Oral, Fecal and Intratumoral Microbiome Atlas in Colombian Patients With Advanced Solid Tumors Receiving First-Line Immunotherapy

Single-center, prospective, observational cohort study. 120 patients with advanced (stage III unresectable or IV) solid tumors candidates for first-line immunotherapy and 30 healthy controls are enrolled (total N=150). Patients provide saliva, stool and tongue-scraping samples plus archival FFPE tumor tissue at baseline (V0) and at 6 (V1) and 12 (V2) months; controls provide saliva and stool at V0 only. Microbiomes are profiled by PacBio HiFi shotgun metagenomics and full-length 16S; tumor transcriptome by RNA-Seq; and saliva/stool metabolome by GC-MS in a subcohort (n=60). Tumor response is assessed by RECIST 1.1. Microbial, transcriptomic and metabolomic features are integrated with clinical outcomes (objective response, PFS, OS) using multivariable and machine-learning models.

Inclusion criteria

• Age 18 years or older.
• Histologically confirmed advanced (stage III unresectable or IV) gastric, colorectal, breast, cervical or head-and-neck cancer.
• Candidate for first-line immunotherapy per current clinical guidelines.
• Available FFPE tumor block in institutional or reference pathology archive.
• Able to provide saliva and stool samples at V0 and follow-up.
• ECOG performance status within protocol limits; life expectancy over 3 months.
• Cognitive capacity to give informed consent; signed EVA-BIOBANCO and Atlas consents.

Inclusion criteria

(healthy controls)

• No prior cancer diagnosis.
• No active autoimmune disease; no inflammatory bowel disease.
• No antibiotics, invasive dental treatment, immunosuppressants or corticosteroids in the prior 3 months; no severe active periodontal disease.

Exclusion criteria

• Systemic antibiotics within 3 months (except short course under 5 days for uncomplicated infection).
• Probiotics or prebiotics within 30 days.
• Chronic proton-pump inhibitors for more than 3 continuous months.
• Inflammatory bowel disease (Crohn, ulcerative colitis) or extensive bowel resection.
• Pregnancy or lactation.
• BMI under 18.5 or over 40 kg/m².
• Uncontrolled diabetes (HbA1c at or above 9% in prior 3 months).
• Invasive dental treatment within 3 months.
• Patients: simultaneous randomized trial of a non-INVIMA-approved experimental immunotherapy; or no evaluable FFPE block meeting quality thresholds.
• Inability to ensure 12-month clinical follow-up.