This chapter consolidates the functional pathway scores and ecological function metrics derived from the two shotgun metagenomic datasets (August 2024 and September 2025). These values are presented as raw functional outputs without interpretation. They serve as the functional reference archive for all mechanistic reasoning in Parts I–IV.
Functional categories include SCFA pathways, bile-acid conversion pathways, mucin-related functions, redox-associated pathways, biofilm functions, and cross-feeding network indicators.
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1. SCFA Production Pathways
Butyrate Pathways
| Pathway | Aug 2024 | Sep 2025 |
|———|———–|———–|
| Acetyl-CoA → Butyrate (classical route) | Severely low | Low |
| Butyryl-CoA:acetate CoA-transferase | Near-zero | Near-zero |
| Butyrate kinase pathway | Absent | Absent |
| Aggregate butyrate potential | 20–30th percentile | 20–30th percentile |
Acetate Pathways
| Pathway | Status |
|———|——–|
| Pyruvate → Acetate | Depressed |
| Acetogenic guild representation | Low |
| Acetate cross-feeding availability | Disrupted |
Propionate Pathways
| Pathway | Status |
|———|——–|
| Succinate → Propionate | Depressed |
| Propanediol route | Depressed |
| Acrylate pathway | Near-zero |
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2. Bile-Acid Conversion Functions
| Function | Aug 2024 | Sep 2025 |
|———-|———–|———–|
| Bile Salt Hydrolase (BSH) | Low | Low |
| 7α-Dehydroxylation | Near-absent | Near-absent |
| Primary → Secondary conversion potential | Severely impaired | Severely impaired |
| Taurine/glycine deconjugation | Low | Low |
| Bile-acid transporter gene prevalence | Elevated relative to commensals | Elevated |
These values reflect impaired microbial processing of bile acids.
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3. Redox-Linked Functional Pathways
| Pathway | Status |
|———|——–|
| Nitrate reduction | Elevated |
| Nitrite reduction | Elevated |
| Oxidative stress response pathways | High |
| Aerobic respiration associated pathways | High |
| Obligate anaerobe pathways | Severely suppressed |
| Hydrogenotrophic cross-feeding | Absent |
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4. Mucin and Barrier-Related Functional Categories
| Function | Status |
|———-|——–|
| Mucin-degrading enzyme pathways | Elevated relative influence |
| Glycan-foraging pathways (commensal) | Depressed |
| Goblet-cell–adjacent microbial pathways | Low |
| Barrier-supportive guild enzyme pathways | Near-zero |
| Mucin-layer reinforcement pathways | Depressed |
These functional data represent the biochemical signature of mucin-layer erosion and impaired barrier ecology.
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5. Biofilm-Associated Functional Pathways
| Pathway | Aug 2024 | Sep 2025 |
|———|———–|———–|
| Enterobacter biofilm structural genes | High | High |
| Quorum-sensing pathways (AI-2) | Elevated | Elevated |
| Adhesion pathways | High | High |
| Biofilm disassembly pathways (commensal) | Minimal | Minimal |
| EPS synthesis (anaerobic guilds) | Absent | Absent |
Biofilm pathways reflect the resilience of pathobiont-dominant structures.
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6. Cross-Feeding Network Indicators
Lactate Production and Utilization
| Pathway | Status |
|———|——–|
| Lactate production | Present but unbalanced |
| Lactate → Butyrate conversion | Absent |
Acetate Availability
| Indicator | Status |
|———–|——–|
| Acetate production | Low |
| Acetate cross-feeding | Severely disrupted |
Hydrogen Cycling
| Function | Status |
|———-|——–|
| Hydrogen consumption (methanogens, acetogens) | Absent |
| Hydrogen-linked SCFA pathways | Absent |
Collapse of cross-feeding networks is reflected in these indicators.
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7. Competitive Advantage Pathways (Proteobacteria-Linked)
| Pathway | Status |
|———|——–|
| Siderophore-mediated iron acquisition | Elevated |
| Oxygen-utilization pathways | High |
| Bile-acid resistance genes | Elevated |
| LPS biosynthesis | High |
| Stress-induced virulence factors | Elevated |
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8. Secondary Metabolite and Irritant-Producing Pathways
| Function | Status |
|———-|——–|
| Phenol production pathways | Elevated |
| Amine production pathways | Elevated |
| Indole pathways | Distorted; elevated precursors |
| Reactive nitrogen species pathways | High |
These pathways reflect irritant metabolite production typical of collapses with suppressed SCFA networks.
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9. Functional Summary Tables
Aggregate Functional Status (2024–2025)
| Category | Status |
|———-|——–|
| SCFA synthesis | Severely impaired |
| Bile-acid transformation | Severely impaired |
| Redox stability pathways | Distorted, high oxidative weighting |
| Mucin-associated functions | Depressed or pathobiont-skewed |
| Biofilm resilience | Pathobiont-favoring |
| Cross-feeding | Collapsed |
| Irritant production | Elevated |
| Ecological buffering | Absent |
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10. Notes on Functional Interpretation
This chapter provides raw functional outputs only.
Interpretation, ecological mapping, and mechanistic integration appear in:
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