK 'Collateral sensitivity cycling of antibiotics for cystic fibrosis airway infections' (2017) Journal of Cystic Fibrosis - DOI:10.1016/S1569-1993(16)30365-4 - Download link
  • Rugbjerg P, Knuf C, Förster J,Sommer MOA", 'Recombination-stable multimeric green flourescent protein for characterization of weak promoter outputs in Saccharomyces cerevisiae' (2015) FEMS yeast research - fov085 - Download link
  • van Der Helm E, Geertz-Hansen HM, Genee HJ, Malla S, Sommer MOA, 'deFUME: Dynamic exploration of functional metagenomic sequencing data' (2015) Biomed Central - 10.1186/s13104-015-1281-y - Download link
  • Kjeldsen TSB, Sommer MOA, Olsen JE # 'Extended spectrum β-lactamase-producing Escherichia coli forms filaments as an initial response to cefotaxime treatment' (2015) Bio Med Central - DOI: 10.1186/s12866-015-0399-3 - Download link
  • Lennen R, Nilsson W, Pedersen M, Bonde MT, Luo H, Herrgard M, Sommer MOA# 'Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects' (2015) Nucleic Acids Research - DOI: 10.1093/nar/gkv1090 - Download link
  • Sommer MOA, 'Advancing gut microbiome research using cultivation' (2015) Current opinion in Microbiology - V. 27 pp 127-132 - Download link
  • Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH,Sommer MOA#, 'Limited dissemination of the wastewater treatment plant core resistome' (2015) Nature Communications - Vol. 6, p. 9452 - Download link
  • Rugbjerg P, Myling-Petersen N,Sommer MOA", 'Flexible metabolic pathway construction using modular and divisible selection gene regulators' (2015) Metabolic Engieering - 10.1016/j.ymben.2015.08.004 - Download link
  • Rodriguez de Evgrafov M, Gumpert H, Munck C, Thomsen TT, Sommer MOA #, 'Collateral ressistance and sensitivity modulate evolution of high-level resistance to drug combinations treatment in Staphylococcus aureus ' (2015) Molecular Biology and Evolution - - Download link
  • Munck C, Gumpert HK, Wallin Al, Wang HH, Sommer MOA #, 'Prediction of resistance development against drug combications by collateral responses to component drugs' (2014) Science Translational Medicine - - Download link
  • Kjeldsen TSB, Overgaard M, Nielsen SS, Bartolaia V, Jelsbak L, Sommer MOA, Guardabassi L, Olsen JE # 'CTX-M-1 β-lactamase expression in Escherichia coli is dependent on cefotaxime concentration, growth phase and gene location' (2015) Journal of Antimicrobial Chemotherapy - DOI: 10.1093/jac/dku332 - Download link
  • Rettedal EA, Gumpert H, Sommer MOA 'Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria' (2014) Nature Communication - - Download link
  • Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgaard, MJ, Palsson BO, Sommer MOA, Feist AM# 'Evolution of Escherichia coli to 42 degrees C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations' (2014) Molecular Biology and Evolution - - Download link
  • Bonde MT, Makransky G, Wandell J, Larsen MV, Morsing M, Jarmer H, Sommer MOA 'Improving biotech education through gamified laboratory simulations' (2014) Nature Biotechnology - Vol. 32, issue 7 P 694-697 - Download link
  • Machado AMD, Sommer MOA# 'Human Intestinal Cells Modulate Conjugational Transfer of Multidrug Resistance Plasmids between Clinical Escherichia coli Isolates' (2014) Plos ONE - Vol. 9, issue 6 e1007339 - Download link
  • Bonde MT, Kosuri S, Genee HJ, Sarup-Lytzen K, Church GM, Sommer MO, Wang HH 'Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides' (2014) ACS Synth Biol. - 2014 May 23 - Download link
  • Genee HJ, Bonde MT, Bagger FO, Jespersen JB Sommer MO, Wernersson R, Olsen LR 'Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly' (2014) ACS Synth Biol. - 2014 May 9 - Download link
  • Bonde MT, Klausen MS, Anderson MV, Wallin Al, Wang HH, Sommer MO 'MODEST: a web-basd design tool for ligonucleotide-mediated genome engineering and recombineering' (2014) Nucleic Acids Res. - 2014 May 16 - Download link
  • Sommer MO 'Microbiology: Barriers to the spread of resistance' (2014) Nature - Vol 509 issue 7502 p.. 567-8 - Download link
  • Malla M, Sommer MOA# 'A sustainable route to produce the scytonemin precursor using Escherichia coli' (2014) Green Chem. - Vol. 16 p 3255-3265 - Download link
  • Dantas G, Sommer MOA 'How to Fight Back Against Antibiotic Resistance' (2014) American Scientist - Vol. 102, P 42-51 - Download link
  • Marvig RL, Jochumsen N, Johansen NK, Høiby N, Molin S, Sommer MO 'Draft Genome Sequences of Pseudomonas aeruginosa B3 Strains isolated from a Cystic Fibrosis Patient Undergoing Antibiotic Chemotherapy' (2013) Genome Announc. - Vol. 1, Issue 5, p. e00804-13 - Download link
  • Imamovic L & Sommer MOA# 'Use of Collateral Sensitivity Networks to Design Drug Cycling Protocols that Avoid Resistance Development' (2013) Science Translational Medicine - Vol. 5, Issue 204, p. 204ra132 - Download link
  • Dantas G, Sommer MOA, Degnan PH, Goodman AL 'Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut' (2013) Annual Review of Microbiology - Vol. 67: 459-475 - Download link
  • Dantas G, Sommer MO 'Context matters - The complex interplay between resistome genotypes and resistance phenotypes' (2012) Curr Opin Microbiol. - Vol. 5, Issue 5, p. 577-82 - Download link
  • Forsberg KJ*, Reyes A*, Wang B, Selleck EM, Sommer MOA#, Dantas G# 'The shared antibiotic resistome of soil bacteria and human pathogens' (2012) Science - 337:1107-1111. - Download link
  • Dantas G#, Sommer MOA#, 'Ecological and clinical consequences of antibiotic subsistence by environmental microbes' (2012) in Antimicrobial Resistance in the Environment Eds. P. Keen and M Monforts. Wiley-VCH - Download link
  • Sommer MOA#, Dantas G#, 'Antibiotics and the resistant microbiome' (2011) Current Opinion in Microbiology - doi:10.1016/j.mib.2011.07.005 - Download link
  • Moore AM*, Munck C*, Sommer MO#, Dantas G.#, 'Functional metagenomic investigations of the human intestinal microbiota' (2011) Frontiers Microbiology 2:118 - Download link
  • Stojanoff V, Jakoncic J, Oren DA, Nagarajan V, Poulsen JCN, Adams-Cioaba MA, Bergfors T, Sommer MOA#, 'From screen to structure with a harvestable microfluidic device' (2011) Acta Cryst. F67:971-975 - Download link
  • Yang L*, Jelsbak L*, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MOA, Molin S, 'Evolutionary dynamics of bacteria in a human host environment' (2011) Proceedings of the National Academy of Science USA 108:7481-7486. - Download link
  • Sommer Mo, Church GM, Dantas G, 'The human microbiome harbours a diverse reservoir of antibiotic resistance genes' (2010) Virulence, Vol. 1, Issue 4, p. 299-303 - Download link
  • Sommer MOA#, Church GM, Dantas G.#, 'A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion' (2010). Nature/EMBO Molecular Systems Biology 6:360 - Download link
  • Sommer MOA*#, Dantas G*#, Church GM. 'Metagenomic functional characterization of the antibiotic resistance reservoir of human microbiomes' (2009). Science, 325:1128-31 - Download link
  • Dantas G*, Sommer MOA*, Oluwasegun R, Church GM#. 'Bacteria Subsisting on Antibiotics' (2008) Science 320:100-103 * Denotes equal contribution - Download link
  • Sommer MOA, Larsen S#. 'Crystallizing proteins on the basis of their precipitation diagrams determined using a microfluidic formulator' (2005) Journal of Synchrotron Radiation 12:779-785 - Download link
  • Hansen, C.L., Sommer, M.O.A., Self, K., Berger, J. and Quake, S.R.: 'Micro-crystallization' in Protein Crystallization in Drug Discovery Edited by Babine and Abdel-Meguid, (2004) Wiley-VCH
  • Hansen, C.L., Sommer, M.O.A. and Quake, S.R.: 'Systematic Investigation of Protein Phase Behavior with a Microfluidic Formulator'. (2004) Proceedings of the National Academy of Science USA 101:14431-14436. - Download link

Tools:

Bioinformatic tools

The laboratory has developed a range of bioinformatic tools that are freely available online:

  • MODEST for designing oligos for multiplex genome engineering.
  • AMUSER for automated design of primers for USER cloning strategies and mutagenesis
  • EMOPEC for tuning protein expression levels in E.coli.
  • deFUME for exploration and annotation of functional metagenomic datasets.
  • poreFUME for analysis of functional metagenomic nanopore dat.
  • NetSURF 2.0 server predicts the surface accessibility, secondary structure, disorder, and phi/psi dihedral angles of amino acids in an amino acid sequence.

Reagents

The laboratory is happy to share any published strains or plasmids.

To simplify this process some of our published reagents have been deposited to AddGene for easy access.

For other reagents not available from AddGene, please contact Morten Sommer.

Joining the Lab

Post docs and PhD students

Talented and motivated applicants interested in joining our lab as a post doctoral fellow or a PhD-student should send their application, including CV and references to:

Morten Sommer
msom@bio.dtu.dk

We have no positions posted at the moment.
While funding is available for some positions, we encourage candidates to apply for their own funding (salary).

Undergraduate and Master student projects

The Sommer lab has a wide range of projects available for master students (speciale) and undergraduates. If you are interested in our research and would like to do a project in the lab please contact Morten Sommer for further information. Please include CV and your grades from your studies so far.

Get in touch

Novo Nordisk Foundation Center for Biosustainability – Bacterial Synthetic Biology Section

Novo Nordisk Foundation Center for Biosustainability
Kemitorvet, Building 220
DK-2800 Kongens Lyngby
Denmark

Lab: E306, E310 and E314
Offices: E316F, E319F, E321F, E323F and E324F

Morten Sommer contact info

Email: msom@bio.dtu.dk
Phone: +45 4525 8000
Mobile: +45 2151 8340
Office: E318F

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