Publications

Full list of publications from the group.

Galgano, S., Kettle, H., Free, A. and Houdijk, J.G.M. Estimating the contribution of the porcine fecal core microbiota to metabolite production via mathematical modelling and in vitro fermentation. mSystems, in press.
Sweeny, A.R., Lemon, H., Ibrahim, A., Watt, K.A., Wilson, K., Childs, D.Z., Nussey, D.H., Free, A. and McNally, L. (2023) A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance. mSystems e0004023, doi: 10.1128/msystems.00040-23.
Watkins, C.A., Gaines, T., Strathdee, F., Baily, J.L., Watson, E., Hall, A.J., Free, A. and Dagleish, M.P. (2022) A comparative study of the fecal microbiota of gray seal pups and yearlings - a marine mammal sentinel species. MicrobiologyOpen 11: e1281.
Watkins, C.A., Bartley, D.J., Günduz Ergün, B., Yıldızhan, B, Ross-Watt, T., Morrison, A.A., Rosales Sanmartín, M.J., Strathdee, F., Andrews, L. and Free, A. (2021) Interactions between Teladorsagia circumcincta infections and microbial composition of sheep with or without successful monepantel treatment - a preliminary study. Ruminants 1: 31-45.
Angelova, A.G., Berx, B., Bresnan, E., Joye, S.B., Free, A. and Gutierrez, T. (2021) Inter- and intra-annual bacterioplankton community patterns in a deepwater sub-Arctic region: persistent high background abundance of putative oil degraders. mBio 12: e03701-03720.
Assil, Z., Esegbue, O., Mašek, O., Gutierrez, T. and Free, A. (2021) Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles. Sci. Tot. Env. 762: 143084.
Free, A., McDonald, M.A. and Pagaling, E. (2018) Diversity-function relationships in natural, applied and engineered microbial ecosystems. Adv Appl Microbiol 105: 131-189.
Bird, C., Darling, K.F., Russell, A.D., Fehrenbacher, J.S., Davis, C.V., Free, A. and Ngwenya, B.T. (2018) 16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer). PLoS ONE 13: e0191653.
Pagaling, E., Vassileva, K., Mills, C.G., Bush, T., Blythe, R.A., Schwarz-Linek, J., Strathdee, F., Allen, R.J. and Free, A. (2017) Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states. Env Microbiol 19: 3374–3386.
Bird, C., Darling, K.F., Russell, A.D., Davis, C.V., Fehrenbacher, J., Free, A., Wyman, M. and Ngwenya, B.T. (2017) Cyanobacterial  endobionts within a major marine, planktonic, calcifier (Globigerina bulloides, Foraminifera) revealed by 16S rRNA metabarcoding. Biogeosciences 14: 901-920.
Robinson, G., Caldwell, G.S., Wade, M.J., Free, A., Jones, C.L.W. and Stead, S.M. (2016) Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes. Scientific Rep 6: 38850. doi: 10.1038/srep38850.
Widder, S., Allen, R., Pfeiffer, T., Curtis, T., Wiuf, C., Sloan, W., Cordero, O., Brown, S., Momeni, B., Shou, W., Kettle, H., Flint, H., Haas, A., Kreft, J., Laroche, B., Rainey, P., Milferstedt, K., Grosskopf, T., Jin, Q., Freilich, S., Schuster, S., Huisman, J., Free, A., Quince, C., Labarthe, S., Wang, H., Smeths, B., Klapper, I., Picioreanu, C., Isaac Newton Institute Fellows and Soyer, O. (2016) Challenges in microbial ecology: building predictive understanding of community behaviour. ISME J 10: 2557-2568.
Bush, T., Butler, I.B., Free, A. and Allen, R.J. (2015) Redox regime shifts in microbially mediated biogeochemical cycles. Biogeosciences 12: 3713-3724.
Glendinning, L., Nausch, N., Free, A., Taylor, D.W. and Mutapi, F. (2014) The microbiota and helminths: Sharing the same niche in the human host. Parasitology 141: 1255-1271.
Glendinning, L. and Free, A. (2014) Supra-organismal interactions in the human intestine. Front Cell Infect Microbiol 4: 47. doi: 10.3389/fcimb.2014.00047.
Pagaling, E., Strathdee, F., Spears, B.M., Cates, M.E., Allen, R.J. and Free, A. (2014) Community history affects the predictability of microbial ecosystem development. ISME J 8: 19-30.
Strathdee, F. and Free, A. (2013). Denaturing gradient gel electrophoresis. In DNA Electrophoresis: Methods and Protocols. Ed: S. Makovets. Methods in Molecular Biology series, Humana Press, USA, pp. 145-157.
Pereira-Medrano, A., Knighton, M., Fowler, G.J.S., Ler, Z.Y., Pham, T.K., Ow, S.W., Free, A., Ward, F.B. and Wright, P.C. (2013).
Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode. J Proteomics 78: 197-210.
Khatri, B.S., Free, A. and Allen, R.J. (2012). Oscillating microbial dynamics driven by small populations, limited nutrient supply and high death rates. J Theor Biol 314: 120-129.
Toh, H., Sharma, V.K., Oshima, K., Kondo, S., Hattori, M., Ward, F.B., Free, A. and Taylor, T.D. (2011) Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp.-L, isolated from a microbial fuel cell. J Bacteriol 193: 6411-6412.
Tota-Maharaj, K., Scholz, M., Ahmed, T., French, C. and Pagaling, E. (2010) The synergy of permeable pavements and geothermal heat pumps for stormwater treatment and reuse. Env Technol 31: 1517-1531.
Fedorovich, V., Knighton, M.C., Pagaling, E., Ward, F.B., Free, A. and Goryanin, I. (2009) A novel electrochemically active bacterium phylogenetically related to Arcobacter butzleri isolated from a microbial fuel cell. Appl Env Microbiol 75: 7326-7334.
Stoebel, D.M., Free, A. and Dorman, C.J. (2008) Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154: 2533-2545.
Free, A. and Barton, N.H. (2007) Do evolution and ecology need the Gaia hypothesis? Trends Ecol Evol 22: 611-619.

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