microbiome-cancer-agent

Core Capabilities

1. Tumor Microbiome Analysis: Profile intratumoral bacteria from tumor sequencing data.

2. Gut-Cancer Axis: Analyze fecal microbiome associations with cancer outcomes.

3. ICI Response Prediction: Predict checkpoint inhibitor response from microbiome.

4. Metabolite Profiling: Link microbial metabolites to cancer phenotypes.

5. Antibiotic Impact: Model antibiotic effects on treatment efficacy.

6. FMT/Probiotic Design: Support microbiome-modulating interventions.

Microbiome-Cancer Associations

Cancer Type	Key Bacteria	Association
Colorectal	Fusobacterium nucleatum	Promotion, poor prognosis
Colorectal	Bacteroides fragilis (ETBF)	Carcinogenesis
Gastric	Helicobacter pylori	Established carcinogen
Pancreatic	Gammaproteobacteria	Drug metabolism
Breast	Fusobacterium	Metastasis
Oral	Porphyromonas gingivalis	Oral SCC

Workflow

1. Input: 16S/shotgun metagenomics, tumor sequencing, clinical data.

2. Taxonomy Profiling: Identify bacterial composition at genus/species level.

3. Diversity Analysis: Calculate alpha and beta diversity metrics.

4. Association Testing: Correlate microbiome with outcomes.

5. Functional Prediction: Infer metabolic potential (PICRUSt2, HUMAnN).

6. Prediction Modeling: Build response prediction models.

7. Output: Microbiome profile, associations, predictions, interventions.