Skip to content

SynCom35 graph: distinguish community immunity from strain mechanisms and unsupported exchanges #1375

Closed

Description

@realmarcin

Review of Dangl_SynComm_35.yaml (CommunityMech:000022) against Teixeira et al., PMID:33879573, complete main body and figure captions.

Whole-community transcription results are assigned to a Dyella/Arabidopsis pair, while the colonization node asserts Dyella/Pseudomonas mutualism. The evidence instead distinguishes SynCom35, five-strain precolonization experiments and the Dyella MF79 secretion-system experiments. Reciprocal fitness was not measured. The WRKY observation is supported, but its proposed regulatory/homeostasis role is not established by that observation.

Three nodes assert generic taxonomic metabolic complementarity, Microbacterium/Stenotrophomonas nutrient exchange, and E. coli/Dyella competition. Their snippets do not support those mechanisms. Remove these unsupported graph claims while retaining the positive suppression, WRKY and colonization observations. Bound the existing two arrows to the actual experiments, including the MF79 retentate result. Do not imply that all 35 strains require T2SS or that a resolved secreted effector was identified. Supplements and figure images were not inspected; the main body does not verify the claimed E. coli negative-control phenotype.

Deduplication: 706 all-state issue titles/bodies and ignored/hidden-inclusive local reports, research, history, tests and scripts; relevant #401 and #754 read. Not every issue comment was searched.

Activity

  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Addressed in graph-only #1381 at a4ca06d433a89666e12c662b24e7fa488c200355 with exact-head self-adversarial COMMENT #1381 (review). 342 passed in 165.07s (0:02:45); actual post-commit docs-current passed. Source-bounded decisions and validation are committed. Non-graph follow-ups #1378, #1379 and #1380 remain open. This graph issue closes only after protected main merge.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions