Eneas Aguirre Von Wobeser



  • Doctor in Biology (University of Amsterdam)
  • CONACyT Chair Researcher (CIAD)
  • National Researcher level 1 (SNI)


My interest in Microbial Ecology started at my PhD at the University of Amsterdam, Netherlands, where I studied the responses of a model cyanobacterium to different environmental stimuli, using microarrays (an ancient technology to measure genome-scale gene expression). There, I was tutored by Hans Matthijs, Bas Ibelings and Jef Huisman.

I have done two postdocs at UNAM. During the first one, I studied antagonistic interactions between aquatic gammaproteobacteria from a water pond in a desert-oasis at Cuatro Ciénegas, Cohahuila, with the guidance of Valeria Souza and Gloria Soberón. In my second postdoc, I worked with a group of physicists lead by Alejandro Frank, to try to understand how antagonistic interactions can promote biodiversity, using agent-based modeling.

I worked for two years as a research scientist at Instituto de Ecología (INECOL), studying avocado microbiomes, in a broader project aimed at combating two emergent beetle-pests. As part of my stay at INECOL, I contributed to the setup of a new laboratory complex and to the establishment of new research lines.

Since 2016, I work at Centro de Investigación en Alimentación y Desarrollo (CIAD) as a CONACyT Chair Researcher.


PhD in Biology, University of Amsterdam, 2011


My current research is focused on microbial ecology of agroecosystems, to understand how their microbial communities are structured and interact with plants, mainly in low-input traditional farms in Mexico, working closely with local farmers. Many of my projects involve metagenomics and microbiome analyses. At present, my active projects include the study of the potential contribution of microorganisms to drought-stress in plants and the interactions in fruit-tree microbiomes.  Through this research, I aim at contributing to the development of strategies for the management of plant-associated microorganisms, which could provide alternatives to agrochemicals in the future.

In the near future, I would like to apply the recent advances of artificial intelligence in the prediction of protein structure to microbial ecology. In particular, I am interested in exploring genes found in Metagenomic Assembled Genomes from yet-uncultured, abundant strains, to try to increase our understanding of their metabolic potential. The inference of function from predicted protein structure will certainly be a challenge, but the field (and available software) is advancing.

Selected Publications:

  • Aguirre-von-Wobeser E. 2021. Type II photosynthetic reaction center genes of avocado (Persea americana Mill.) bark microbial communities are dominated by aerobic anoxygenic Alphaproteobacteria. Current Microbiology 78: 2623–2630.
  • Aguirre-von-Wobeser E, Alonso-Sanchez A, Mendez-Bravo A, Espino LAV, Reverchon F. 2020. Barks from avocado trees of different geographic locations have consistent microbial communities. Archives of Microbiology 203:4593-4607.
  • Aguirre-von-Wobeser E, Rocha-Estrada J, Shapiro LR, de la Torre M. 2018. Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem. PloS One 13:e0208852.
  • Aguirre-Von-Wobeser E, Eguiarte LE, Souza V, Soberón-Chávez G. 2015. Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments. Frontiers in Microbiology 6:490.
  • Aguirre-von-Wobeser E, Soberón-Chávez G, Eguiarte L, Ponce-Soto GY, Vázquez-Rosas-Landa M, Souza V. 2014. Two-role model of an interaction network of free-living gamma-proteobacteria from an oligotrophic environment. Environmental Microbiology 16:1366-1377.


Erika Dulce Olivares García (Maestría)

Fred Eduardo Hernández Perea (Doctorado)


Jean-Baptiste Daniel Horby (Licenciatura)

Eduardo Barrera Bautista (Licenciatura)

Karla Arely Veloz Badillo (Licenciatura)