kin discrimination

traitmech:000716 · CLASS · PROPOSED

An ecological phenotype in which microbial cells preferentially associate with kin or exclude nonkin through differential interactions according to genetic similarity or relatedness.

Trait evidence (3)

DOI:10.1371/journal.pbio.0060287
Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals

Ostrowski et al. 2008, PMID:19067487; scientific abstract, publisher PDF page 1, contiguous span visually checked. Mixtures with AX4-GFP and natural-isolate dye controls support partial sorting during aggregation, not complete clonal exclusion. The measured endpoint is variation in fluorescent spore proportions among fruiting bodies; genetic distance uses 12 microsatellite loci, not genome-wide identity. Main text and all four figures were inspected; Figure 1 is hypothetical. Supplementary Tables S1 and S2 were read by text extraction. Main Methods names QS45, absent from the retrieved S1 strain table; no strain alias is inferred. Kin-selected benefit is an interpretation, not a measured fitness endpoint here. Natural provenance of every laboratory derivative and a molecular recognition mechanism remain unresolved. Native abstract verifier: VERIFIED.
DOI:10.1073/pnas.1512671112
Some swarms did merge, and most interestingly, this behavior was only seen in the most highly related strain pairs.

Stefanic et al. 2015, PMID:26438858, PMC4653157; directly retrieved scientific abstract from Europe PMC with the namespace-qualified query EXT_ID:26438858 AND SRC:MED. Title, PMID and DOI were checked together. The authors define a conspecific scope and report relatedness-associated swarm merging versus boundary formation among sympatric Bacillus subtilis isolates. The separately reported root-colonization outcome is not a direct killing measurement. Full text, figures and supplements were inaccessible and are not claimed as inspected; indexed search passages were not used as excerpts or quantitative evidence. Native abstract verifier: VERIFIED. Linked PMID:26512099 is commentary, not a correction or experimental replication.
DOI:10.1128/mBio.00723-17
The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin.

Lyons and Kolter 2017, PMID:28679746, PMC5573675; scientific abstract, NLM version 1 PDF page 1 and JATS article-meta abstract without abstract-type. This is not the separate IMPORTANCE summary. Introduction distinguishes preferential kin association from nonkin exclusion and supports the definition's two modes; the paper's own experiments support the nearby-species extension. The comparison concerns interactions with B. subtilis NCIB3610: nearby species can be antagonized, while more distant lineages show varied outcomes. This is not a universal monotonic relation between distance and antagonism. Relatedness uses type-strain 16S, not whole-genome identity of every isolate. Swarm, biofilm and halo assays differ in medium and endpoint. Figure 2A and 2C assign WNC032 to different species; Data Set S1 identifies it as B. megaterium. No silent panel correction or taxon anchor is inferred. Actual Figures 2 and 4 and selected spreadsheet rows/totals were inspected, not all figures or raw assays. Native abstract verifier: VERIFIED. Shares an investigator with 2015; not an independent-laboratory replication.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1128/mBio.00723-17

Parent traits (1)

phenotype METPO:1000059

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Preserve relational phenotype scope without equating all recognition or cooperation.

CURATION TODO OPEN kin-discrimination-scope-and-hierarchy · raised by codex · 2026-10-13

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Stefanic 2015 defines conspecific discrimination, whereas Lyons 2017 explicitly extends exclusion to nearby species. The record retains that attributed extension without a universal kin threshold, obligate killing, cognition or monotonic distance-response rule. Kin recognition, allorecognition and self/nonself discrimination are not asserted as exact synonyms. An interaction phenotype is required; a recognition locus, allele match, isolated pairing or spatial assortment alone is insufficient. Recognition-allele specificity, measured relatedness proxies and genome-wide relatedness must not be conflated. METPO:1000059 phenotype is the conservative parent. Mutualism (traitmech:000041) requires reciprocal benefit; biofilm formation (traitmech:000053) is neither necessary nor sufficient. Contact-dependent outer membrane exchange (traitmech:000650) is material transfer, and its existing negative kin-discrimination evidence remains a boundary, not a parent gap. Heterokaryon incompatibility (traitmech:000606) concerns postfusion restriction and is not automatically equivalent or reparented. Predation requires trophic benefit; DNA self/nonself defense has a different target and endpoint. No organism-level disjointness is implied.

Resolve strain, assay and source gaps before assigning canonical taxa or molecular mechanisms.

KNOWLEDGE GAP OPEN kin-discrimination-evidence-and-mechanism-limits · raised by codex · 2026-10-13

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The QS45 strain-table gap and WNC032 figure-label conflict remain unresolved. The 2015 scientific abstract was read directly, but full text was not. The 2017 scientific abstract and IMPORTANCE summary were distinguished; the corrected excerpt is from the scientific abstract, not IMPORTANCE. Selected supplemental spreadsheet checks are not raw-image reanalysis or a statistical replication; supplementary EPS figures remain unread. Bounded MED, PLOS and NLM metadata checks are not exhaustive clearance of corrections or retractions; some publisher routes were inaccessible. No canonical taxa, exact external mappings, protein examples or causal graph are asserted. Allele-specific adhesion in engineered systems requires separate provenance and mechanism review, not inference of natural species-wide possession. Source URLs, hashes, access limits and native snippet outcomes are retained in the source-verification sidecar.

Curation history

2026-10-13T09:09:53Z · MINTED_TRAITMECH_ID · codex
Added kin discrimination with three DOI-backed contiguous snippets and bounded assay, source and hierarchy discussions. Reserved 000716, v592 and 1066900-1066999 after ignored/hidden current-file, retained-history, independent-copy and open/draft PR checks; numeric false positives were adjudicated. No exact active METPO counterpart identified in inspected sources. No taxa or causal graph inferred; prior records unchanged. Timestamp is observed post-audit acceptance, not an estimated write time.
2026-10-13T09:17:32Z · EVIDENCE_CORRECTED · codex
Addressed adversarial findings #1909 and #1910: replaced two source-matching but insufficiently self-contained excerpts with explicit swarm-merging and antagonism results. Changed sole definition authority to Lyons 2017 for the attributed nearby-species extension, preserving the explicit Stefanic 2015 evidence DOI. Updated section and native-verifier notes. Original event, phenotype definition, identifiers, parent, PROPOSED status and remaining source limits are preserved. Timestamp is observed correction decision time, not an estimated write time.

Recorded curation sessions

2026-10-13T09:12:29Z · codex
- CREATE — Add evidence-backed microbial kin discrimination
  Added PROPOSED traitmech:000716 under METPO:1000059 with three DOI-backed snippets (10.1371/journal.pbio.0060287, 10.1073/pnas.1512671112, 10.1128/mBio.00723-17), two OPEN discussions and companion v592 proposal reserving 1066900-1066999. Retained relational scope, nonmonotonic and assay-dependent outcomes, 2015 abstract-only access, strain-label discrepancies and unresolved mechanisms. No canonical taxa, exact mappings or causal graph inferred. Guarded writer dry-run and apply passed; broader validation and review follow. Existing trait records remain unchanged.
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2026-10-13T09:19:03Z · codex
- EDIT — Correct kin-discrimination evidence and definition provenance
  Addresses #1909 and #1910 from the saved initial adversarial review: replaces two insufficiently self-contained snippets with explicit merging and antagonism results, changes definition_source to DOI:10.1128/mBio.00723-17 for the nearby-species scope, preserves DOI:10.1073/pnas.1512671112 for its own excerpt, and updates the 2017 scientific-abstract locator and discussion. Preserves the original event and history/records/kin_discrimination/2026-10-13T091229Z-codex-2c345e.yaml. Does not alter the phenotype definition, identifiers, parent, PROPOSED status or source limitations. Guarded correction dry-run and apply passed; broader validation follows.
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