Gut Diversity Atlas: Comparative Analysis of Healthy Gut Microbiota in the Lebanese Population

Abstract

Introduction: The gut microbiota is a complex community of microorganisms residing primarily in the intestines. It functions as a pseudo-endocrine organ and plays a major role in both health and disease. To better understand its contribution to human health, this study characterizes the gut microbial composition of the healthy Lebanese population—a cohort that remains largely unexplored. Establishing a baseline profile of gut microbial diversity and composition will allow for future comparisons with both healthy individuals from other populations and those affected by diseases. This study employed both culturomics and metagenomics. Culturomics enabled the isolation of bacterial strains, including fastidious or low-abundance organisms that are often undetectable by sequencing. Metagenomics provided a comprehensive overview of microbial community structure and taxonomic composition.

Methods: Stool samples were collected from healthy Lebanese adults and preserved at −80°C. Gut microbiota profiling was performed using metagenomics and culturomics. Metagenomic sequencing was conducted using Oxford Nanopore (16S full-length) and Illumina MiSeq (V3–V4 region) platforms. Bioinformatic analysis included quality control, taxonomic classification, and diversity assessments. Culturomics was used to isolate diverse bacterial strains through serial dilution and anaerobic culturing on various selective media.

Background: Over the last decade, the importance of the gut microbiota in human health and disease has increased. The gut microbiota is composed of trillions of microorganisms. It has multiple roles ranging from the generation of vitamins and short chain fatty acids, bioconversion of nutrients, maintenance of the gut barrier integrity and providing protection against pathogenic microbes amongst other roles. There are numerous factors that interplay together to influence the composition of our gut, including our diet, genetics, age, mode of delivery at birth and usage of medications, especially antibiotics. Alterations in the normal composition of our gut is known as dysbiosis. Dysbiotic states have been shown to contribute to the pathophysiology and prognosis of numerous diseases such as inflammatory bowel disease or colorectal cancer.

The gut microbiota of the Lebanese population remains underexplored, with limited data in the current literature. The Lebanese population is a highly diverse group of people coming from different backgrounds, enjoying different lifestyles and having different dietary intakes. This diversity underscores the importance of studying the gut microbial composition and classification in order to highlight its importance in our health, and to investigate dysbiosis and its potential contribution to the pathophysiology of various diseases.

Aim: • Molecular description of the gut microbiota of the healthy Lebanese population using two different platforms (Nanopore and Illumina) • Creation of a strain collection bank (SCB) of bacteria isolated from the stool samples of healthy donors. This SCB will serve bacterio-therapy development for targeted diseases. • Create a baseline reference of the gut microbial composition and diversity that will be used for comparisons with other populations and disease cohorts, as well as for future studies. Conclusion: This study provides the first in-depth characterization of the healthy Lebanese gut microbiota using both metagenomics and culturomics. Across samples, Bacillota emerged as the dominant phylum, with genera such as Faecalibacterium, Blautia, and Ruminococcoides consistently abundant. Culturomics enabled the isolation of 726 bacterial strains, including potentially novel species, enriching our local microbial library. Notably, metagenomic comparison between Oxford Nanopore and Illumina platforms revealed differences in taxonomic resolution and detection of low-abundance taxa. These findings establish a foundational gut diversity reference for the Lebanese population and support future development of targeted bacteriotherapies.