In the last decade, round the world sampling programs have been launched and massive sequencing has been used to tackle the enormous diversity of marine microbes. The International Census of Marine Microbes (2005-2010) was the first to use high throughput sequencing to retrieve marine diversity. At about the same time, the Sorcerer II Global Ocean Sampling expedition (http://www.jcvi.org/cms/research/projects/gos/overview/) collected surface samples from several oceans. More recently TARA Oceans (https://www.embl.de/tara-oceans/start/) and Malaspina 2010 (http://www.expedicionmalaspina.es/Malaspina/Main.do#content:Home), have collected samples down to 1000 and 4000 meters respectively, mostly in the tropical and subtropical oceans. All of these efforts have resulted in a huge data set of sequences from the oceans that can now be queried for different ecological questions.

We use marine data to identify potentially interacting microbial taxa through co-occurrence networks. Link to projects.

Stations sampled during circumnavigation cruises Maslapina 2010 and Tara Oceans.

We use metagenomes to assemble genomes of environmentally relevant bacteria and to look at seasonal changes in the abundance of different taxa and different functions.

We also use sequence information to analyze microdiversity. We analyze the existence of different strains of chosen organisms adapted to different ecological situations. We use metagenomic information of genes and deconvolution to reconstruct the genetic variability within particular species. Link to projects.

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 7:433, pp 1-12. http://dx.doi.org/10.3389/fmicb.2016.00433

Yelton, Alexis P., Silvia G. Acinas, Shinichi Sunagawa, Peer Bork, Carlos Pedrós-Alió, Sallie Chisholm (2016). Global genetic capacity for mixotrophy in marine picocyanobacteria. The ISME Journal, 10: 2946-2957. doi:10.1038/ismej.2016.64

Pinhassi, Jarone, Edward F. DeLong, Oded Béjà, José M. González, Carlos Pedrós-Alió (2016). Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology and ecology. Microbiology and Molecular Biology Reviews 80:1-26. doi:10.1128/MMBR.00003-16

Ghiglione, J-F, P E. Galand, T Pommier, C Pedrós-Alió, E W Maas, K Bakker, S Bertilson, D L. Kirchman, C Lovejoy, P L. Yager, A E. Murray (2012). Pole to pole biogeography of surface and deep marine bacterial communities. Proceedings of the National Academy of Sciences USA 109 (43) 17633-17638; published ahead of print October 8, 2012, doi:10.1073/pnas.1208160109

Ugo Bastolla, Centro de Biología Molecular Severo Ochoa, CSIC, Madrid, Spain


Silvia G. Acinas and Josep M. Gasol. Institut de Ciències del Mar, CSIC, Barcelona, Spain


Extreme Environments

Extreme environments demand specific adaptions of the organisms living in them. Along evolution, only a small set of microbial taxa has been able to adapt to such conditions. Therefore, microbial communities are simplified in extreme environments. As an example, there may be 3,000 bacterial and archaeal taxa in a sample of marine water. A similar sample from our gut will contain 300 taxa and a sample from a hypersaline environment has only 10 to 30 taxa. This simplifies the potential interactions among microorganisms and facilitates our objective of analyzing microbial communities

Geyser and microbial mats at El Tatio (4200 masl, northern Chile)

Human body

The fundamental importance of our microbiota has not been realized until the last couple of decades. Microorganisms cover our body and live inside it. Their contribution to our health depends on a delicate balance with pathogens and the immune system. We are interested in the interactions between pairs of microorganisms in our body, since these interactions will be similar to those in other environments.

We study physical interactions among gut bacteria by encapsulating them in microspheres and looking at their capacity for growing together. We are also interest in the diversity and metabolic interactions of the normal microbiota in the mouth and the vagina.

  1. Identification of interacting species by encapsulating and growing gut bacteria.
  2. Building metabolic models of interacting body microbes.

In Madrid, Spain (gut):

Fernando Baquero and Teresa M. Coque, Hospital Ramon y Cajal



In Valencia, Spain:

Alex Mira, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO) (human milk).


María Carmen Belloch, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), Generalitat Valenciana (foods).


In Montpellier, France:

Samuel Alizon, Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC), CNRS, Centre IRD de Montpellier (vagina)


In Galicia, Spain:

Inmaculada Tomás, Universidad de Santiago de Compostela (mouth)


Art by Charis Tsevis (http://tsevis.com/; reproduced with permission)

Other environments

Our techniques can be applied to any environment. Thus, we collaborate with scientist interested in several other environments, such as wastewaters, bioleaching piles, or plastics.

  1. Evaluation of treatments on the composition of the microbial community.
  2. Antibiotic resistance genes in waste waters.

Rocha, C., Vaz, I., Henriques, I., Tamames, J., Lira, F., Martínez, JL., ;Manaia, C. Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant. Environment International 118:179-188. doi: 10.1016/j.envint.2018.05.040.

In Porto, Portugal:

Waste water microbes and antibiotic resistance

Célia M. Manaia, Universidade Católica Portuguesa


In Madrid, Spain:

José Luis Martínez, Centro Nacional de Biotecnología, CSIC (Waste water microbes and antibiotic resistance).


Víctor de Lorenzo, Centro Nacional de Biotecnología, CSIC (Plastics and microbes).

In Antofagasta, Chile:

Cecilia Demergasso, Centro de Investigación Científico y Tecnológico para la Minería (CICITEM), Universidad Católica del Norte (biolixiviation).


Wastewater treatment plant in Antwerpen-Zuid, Belgium (picture by Annabel).