Fernando Puente Sanchez

My area of expertise is the study of microbial ecosystems using metagenomics, metatranscriptomics and 16S rRNA gene profiling. I have worked in several settings (deep-subsurface, acidic rivers, ocean, lakes, host-associated...), and I strive to find common patterns in the way that microorganisms interact between themselves and with the environment.

To achieve this, I apply (and if necessary, develop) bioinformatics methods in order to integrate the vast amount of information generated by modern approaches (large-scale spatial and temporal series comprised of functional, taxonomic and physicochemical profiles) and form a coherent picture of what drives the behaviour of the community. Ultimately, I want to find interesting and hopefully useful stories about how microbes and ecosystems work.

At SLU, I study the diversification trajectories of microorganisms from different habitats, their relationship with environmental constraints, and the internal structure of the resulting microbial species. I also study microbiome dynamics in aquaculture systems, aiming to identify the risk factors leading to the overgrowth of harmful bacteria.

I develop and mantain software packages for metagenomic analyses such as SqueezeMeta, SQMtools and SuperPang.

- Jay Håkansson (PhD, co-supervisor, starting year 2025): A global study on freshwater prokaryotic intra-species diversity

- Ricardo Parizotto Ribeiro (PhD, co-supervisor, starting year 2025): Revealing population traits of locally adapted filamentous cyanobacteria – using multiomics

- Sofia Larsson (PhD, main supervisor, starting year 2024): Scaling up single molecule variant-detection for aquatic pathogen surveillance

- Bella Safitri (PhD, main supervisor, starting year 2024): Environmental impact of open water aquaculture in hydropower reservoirs from a microbiome perspective

- Nhat Ton Nguyen (PhD, main supervisor, starting year 2024): Microbial response to organic matter in Recirculating Aquaculture Systems (RAS) at a genome level resolution

Past students

- Natalia García-García (PhD, co-supervisor, 2018-2023): The role of microdiversity in aquatic systems

- Nhat Ton Nguyen (MSc, 2023): Time series analysis of fish gut microbiota using Oxford Nanopore 16S rRNA gene sequencing and influence of instect-derived feed

- Aliecha van 't Spijker (BSc, 2022): Pigment characterization of lake cyanobacteria subpopulations

- Luis Alberto Macías Pérez (MSc, 2018): Identification of clusters co-varying microbial functions across a time-series of Arctic Ocean samples

- Natalia García García (MSc, 2018): Network Analysis of Microbial Ecosystems at Multiple Taxonomic Resolutions

- Puente-Sánchez, F., Pascual-García, A., Bastolla, U., Pedrós-Alió, C., & Tamames, J. (2024). Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. Communications biology, 7(1), 1046.

- Hoetzinger, M., Hahn, M. W., Andersson, L. Y., Buckley, N., Ramsin, C., Buck, M., ... , Puente-Sánchez, F., & Bertilsson, S. (2024). Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria. The ISME Journal, 18(1).

- Puente‐Sánchez, F., Hoetzinger, M., Buck, M., & Bertilsson, S. (2023). Exploring environmental intra‐species diversity through non‐redundant pangenome assemblies. Molecular Ecology Resources, 23(7), 1724-1736.

- Arce-Rodríguez, A., Libby, E., Castellón, E., Avendaño, R., Cambronero, J. C., Vargas, M., ... & Puente-Sánchez, F. (2023). Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river. Environmental Microbiome, 18(1), 6.

- Puente-Sánchez, F., García-García, N., & Tamames, J. (2020). SQMtools: automated processing and visual analysis of’omics data with R and anvi’o. BMC bioinformatics, 21(1), 1-11.

- García-García, N., Tamames, J., Linz, A. M., Pedrós-Alió, C., & Puente-Sánchez, F. (2019). Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions. The ISME journal, 13(12), 2969-2983.

- Blanco, Y., Rivas, L. A., González-Toril, E., Ruiz-Bermejo, M., Moreno-Paz, M., Parro, V., ... & Puente-Sánchez, F. (2019). Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments. Science of the Total Environment, 650, 384-393.

- Tamames, J., & Puente-Sánchez, F. (2019). SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline. Frontiers in microbiology, 9, 3349.

- Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M., García-Villadangos, M., Moreno-Paz, M., Blanco, Y., ... & Parro, V. (2018). Viable cyanobacteria in the deep continental subsurface. Proceedings of the National Academy of Sciences, 115(42), 10702-10707.

- Puente-Sánchez, F., Díaz, S., Penacho, V., Aguilera, A., & Olsson, S. (2018). Basis of genetic adaptation to heavy metal stress in the acidophilic green alga Chlamydomonas acidophila. Aquatic Toxicology, 200, 62-72.

- Puente-Sánchez, F., Aguirre, J., & Parro, V. (2016). A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies. Nucleic acids research, 44(4), e40-e40.

- Puente‐Sánchez, F., Moreno‐Paz, M., Rivas, L. A., Cruz‐Gil, P., García‐Villadangos, M., Gómez, M. J., ... & Parro, V. (2014). Deep subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt revealed through geochemistry and molecular biomarkers. Geobiology, 12(1), 34-47.