Data and Code for Rethinking the Soil Core Microbiome

Lee, J., Aponte Rolón, B., de Lorimier, P., Ané, J-M., Niccolò Benucci, G.M., Carrell, A.A., Chai, Y.N., Chandrasoma, J., Geerdes, N., Infante, V., Kristy, B., Martin, S., Pascoe, I., Patra, R., Radmer, L., Rush, T.A., Shita, N.S., Suratt, A., Suthers, P.F., Cregger, M.A., Howe, A., Lebeis, S, Scheller, H.V. July 10, 2026. Data and Code for: “Rethinking the Soil Core Microbiome.” GitHub.

The data repository contains the reproducible analysis workflow associated with the New Phytologist Viewpoint “Rethinking the soil core microbiome.”

The central argument of the Viewpoint publication is that taxa selected by occurrence, abundance, Bray-Curtis contribution, clustering threshold, or other analytical filters should not automatically be called a biological “core microbiome.” In the data repository, such taxa are therefore described as operationally selected taxa unless there is independent evidence for biological conservation.

The repository is intended for manuscript reproducibility, not as a general-purpose core microbiome detection package.

GitHub:  R script and data for reproducible analysis