Datasets for SynCom101 paper

These are datasets used in SynCom101 as example datasets. They can be loaded in the data input page through input method “Public Bacterial Collections”. It included pickle file format input data generated from following dataset:

(1) Crop Rhizosphere Bacterial Collections (CRBC) – 4,618 genomes

Reference genomes of root microbes from wheat, rice, maize, and Medicago. The collection includes 6,699 bacterial genomes (68.9% from isolates) and 1,817 potentially novel species, expanding crop root bacterial diversity by 290.6%.

Reference: https://doi.org/10.1016/j.cell.2025.02.013 | Website: www.cropmicrobiome.com

(2) proGenomes v3 – ~130 host-plant associated representative strains

Consistently annotated bacterial and archaeal genomes with strict quality controls. Part of a larger database with over 900,000 genomes from 40,000+ species.

Reference: https://doi.org/10.1093/nar/gkac1078

(3) AtSphere

Reference: https://doi.org/10.1038/nature16192

Soil – Bacterial isolates from bulk soil

Comprehensive collection of soil bacterial isolates for studying plant-microbe interactions.

Rhizosphere (Root Zone) – Bacterial isolates from plant root zone

Collection focused on rhizosphere bacteria for studying root-microbe interactions.

Phyllosphere (Leaf Surface) – Bacterial isolates from leaf surface

Collection of phyllosphere bacteria for studying leaf-microbe interactions.