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Microbial ecosytems and interactions

Dynamic diatom-bacteria consortia in synthetic plankton communities 

Y. Deng, M. Mauri, M. Vallet, M. Staudinger, R. J. Allen and G. Pohnert

Appl. Env. Microbiol. (2022)


Resource spectrum engineering by specialist species can shift the specialist-generalist balance

C. G. Mills, R. J. Allen* and R. A. Blythe* 

Theoretical Ecology 1-15 (2019)


Bacterial growth: a statistical physicist's guide

R. J. Allen and B. Waclaw

Reports on Progress in Physics  82, 016601 (2019)


Oxic-anoxic regime shifts induced by biogeochemical feedbacks in microbial communities

T. Bush, M. Diao, R. J. Allen, R. Sinnige, G. Muyzer and J. Huisman 

Nature Communications 8, 789 (2017)


Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

E. Pagaling, K. Vassileva, C. G. Mills, T. Bush, R. A. Blythe, J. Schwarz-Linek, F. Strathdee, R. J. Allen and A. Free 

Environmental Microbiology 19: 3374–3386 (2017)


Resource spectrum engineering by specialist species can strongly disfavour generalists

C. G. Mills, R. J. Allen and R. A. Blythe (submitted)


Challenges in microbial ecology: building predictive understanding of community function and dynamics

            S. Widder, R. J. Allen et al.

ISME Journal 10, 2557-2568 (2016)

              This review article results from a 4-month programme "Understanding Microbial Communities" at the Isaac Newton Institute, Cambridge University, which I co-organised in August-December 2014.


Redox regime shifts in microbially-mediated biogeochemical cycles

    T. Bush, T. B. Butler, A. Free and R. J. Allen 

Biogeosciences 12, 3717-3724 (2015)


Competition for space during bacterial colonisation of a surface

    D. P. Lloyd and R. J. Allen 

J. R. Soc. Interface 12, 20150608 (2015)


Selection history affects the predictability of microbial ecosystem development

        E. Pagaling, F. Strathdee, B. Spears, M. E. Cates, R. J. Allen* and A. Free* 

ISME J. 8, 19-30 (2013) (*=equal contribution)


Oscillating microbial dynamics driven by small populations, limited nutrient supply and high death rates

        B. S. Khatri, A. Free and R. J. Allen 

J. Theor. Biol. 314, 120-129 (2012)



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A warm welcome to our new group assistant Mr Moritz Wiegand!


Congratulations to Nia Verdon who has submitted her PhD thesis!


We are advertising an experimental postdoc position on biophysics of microbial aggregation in the context of the human gut microbiome. Please publicise it! Deadline is 22nd November.


Check out our student Patrick Sinclair's paper in Physical Review Letters presenting a model for stochastic initiation of bacterial biofilms - and a commentary on it in Nature Reviews Physics.


Congratulations to Patrick Sinclair who has successfully defended his PhD thesis!




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