Dr. Rubén Garrido-Oter

We are interested in the evolutionary and ecological principles that govern the structure and dynamics of complex microbial communities, in particular those associated with photosynthetic organisms, such as land plants and terrestrial microalgae.

In this context, we focus on two main research questions:

• what are the principles that govern microbiota establishment, stability and dynamics and,
• how adaptation occurs in a community context, where multipartite microbe-microbe as well as host-microbe interactions exert selective pressure in all interacting partners.

To address these questions, we develop and apply reductionist experimental approaches and computational tools. Using tractable experimental systems based on large-scale microbial culture collections we aim at developing a mechanistic understanding of how microbiota members interact with each other and with their host. Our ultimate goal is to reveal fundamental, quantitative principles governing the dynamic behaviour of host-associated microbial communities.

1. Duran P, Flores-Uribe J, Wippel K, Zhang P, Guan R, Melkonian B, Melkonian M, Garrido-Oter R (2022) Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nat Commun 13(1):406. doi: 10.1038/s41467-022-28055-8.
2. Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R (2021) Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Commun 1(1):73. doi: 10.1038/s43705-021-00077-1.
3. Zhang J, Liu YX, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y (2021) High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat Protoc 16(2):988-1012. doi: 10.1038/s41596-020-00444-7.
4. Wippel K, Tao K, Niu Y, Zgadzaj R, Kiel N, Guan R, Dahms E, Zhang P, Jensen DB, Logemann E, Radutoiu S, Schulze-Lefert P, Garrido-Oter R (2021) Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nat Microbiol 6(9):1150-1162. doi: 10.1038/s41564-021-00941-9.
5. Garrido-Oter R, Nakano RT, Dombrowski N, Ma KW, AgBiome T, McHardy AC, Schulze-Lefert P (2018) Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host Microbe 24(1):155-167 e155. doi: 10.1016/j.chom.2018.06.006.
6. Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17(3):392-403. doi: 10.1016/j.chom.2015.01.011.
7. Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528(7582):364-369. doi: 10.1038/nature16192.