Exploring the Gut Microbiome Signature in Inflammatory Bowel Disease Patients: Metagenomic Analysis and Functional Profiling

Valentina Borriello^*
*Correspondence: Valentina Borriello, Department of Clinical and Experimental Medicine, Gastroenterology Section, “Gaspare Rodolico” Policlinico Hospital, University of Catania, 95100 Catania, Italy, Email:

Keywords

Inflammatory bowel disease • IBD • Gut microbiome • Metagenomic analysis • Functional profiling • Crohn's disease • Ulcerative colitis

Introduction

Inflammatory Bowel Disease (IBD) is a group of chronic inflammatory disorders of the gastrointestinal tract, primarily including Crohn's disease and ulcerative colitis. Despite extensive research, the precise etiology of IBD remains elusive, though it is widely accepted that a combination of genetic, environmental, and immunological factors contribute to its pathogenesis. The gut microbiome, consisting of trillions of microorganisms, has emerged as a key player in maintaining intestinal health and influencing disease states. Dysbiosis, or microbial imbalance, has been frequently observed in IBD patients, suggesting a potential link between microbiome composition and disease pathology. This study aims to delineate the gut microbiome signature associated with IBD through comprehensive metagenomic analysis and functional profiling, offering new insights into microbial roles in IBD and identifying potential therapeutic targets [1].

Literature Review

To explore the gut microbiome signature in IBD patients, we conducted a metagenomic analysis on stool samples collected from both IBD patients (comprising individuals with Crohn's disease and ulcerative colitis) and healthy controls. High-throughput sequencing was employed to generate comprehensive microbial profiles, identifying taxonomic composition and relative abundances of microbial communities. Advanced bioinformatics tools were used to analyze the sequencing data, revealing significant differences in microbial diversity and composition between IBD patients and healthy individuals [2].

Key findings included a marked reduction in microbial diversity in IBD patients, with specific taxa being significantly underrepresented or overrepresented compared to controls. For instance, beneficial commensal bacteria such as Bacteroides and Faecalibacterium were notably decreased, while potentially pathogenic bacteria like Escherichia and Fusobacterium were elevated in IBD samples. Functional profiling, performed using tools such as HUMAnN2, provided further insights by mapping microbial genes to metabolic pathways. This analysis revealed disruptions in key metabolic functions, including amino acid metabolism, short-chain fatty acid production, and immune-modulatory pathways, underscoring the potential impact of microbiome alterations on IBD pathophysiology [3].

Discussion

The results of our metagenomic analysis and functional profiling underscore the significant alterations in the gut microbiome of IBD patients compared to healthy controls. The observed decrease in microbial diversity and the dysbiotic shift towards pathogenic bacteria highlight the potential role of the microbiome in perpetuating intestinal inflammation. The functional disruptions identified, particularly in metabolic and immune-related pathways, suggest mechanisms by which microbial dysbiosis may contribute to IBD pathogenesis [4]. These findings align with previous research indicating that the gut microbiome plays a critical role in maintaining mucosal immunity and intestinal barrier function. The reduction in beneficial microbes such as Faecalibacterium, known for its anti-inflammatory properties, and the increase in pathogenic species may exacerbate inflammation and compromise gut integrity. Furthermore, the disrupted metabolic pathways could impact the availability of key metabolites, such as short-chain fatty acids, which are vital for maintaining gut health and modulating immune responses [5].

Future research should focus on longitudinal studies to track microbiome changes over time in IBD patients and explore the causal relationships between microbial alterations and disease progression. Additionally, therapeutic strategies aimed at restoring microbial balance, such as probiotics, prebiotics, and fecal microbiota transplantation, hold promise and warrant further investigation [6].

Conclusion

Our study provides a comprehensive analysis of the gut microbiome signature in IBD patients through metagenomic and functional profiling. The significant alterations in microbial diversity, composition, and functional pathways observed in IBD patients underscore the potential role of the microbiome in disease pathogenesis. These insights not only enhance our understanding of IBD but also highlight potential microbial targets for therapeutic intervention. Addressing microbial dysbiosis and restoring a healthy gut microbiome may offer novel approaches for managing and treating IBD, ultimately improving patient outcomes.

Acknowledgement

None.

Conflict of Interest

None.

References

1. Ng, Siew C., Hai Yun Shi, Nima Hamidi and Fox E. Underwood, et al. "Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: A systematic review of population-based studies." Lancet 390 (2017): 2769-2778.

Google Scholar, Crossref, Indexed at

2. Molodecky, Natalie A., Shian Soon, Doreen M. Rabi and William A. Ghali, et al. "Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review." Gastroenterol 142 (2012): 46-54.

Google Scholar, Crossref, Indexed at

3. Gajendran, Mahesh, Priyadarshini Loganathan, Anthony P. Catinella and Jana G. Hashash. "A comprehensive review and update on Crohn's disease." Disease-a-month 64 (2018): 20-57.

Google Scholar, Crossref, Indexed at

4. Olfatifar, Meysam, Mohammad Reza Zali, Mohamad Amin Pourhoseingholi and Hedieh Balaii, et al. "The emerging epidemic of inflammatory bowel disease in Asia and Iran by 2035: A modeling study." BMC Gastroenterol 21 (2021): 204.

Google Scholar, Crossref, Indexed at

5. Jewell, Derek P., Lloyd R. Sutherland, John WD McDonald and Brian G. Feagan. "Ulcerative colitis." Evidence‐based Gastroenterol Hepatol (2010): 232-247.

Google Scholar, Crossref, Indexed at

6. Zallot, Camille, Didier Quilliot, Jean‐Baptiste Chevaux and Carina Peyrin‐Biroulet, et al. "Dietary beliefs and behavior among inflammatory bowel disease patients." Inflamm Bowel Dis (2012).

Google Scholar, Crossref, Indexed at