Additional file 3 of Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Bibliographic record
Abstract
Supplementary Material 3. Supplementary Figure 3. Characteristics of 237 reconstructed MAGs. A-C. Boxplots showing beta-dispersion analysis results - the distances from each sample to the centroid of its respective group (HB or NB). Lower values indicate samples within that group are more similar to each other, while higher values indicate greater within-group variability. The significant differences in dispersion between HB and NB communities (particularly for reaction and pathway abundance) reveal that NB communities exhibit more variable metabolic profiles than HB communities, suggesting that Bacteroides presence may constrain metabolic variability. Distances were calculated from: (A) PCoA based on reaction content (top: Jaccard distances for presence/absence; bottom: Bray-Curtis dissimilarities for abundance-weighted data); (B) PCoA based on pathway content (top: Jaccard distances; bottom: Bray-Curtis dissimilarities); and (C) taxonomic composition at the family level. (). Significance determined using beta-dispersion (TukeyHSD) test. * - p-value < 0.05, ** - p-value <0.01, *** - p-value < 0.001. D. Major characteristics of 237 MAGs reconstructed in this study: completeness, contamination, N50 and genome size.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.007 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.750 | 0.187 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".