The gut microbiome in the Lebanese population and its alterations in metastatic colorectal cancer: benchmarking and application

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BACKGROUND: Colorectal cancer (CRC) is a rising health concern in Lebanon and across the Arab world, concomitant with dietary and lifestyle transitions. The gut microbiome may contribute to CRC progression and treatment response, and it remains understudied in Arab populations. This pilot study investigates gut microbiome dynamics in a cohort of stage IV CRC patients and cancer-free individuals from Lebanon, benchmarking computational tools for 16S rRNA sequencing and analyzing microbial and functional shifts associated with cancer development and therapy. METHODS: Stool samples were collected from cancer-free individuals (n = 32) and newly diagnosed stage IV CRC patients before therapy (n = 17). A subset of CRC patients (n = 10) provided follow-up samples 3-6 months after therapy. 16S rRNA microbial profiling was conducted using the Illumina MiSeq platform. Computational tools were benchmarked using a mock community, with a defined microbial composition. Microbiome and functional analyses included diversity metrics, differential abundance testing, and pathway prediction, with adjustments for age and sex, followed by sensitivity analyses accounting for antibiotic use and immunotherapy. RESULTS: Among the evaluated computational tools, USEARCH was selected for downstream CRC microbiome analyses based on its performance. CRC patients exhibited progressive dysbiosis, characterised by distinct beta diversity profiles, reduced alpha diversity and a declining Firmicutes/Bacteroidota ratio from cancer-free controls to baseline CRC and post-therapy samples. Differential abundance analysis identified taxa associated with CRC development and therapy response, including Fusobacterium, Muribaculaceae, Intestinimonas, Intestinimonas butyriciproducens and Lactobacillus fermentum. Notably, some potentially beneficial taxa increased progressively across the disease and treatment continuum, suggesting that therapy may promote specific favorable microorganisms while coinciding with broader microbiome dysregulation. Functional pathway analysis revealed widespread alterations in microbial functional capacity, including potential therapy-associated shifts. CONCLUSION: This study represents a pioneering effort in gut microbiome profiling of Lebanese population with advanced CRC, establishing a molecular reference map during a period of rising CRC incidence and dietary transition. Computational benchmarking using a mock community supported the robustness of the analytical workflow. The results may facilitate the discovery of microbial signatures associated with CRC development and therapy response, providing insights into cancer prevention and clinical intervention.

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