Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease

Abstract

Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.

Keywords: biomarkers; bowel disease; inflammation; metagenomic; microbiota.

Figure 1

Changes in the intestinal microbiota of patients with inflammatory bowel disease (IBD) are characterized by a decrease in diversity, a reduction in probiotics, and an increase in pathogenic bacteria, which contribute to the onset of intestinal inflammation (modified figure derived from [28] and created in https://BioRender.com).

Figure 2

Alterations in the intestinal microbiota of patients with CRC are characterized by an imbalance in microbial composition, with an increase in pathogenic bacteria and a decrease in beneficial microbes, which may contribute to tumorigenesis (modified figure derived from [107] and created in https://BioRender.com).

Figure 3

Genetic predisposition (HLA-DQ2/DQ8) and the presence of gluten are necessary factors for developing celiac disease (CeD). However, environmental factors, including microorganisms, play a significant role in the pathogenesis of celiac disease. Changes in the microbiome, such as a reduction in beneficial bacteria (such as Lactobacillus and Bifidubacterium) and an increase in pathogenic microorganisms (either bacterial, such as Proteobacteria, viral, such as Enterovirus and Reovirus, or fungal, such as Candida or Saccharomycetes), are linked to disease onset and persistence, even in patients following a gluten-free diet. Other environmental factors lead to microbiota modification, such as early-life feeding patterns, including breastfeeding or the method of birth (cesarean section vs. vaginal delivery). Created in https://BioRender.com.