The plant microbiome ecotypes project assigned bacterial species to genome-based cohorts (dual-nature, pathogenic, beneficial, neutral) and found that the dual-nature cohort is the largest one, both across all species analysed and, more strongly, among plant-associated species 1. Detailed results are in Plant Microbiome Ecotypes — Compartment-Specific Functional Guilds and Their Genetic Architecture.
Cohort Distribution Across Species
Across the refined cohort distribution of 25,660 species, dual-nature species numbered 12,463 (48.6%), pathogenic 6,272 (24.4%), beneficial 3,394 (13.2%) and neutral 3,531 (13.8%) 1.
Among the 1,115 plant-associated species, dual-nature species numbered 878 (78.7%), pathogenic 108 (9.7%), beneficial 94 (8.4%) and neutral 35 (3.1%) 1. This refines the all-species result: the dual-nature share is higher in the plant-associated subset than in the full species set, while the pathogenic, beneficial and neutral shares are each lower 1.
Interpretation and Evidence Grade
The cohort counts are direct tallies from one project’s genome-based classification 1. They suggest the hypothesis that, at the gene-content resolution used for cohort assignment, a strict beneficial-versus-pathogen dichotomy is not recoverable for most plant-associated species; this interpretation rests on a single project and on how the cohort rules define a “dual-nature” signature, so it is not yet an established finding 1.
Open Directions
- Within the dual-nature cohort of Plant Microbiome Ecotypes — Compartment-Specific Functional Guilds and Their Genetic Architecture, test whether the beneficial and pathogenic marker sets co-occur on the same mobile elements or in the core genome, to ask whether dual-nature status reflects accessory-gene mixing or shared core functions 1.
- Compare cohort assignments against curated host-interaction phenotypes (where available) for plant-associated species, to measure how often a dual-nature genomic call corresponds to an observed beneficial or pathogenic lifestyle 1.
- Re-run cohort assignment under stricter or weighted marker thresholds to test whether the dual-nature majority among plant-associated species is robust to marker-definition choices 1.