Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.
Highlights
The gastrointestinal microbiota comprises a collection of microbial communities, including viruses, bacteria, archaea and fungi, inhabiting the gastrointestinal tract [1]
inflammatory bowel disease (IBD) encompasses a group of chronic inflammatory bowel pathologies of idiopathic origin that affect millions of people throughout the world; the two most important pathologies covered by this term are Crohn’s disease (CD) and ulcerative colitis (UC) [5]
Studies in animal models and humans have shown that there is a persistent imbalance of the intestinal microbiome related to IBD, with a substantial body of literature providing evidence for the relation of the human gut microbiome and IBD [4,6,7,8,9,10]
Summary
The gastrointestinal microbiota comprises a collection of microbial communities, including viruses, bacteria, archaea and fungi, inhabiting the gastrointestinal tract [1]. The constitution and diversity of the microbiota in different sections of the gastrointestinal tract are highly variable and its concentration increases steadily along it, with small numbers in the stomach and very high concentrations in the colon [2,3] This community has been linked to many diseases, including inflammatory bowel disease (IBD) [4]. Studies in animal models and humans have shown that there is a persistent imbalance of the intestinal microbiome (which refers to the gut microbiota and their collective genetic material) related to IBD, with a substantial body of literature providing evidence for the relation of the human gut microbiome and IBD [4,6,7,8,9,10] Despite all this evidence, it has been difficult to determine whether these changes in the microbiome are the cause of IBD or rather the result of inflammation after. Our objective was to describe the associations between IBD and dysbiosis and the potential clinical translation of microbiome-based biomarkers
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