MEG Lab

Department of Experimental Medical Science, Lund University - SciLifeLab - TCSMT, University of Turku

The Microbial Evolutionary Genetics (MEG) Lab develops predictive, quantitative understanding of how microbial populations and communities evolve, with a particular focus on antimicrobial resistance, community resilience, and infection dynamics. We investigate when resistance evolution and treatment outcomes are predictable, and when they depend critically on ecological interactions among coexisting microbes.

Our research integrates experimental evolution, synthetic and clinically inspired microbial communities, genetic engineering, genomics, and bioinformatics. By combining ecological realism with experimental control and data-driven modelling, we aim to generate evolution-aware principles that inform antimicrobial therapy and improve understanding of persistent and treatment-resistant infections.

The lab is led by Assistant Professor (DDLS Fellow) Johannes Cairns and operates between Lund University and the University of Turku, in close collaboration with interdisciplinary infection research and data-driven life science environments in Sweden and Finland.

news

Mar 01, 2026	Johannes was appointed Assistant Professor (DDLS Fellow) at the Faculty of Medicine, Lund University, and SciLifeLab. Here is his interview on the appointment at Lund.
Jan 10, 2026	Aava is joining the MEG Lab to implement high-resolution lineage tracking in synthetic community members as her MSc thesis project. Welcome!
Oct 09, 2025	Inga-Katariina received a doctoral research grant from the Jenny and Antti Wihuri Foundation. Congratulations!
Jan 01, 2025	Johannes was appointed Collegium Researcher at the Turku Collegium for Science, Medicine and Technology.
May 23, 2024	Inga-Katariina received a doctoral research grant from the Finnish Cultural Foundation. Congratulations!

selected publications

2025

Evolution induced state shifts in a long-term microbial community experiment

Mikko Kivikoski, Johannes Cairns, Shane L Hogle, and 4 more authors

bioRxiv, 2025

Abs DOI

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evolution shapes these systems through eco-evolutionary feedbacks is a central challenge in ecology and evolution. Experimental studies using simplified microbial assemblages have yielded important insights into the ecological principles governing community states. However, an important knowledge gap is how selection within member species drives changes of community state in multispecies systems. Here, we present a fouryear evolution experiment involving a 23-species synthetic bacterial community propagated in two environments: a control medium and the same medium supplemented with the antibiotic streptomycin. Through combined analyses of community composition and genome evolution, we quantified the temporal changes in species abundances and the evolutionary trajectories of individual community members. The extended duration of the experiment enabled the detection of adaptive mutations and community state shifts that occur only over long evolutionary timescales. We show that community dynamics are environment dependent and reproducible across replicates, and that evolution of streptomycin resistance in a previously streptomycin-sensitive species on its own can induce abrupt community state shifts. Our results provide a direct demonstration of eco-evolutionary feedbacks within a multi-species community, revealing how a single adaptive mutation can reorganize complex ecological networks.Competing Interest StatementThe authors have declared no competing interest.Research Council of Finland, https://ror.org/05k73zm37, #346126, #330886, #327741, #346128, #364234
Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities

Johannes Cairns, Shane Hogle, Elizaveta Alitupa, and 2 more authors

Nature Ecology & Evolution, 2025

DOI

2022

Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

Johannes Cairns, Florian Borse, Tommi Mononen, and 2 more authors

Evolution Letters, 2022

2020

Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation

Johannes Cairns, Roosa Jokela, Lutz Becks, and 2 more authors

Nature Ecology & Evolution, 2020

2018

Dual-stressor selection alters eco-evolutionary dynamics in experimental communities

Teppo Hiltunen, Johannes Cairns, Jens Frickel, and 6 more authors

Nature Ecology & Evolution, 2018

2017

Genomic evolution of bacterial populations under coselection by antibiotics and phage

Johannes Cairns, Jens Frickel, Matti Jalasvuori, and 2 more authors

Molecular Ecology, 2017