Microbial community modelling



Javier Tamames de la Huerta

Group Leader



Carlos Pedrós Alió

Group Leader







Research summary

We are interested in providing a description of the rules governing the assembly of natural bacterial communities. This will allow us to determine the best combination of species suited to fulfil a particular goal, mainly in the biotechnological scenario.

We also aim to understand the ecology of aquatic microorganisms. We are interested in learning how they survive in unusual environments to throw light on the functioning of more conventional ones. Another interest is in understanding the diversity of microorganisms, in particular the mechanisms maintainig a large number of rare bacteria in aquatic ecosystems.



Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M (2013). Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME J; 7:122-136

Pascual-García A, Tamames J, Bastolla U (2014) Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions? BMC Microbiol; 14:284

Palovaara, Joakim, Neelam Akram, Federico Baltar, Carina Bunse, Jeremy Forsberg, Carlos Pedrós-Alió, José M. González and Jarone Pinhassi (2014) Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria. Proceedings of the National Academy of Sciences USA, 111 (35) E3650-E3658, doi:10.1073/pnas.1402617111 doi: 10.1073/pnas.1402617111

Pedrós-Alió, Carlos, Marianne Potvin & Connie Lovejoy (2015) Diversity of planktonic microorganisms in the Arctic Ocean. A review. Progress in Oceanography 139: 233-243. doi: 10.1016/j.pocean.2015.07.009

Tamames, Javier, Pablo D. Sánchez, Pablo I. Nikel, Carlos Pedrós-Alió (2016). Quantifying the relative importance of phylogeny and environmental preferences as drivers of gene content in prokaryotic microorganisms. Frontiers in Microbiology doi: 10.3389/fmicb.2016.00433



In these two years, our group has established a solid methodology for the analysis of genomes, metagenomes and metatranscriptomes that has been applied successfully in several instances. We are particularly interested in ecological scenarios such as the detoxification of polluted environments (Guazzaroni et al 2013), function of hypersaline environments (López-López et al 2013), and responses to temperature gradients in thermophilic microbial mats (in collaboration with the Pontificia Universidad Católica de Chile, 2014). We also collaborate with several groups on the clinical importance of genomes and microbiomes, such as the groups of Dr F. Baquero (Hospital Ramón y Cajal, Madrid) in cystic fibrosis, and that of Dr I. Tomás (Universidad de Santiago de Compostela, Spain) in the role of oral microbiomes in periodontal health.

We also study the rules that govern assembly of natural bacterial communities, by defining the relationships between environmental factors and species presence or co-ocurrence. This led us to define patterns of functional redundancy in metagenomes, that is, in which cases particular species can be replaced by counterparts with no influence on the overall performance of the microbiome. We also developed predictive systems to determine environmental preferences of individual species based on their genomic compositions. We are now working to extend these tools to predict possible compatibilities and co-ocurrences between species in given settings. In the future, we expect to be able to accurately predict the effect of specific perturbations in the performance of the microbiome, and therefore to propose optimal combinations of species for living in defined conditions or fulfilling given roles.





Javier Tamames de la Huerta Principal investigator
Carlos Pedrós-Alió Principal investigator
Fernando Puente Postdoctoral scientist
Marta Cobo Predoctoral scientist

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