Diet Diversity - Does the Gut Microbiome Differ

Research question

Is reported plant diversity associated with microbial composition after country adjustment?

Assess reported plant-type categories and gut microbial community composition in historical American Gut data, with geography and questionnaire-missingness sensitivity.

Data and comparison design

The analysis compares samples through Bray–Curtis dissimilarity and its corrected geometry, rather than testing one organism in isolation. Read incremental R² with the permutation test and dispersion checks: a detectable association may still explain very little of the variation.

Recorded findings

Analysis element	Recorded result	Meaning
Fixed-seed sample	600 participants	Captured historical American Gut sample.
Main analysis	564 participants	After the archived eligibility and missingness rules.
Incremental R²	0.804%	Country-adjusted corrected Bray–Curtis geometry.
Permutation p-value	.004	A detectable, small association; sensitivities are less conclusive.

The source contains 4,827 matching samples and 22,742 features. Eligibility and participant deduplication leave 2,719 participants, from whom a fixed-seed country-proportional sample of 600 was selected. Main analysis includes 564 respondents with known country; 479 complete cases, 540 US respondents and a 300-person eight-state subset support sensitivity analyses.

All 9,089 nonzero cohort features were retained. Bray–Curtis geometry had 259 materially negative eigenvalues; Lingoes correction yielded 598 retained coordinate dimensions. All dimensions were used for inference; display axes explain 4.40% and 2.47% of corrected inertia.

The primary country-adjusted association has incremental R² 0.0080399356 (0.804%), partial R² 0.0081978586 (0.820%), pseudo-F 1.1344562, and permutation p=.004 using 999 permutations. This is a small association in corrected geometry, not the fraction of raw-count biological variance explained or a causal benefit. Multiplicity-adjusted complete-case and regional sensitivity tests are less conclusive.

The new mean centroid distances decrease from 0.840916 to 0.808207 across increasing plant categories; “More than 30” is correctly identified as the minimum. The previous attempt's range defect is absent. Dispersion F is 2.3986004, with saved permutation p=.046; unequal dispersion limits a pure centroid interpretation.

Artifacts inside the package: analysis_rules.md, analysis.py, study_report.md, plant_diversity_reproducible.zip, ordination.png, and sensitivity_missingness.png. The bundle additionally includes captured inputs, model/cohort/missingness/geometry tables, PDF figures and replay records.

What the comparison shows

The recorded association is small and sensitive to analysis choices. It describes community-composition differences in this cohort, without establishing that dietary diversity caused a healthier microbiome.

Assumptions and limits

The small association is not a causal dietary benefit or a fraction of raw-count biological variance explained. Self-report, missingness, confounding and a heavily US-dominated cohort limit generalization. Unequal dispersion and substantial geometry correction complicate interpretation; original geometry and permutation generation were not independently rerun.

Sources and research materials

The unchanged research package comes from the upstream archive. It retains the original conversation and included scientific artifacts, including analysis code, results and figures. The poster is an AI-generated thematic illustration, not study evidence. This introduction summarizes archived findings; the analysis was not rerun. Later bounded checks do not certify the entire study or mean the original package was corrected.