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 industrial biotechnology and human health. We develop and apply novel technologies within the fields of metagenomics, synthetic biology, lab evolution, microbiomics and multiplexed phenotyping. Our specific areas of interest include: :

Antibiotic resistance in human pathogens and microbial communities
Collateral sensitivity and its relevance to drug treatment strategies
Population heterogeneity in industrial bioprocesses
Microbial evolution and evolutionary constraints
Multiplex genotype to phenotype associations related to microbial production and tolerance
Microbiome therapeutics

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.

Research

Our work is broadly aimed towards understanding how biological systems establish, organize and evolve. 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.

Antibiotic resistance

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 are using 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 study 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.

Synthetic biology for sustainable generation of value chemicals

Increasing concerns related to climate change caused by our reliance on fossil fuels for many processes in our society prompt the need to look for alternatives. Biological systems can be engineered to perform conversions of renewable input substrates to value added products using much less energy than conventional methods. We use a variety of metagenomic and culture based techniques for harnessing biological diversity useful for generation of biofuels and other value chemicals. We build synthetic selection networks that sense and respond to specific metabolites inside the cell. We deploy these tools for pathway discovery, strain optimization for specific metabolic engineering targets. We use synthetic selection systems for multiplexed interrogation of biological phenotypes enhancing our understanding of cellular metabolism and regulation.

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.

People

Here you will find current and past members.

Permanent Staff

  • Morten O. A. SommerMorten O. A. Sommer, Professor
  • Mari Rodriguez de EvgrafovMari Rodriguez de Evgrafov, PhD
  • Gitte MejlhartGitte Mejlhart,
    PA

Post docs

  • Christian MunckChristian Munck, PhD
  • Daniel SimonDaniel Simon, PhD
  • Eric van der HelmEric van der Helm, PhD
  • Eugene FletcherEugene Fletcher, PhD
  • Lejla Imamovic, PhDLejla Imamovic, PhD
  • Lumeng Ye, PhDLumeng Ye, PhD
  • Mareike Bongers, PhDMareike Bongers, PhD
  • Mostafa Ellabaan, PhDMostafa Ellabaan, PhD
  • Peter Rugbjerg, PhDPeter Rugbjerg, PhD
  • Solvej Sieder, PhDSolvej Sieder, PhD
  • Stefano Cardinale, PhDStefano Cardinale, PhD

PhD students

  • Andreas Porse ZsoharAndreas Porse
  • Carola E. H. RosenkildeCarola E. H. Rosenkilde
  • Felipe LinoFelipe Lino
  • Kira Sarup-LytzenKira Sarup-Lytzen
  • Leonie JahnLeonie Jahn
  • Maria-Anna MisiakouMaria-Anna Misiakou
  • Michael Schantz KlausenMichael Schantz Klausen
  • Rachel HickmannRachel Hickmann
  • Ruben Vazquez UribeRuben Vazquez Uribe

Research ass.

  • Gonzalo TuerosGonzalo Tueros

Students

  • Chi U Seak (Leo)Chi U Seak (Leo)
  • Christian NielsenChristian Nielsen
  • Evan ChaberskiEvan Chaberski

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

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 ERC Starting Grant (2015-2019) - Utilizing evolutionary interactions to limit multidrug resistance

DFF Sapere Aude (2014-2018) - Novel treatment strategies for countering durg resistance

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

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

EU H2020 ITN MetaRNA (2015-2018) - RNA-based technologies for single-cell metabolite analysis

SIPROS (2016-2019) - Virtual Laboratory Simulations for Increased Productivity and Occupational Standards in the Biotechnology Industry

Past funders

Lundbeck Foundation (2011-2014) - <VUnderstanding 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

  • 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 Nutrition116, 1356-1368DOI:10.1017/S0007114516003354 - 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 Microbiologyarticle 16152DOI:10.1038/nmicrobiol.2016.152 - 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, 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 Chemotherapy71, 9, p. 2449-2459 11 pDOI:10.1093/jac/dkw198 - 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
  • 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
  • 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
  • Sommer MOA, Suess B '(Meta-)genome mining for new ribo-regulators' (2016) Science - 352 P: 144-145 DOI: 10.1126/science.aaf6189 - Download link
  • Klausen MS, Sommer MOA 'Principles of Systems Biology, No 2' (2016) Cell Systems - P. 60 - 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
  • 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
  • Ronda C, Pedersen LE, Sommer MOA, Toftgaard Nielsen A# 'CRMAGE: CRISPR Optimized MAGE Recombineering' (2016) Scientific Reports - DOI: 10.1038/srep19452 - 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
  • 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
  • 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, 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
  • Sommer MOA, 'Advancing gut microbiome research using cultivation' (2015) Current opinion in Microbiology - V. 27 pp 127-132 - Download link
  • Rugbjerg P, Myling-Petersen N,Sommer MOA", 'Flexible metabolic pathway construction using modular and divisible selection gene regulators' (2015) Metabolic Engieering - - 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 - - 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
  • 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
  • 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
  • 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
  • Sommer MO 'Microbiology: Barriers to the spread of resistance' (2014) Nature - Vol 509 issue 7502 p.. 567-8 - 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
  • 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.

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 a PostDoc position posted at the moment. Please follow the link to see the postings

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