This chapter consolidates the primary shotgun metagenomic outputs used throughout the book. The values are presented without interpretation; they serve as the dataset reference for all ecological and mechanistic reasoning in Parts I–IV.
Two full shotgun metagenomic datasets form the empirical foundation:
- Dataset 1: August 2024
- Dataset 2: September 2025
Both include taxonomic composition, functional pathways, SCFA potential, bile-acid conversion metrics, and guild-level ecological indicators.
1. High-Level Phylum Composition
August 2024
| Phylum | Relative Abundance |
|---|
| Proteobacteria | 86.7% |
| Firmicutes | Depressed |
| Bacteroidetes | Low |
| Actinobacteria | Low |
| Verrucomicrobia | Present at low levels |
| Others | Trace |
September 2025
| Phylum | Relative Abundance |
|---|
| Proteobacteria | 79.24% |
| Firmicutes | Depressed |
| Bacteroidetes | Low |
| Actinobacteria | Low |
| Verrucomicrobia | Minor increase |
| Others | Trace |
2. Family-Level Composition
August 2024
| Family | Relative Abundance |
|---|
| Enterobacteriaceae | 81.9% |
| Bacteroidaceae | Reduced |
| Lachnospiraceae | Near-zero |
| Ruminococcaceae | Near-zero |
| Streptococcaceae | Low |
| Veillonellaceae | Low |
| Akkermansiaceae | Low |
| Others | Trace |
September 2025
| Family | Relative Abundance |
|---|
| Enterobacteriaceae | 72.51% |
| Bacteroidaceae | Reduced |
| Lachnospiraceae | Near-zero |
| Ruminococcaceae | Near-zero |
| Streptococcaceae | Low |
| Veillonellaceae | Low |
| Akkermansiaceae | Low/modest presence |
| Others | Trace |
3. Genus- and Species-Level Highlights
These values represent dominant or ecologically significant taxa.
Low-abundance commensals are omitted unless ecologically relevant.
Dominant Taxa
- Escherichia/Shigella group: dominant
- Klebsiella spp.: elevated
- Enterobacter spp.: elevated
Depressed Anaerobic Guilds
- Faecalibacterium prausnitzii: near-zero
- Roseburia spp.: near-zero
- Eubacterium spp.: near-zero
- Butyrivibrio spp.: absent
- Anaerostipes spp.: absent
Mucin-Linked Taxa
- Akkermansia spp.: low, intermittent
- Mucin-degrading pathobionts: relatively increased due to exposure of mucin niches
Opportunistic or Reactive Taxa
- Enterococcus spp.: low but persistent
- Streptococcus spp.: modest presence
- Veillonella spp.: present at low levels
4. Functional Pathways (Raw Scores)
Functional outputs are reported exactly as defined in the dataset.
SCFA Production Potential
| Pathway | Percentile/Status |
|---|
| Butyrate synthesis (combined pathways) | 20–30th percentile |
| Acetate pathways | Depressed |
| Propionate pathways | Depressed |
| Cross-feeding network potential | Severely impaired |
Bile-Acid Conversion
| Function | Status |
|---|
| BSH (bile salt hydrolase) | Low |
| 7α-dehydroxylation | Near-absent |
| Primary → secondary conversion | Severely impaired |
Redox and Oxygen Handling
| Indicator | Status |
|---|
| Facultative anaerobe metabolic pathways | Extremely high |
| Obligate anaerobe pathways | Severely suppressed |
| Nitrate-reduction pathways | Elevated |
| Oxidative-stress pathways | Overrepresented |
Mucin and Barrier-Related Functions
| Function | Status |
|---|
| Mucin-degrading enzymes | Elevated relative influence |
| Mucin-repair–associated microbes | Depressed |
| Barrier-supporting guilds | Absent or minimal |
5. Ecological Guild Summary
Anaerobic SCFA Producers
- Severely reduced
- Minimal detectable butyrate-producing capacity
Cross-Feeding Guilds
- Disconnected
- Absent second-stage butyrate producers
- Poor acetate → butyrate conversion
Biofilm Guilds
- Strong biofilm-forming Enterobacteriaceae dominance
- No balancing anaerobic biofilm guilds
Mucin-Interacting Guilds
- Commensal mucin consumers suppressed
- Pathobionts exploiting exposed mucin niches elevated
6. Diversity Metrics
| Metric | August 2024 | September 2025 |
|---|
| Alpha diversity | Low | Low |
| Beta diversity (shift) | Minor shift | Pathobiont-dominant pattern maintained |
| Ecological redundancy | Collapsed | Collapsed |
7. Summary Tables
Primary Ecological Pressures Identified
| Pressure | Evidence Source |
|---|
| Pathobiont dominance | Proteobacteria 86.7% → 79.24% |
| Reduced SCFA potential | Butyrate 20–30th percentile |
| Impaired bile conversion | Low BSH, absent 7α-dehydroxylation |
| Mucin-layer erosion | Guild suppression + elevated mucin-degrading enzymes |
| Oxygen-tension disruption | Loss of anaerobes + elevated facultative pathways |
| Biofilm stabilization | Enterobacteriaceae biofilm guild dominance |
8. Notes on Data Handling
- All values are presented as-is from the two available timepoints.
- Values labeled “Depressed” indicate measurable presence but below normative ecological thresholds.
- Part II (Ch-10) details the evidence-stratification rules governing interpretation of these data.
