Ecological distribution and evolutionary value of the global microbiome

Published in the journal Nature the article "Towards the biogeography of prokaryotic genes" with the participation of the Comparative Metagenomics Lab of the CBGP led by Jaime Huerta-Cepas.

Microbial communities dominate life on Earth and have shaped the planet as we know it. As a whole, microorganisms represent a total biomass only surpassed by plants, and can be found in any type of habitat.

In recent decades, exploration of these communities (known as microbiomes) using massive sequencing techniques has revealed enormous microbial biodiversity as well as important implications for ecosystem modeling and human and plant health.

However, many aspects of the dynamics and ecological distribution of these microbiomes on a global scale are still unknown: Can the same species of microorganisms inhabit different ecosystems? What is the genetic variability in the global microbiome? Do the genetic changes observed between species respond to adaptations to the environment?

These and other questions are addressed in the article "Towards the biogeography of prokaryotic genes" published today in the journal Nature. In the article, a unified perspective of the microbiome of 14 ecosystems is presented, and the functional and adaptive value of more than 300 million bacterial genes obtained from 13,000 DNA samples is analyzed.

The study, co-led by the computational biology laboratories of Dr. Peer Bork (EMBL, Germany), Luis P. Coelho (Fudan University, China) and Jaime Huerta-Cepas (CBGP, UPM-INIA/CSIC, Spain), describes the biogeographic distribution and the selective pressure of an extensive catalog of genes, each of which considered unique at the sequence level and representative of a microbial species.

The results show that only a small part of these genes is distributed throughout multiple ecosystems, thus supporting the hypothesis that adaptation to the environment is occurring at very specific taxonomic levels. Likewise, the work goes deep into the analysis of the genetic variability of microorganisms from the point of view of comparative genomics, grouping the genes in the catalog into large families and quantifying the possible degree of functional redundancy between ecosystems. Surprisingly, the results suggest that most of the genes observed would be variants of a small portion of all the gene families explored, and most of these variants would be evolutionarily neutral. However, the work also estimates that a small percentage of these genes (millions, in absolute terms) could have a high adaptive value and, therefore, a greater ecological dispersion.

Together, the work provides a new approach to the study of the planet's microbiome, analyzing it as a single and global system, opening new research pathways aimed at identifying new gene functions and studying the adaptation of certain organisms to specific environmental conditions.

The work has been developed with the participation of the researchers Álvaro Rodríguez del Río, Carlos Pérez Cantalapiedra and Joaquín Giner Lamia from the Comparative Metagenomics Lab of the Centre for Plant Biotechnology and Genomics, CBGP (UPM-INIA/CSIC) led by Jaime Huerta-Cepas (Researcher INIA/CSIC). The CBGP is a joint research center between the Technical University of Madrid (UPM) and the National Institute for Agricultural and Food Research and Technology (INIA) of The Spanish National Research Council (CSIC). This research has received funding from the Severo Ochoa Center of Excellence project, the INPhINIT program of La Caixa Foundation and other funds from the Spanish State Research Agency (AEI).

Crédito de la imagen: Isabel Romero Calvo/EMBL.

Coelho, L.P., Alves, R., del Río, Á.R., Myers, P.N., Cantalapiedra, C.P., Giner-Lamia, J., Schmidt, T.S., Mende, D.R., Orakov, A., Letunic, I., Hildebrand, F., Van Rossum, T., Forslund, S.K., Khedkar, S., Maistrenko, O.M., Pan, S., Jia, L., Ferretti, P., Sunagawa, S., Zhao, X.-M., Nielsen, H.B., Huerta-Cepas, J., Bork, P. 2021. Towards the biogeography of prokaryotic genes. Nature 1–5. DOI: 10.1038/s41586-021-04233-4