Additional file 12 of Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure
Bibliographic record
Abstract
Additional file 12: Supplemental Figure 12. Comparison of changes in pathway-specific gene expression, with changes in taxon abundance and global gene expression for three select pathways. For each pathway (glycolysis, purine metabolism and cell wall biogenesis) we calculate the shift in expression across the four conditions tested (i.e. corn + AGPs v corn; wheat + AGPs v wheat; corn v wheat; and corn + AGPs v wheat + AGPs). The absolute deviation of these changes in pathway-specific expression were then calculated relative to: 1) the relative change in abundance of that taxon (as measured by the log2 fold-change associated with that taxon according to 16S rDNA-based relative abundance); and 2) the total change in RNA for that taxon (as measured by the log2 fold-change in total taxon RNA, calculated by summing RPKM values for all genes for that taxon). Here OTUs are grouped into genera. In the box-plots, taxa with values close to zero, indicate that the shift in pathway gene expression was driven by a general shift in either taxon abundance (16S) and/or global taxon expression. Of the 48 comparisons presented, 42 show that at least 60% of taxa with pathway expression, deviate by greater than a log2 fold change from changes in relative abundance (as measured by 16S rDNA) or global taxon expression (as measured by total taxon RPKM). Note, due to lack of phylogenetic resolution associated with the 16S rDNA datasets, these comparisons feature fewer taxa than the comparisons involving taxon-specific global gene-expression. Single sample Wilcoxon tests further reveal that for 43 of the datasets, pathway-specific gene-expression significantly deviates from either taxon-abundance or global gene expression (* p<0.05; ** p< 0.01; *** p<0.001). The lower panels show the 20 genera exhibiting the greatest divergence in pathway expression relative to global gene expression. For the Corn v Corn+AGP comparison for the glycolysis pathway, we identified ‘Other Bacteria’ and various Proteobacterial groups as possessing the greatest deviation between pathway-specific and global fold change expression. For the Wheat v Wheat+AGP comparison. among the taxa with the greatest deviation between pathway-specific and global fold change expression, were taxa classified as ‘Other Bacteria’, ‘Peptostreptococcaceae’ and ‘Clostridiaceae’.
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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 | 0.018 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.811 | 0.143 |
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".