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Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer

Journal of the Royal Society Interface (2020) 17:20200053. Link

Biogas productivity of anaerobic digestion process is governed by a core bacterial microbiota

Yu Tao, Mustafa Evren Ersahin, Dara S.M. Ghasimi, Hale Ozgun, Haoyu Wang, Xuedong Zhang, Miao Guo, Yunfeng Yang, David C. Stuckey, Jules B. van Lier,

Chemical Engineering Journal. 380:122425 (2020) Link

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers
Maria Westerholm, Jan Dolfing, Anna Schnürer.
Environ. Sci. Technol. 53:5512-5520 (2019) Link

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and asulfate reducer
Chen J, Wade MJ, Dolfing J,Soyer OS.
J. R. Soc. Interface 16:20190129 (2019) Link

Biodiversity-function relationships in methanogenic communities
Sierocinski P, Bayer F, Yvon-Durocher G, Burdon M, Grosskopf T, Alston M, Swarbreck D, Hobbs PJ, Soyer OS, and Buckling A.
Molecular Ecology 27:4641-4651 (2018) Link

Impact of spatial organization on a novel auxotrophic interaction among soil microbes
Jiang X, Zerfass C, Feng S, Eichmann R, Asally M, Schafer P, Soyer OS.
ISME Journal 12:1443-1456 (2018) Link

Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination
Hesse E, O'Brien S, Tromas N, Bayer F, Lujan AM, van Veen EM, Hodgson DJ and Buckling A.
Ecology Letters 21:117-127 (2018) Link

Engineering microbial communities using thermodynamic principles and electrical interfaces
Zerfass C, Chen J and Soyer OS.
Current Opinion in Biotechnology 50:121-127 (2018) Link

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities
Sierocinski P, Milferstedt K, Bayer F, Grosskopf T, Alston M, Bastkowski S, Swarbreck D, Hobbs PJ, Soyer OS, Hamelin J and Buckling A.
Current Biology 27(21):3390-3395 (2017) Link

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water
Oko B, Tao Y and Stuckey DC.
Biotechnology for Biofuels 10:123 (2017)

MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions
Wade MJ, Oakley J, Harbisher S, Parker NG, Dolfing J.
PLoS ONE 12(3): e0173249 (2017) Link

Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes
du Lac M, Scarpelli AH, Bates DG, and Leonard JN
ACS Synthetic biology 6(7):1131-1139 (2017) Link

Generalised approach to modelling a three-tiered microbial food-web
Sari T. and Wade M.
Mathematical Biosciences 291:21-37 (2017)

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community
Gomez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, McElroy K and Buckling A.
Nature Communications 7:12453 (2016) Link

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Grosskopf T, Consuegra J, Gaffe J, Willison JC, Lenski RE, Soyer OS, and Schneider D.
BMC Evolutionary Biology 16:163 (2016) Link

A stable genetic polymorphism underpinning microbial syntrophy
Grosskopf T, Simone Z, Alston M, Folkes L, Swarbreck D, Soyer OS.
ISME Journal 10:2844-2853 (2016) Link

Microbial diversity arising from thermodynamic constraints
Grosskopf T. and Soyer OS.
ISME Journal 10:2725-2733 (2016) Link

Challenges in microbial ecology: building predictive understanding of community function and dynamics.
Widder S, Curtis TP, Grosskopf T, et. al and Soyer OS.
ISME Journal 10:2557-2568 (2016) Link

Perspectives in mathematical modelling for microbial ecology
M.J. Wade, J. Harmand, B. Benyahia, T. Bouchez, S. Chaillou, B. Cloez, J.-J. Godon, B. Moussa Boudjemaa, A. Rapaport, T. Sari, R. Arditi, C. Lobry.
Ecological Modelling 321, 64-74 (2016) Link

Emergent behaviour in a chlorophenol-mineralising three-tiered microbial `food web'
M. J. Wade, R. W. Pattinson, N. G. Parker and J. Dolfing.
Journal of Theoretical Biology 389:171-186 (2016) Link

Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii
K.J. Jones, K. Moore, C. Sambles, J. Love, D.J. Studholme, S.J. Aves.
Genome Announcements 4(1):e01527-15 (2016) Link

Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates
D.S.M. Ghasimi1, Y. Tao, M. de Kreuk1, M. H. Zandvoort and J. B. van Lier.
Biotechnol Biofuels 8:171 (2015) Link

The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments
Jan Dolfing and Igor Novak.
Biodegradation 26(1):15-27 (2015) Link

Some (bacilli) like it hot: genomics of Geobacillus species
David Studholme
Microbial Biotechnology 8(1):40-48 (2015) Link

Syntrophy in Microbial Fuel Cells
Jan Dolfing.
The ISME Journal 8(1):4-5 (2014) Link

Synthetic Microbial Communities
Tobias Grosskopf and Orkun Soyer.
Current Opinion in Microbiology 18:72-77 (2014) Link

The interplay between microevolution and community structure in microbial populations
Siobhan O'Brien, David J Hodgson and Angus Buckling
Current Opinion in Biotechnology 24:821-825 (2013) Link

Syntrophic Propionate Oxidation via Butyrate: a Novel Window of Opportunity under Methanogenic Conditions
Dolfing, J.
Applied and Environmental Microbiology 79(14):4515-4516 (2013) Link