The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease

Abstract

The gut microbiome serves as a signaling hub that integrates environmental inputs with genetic and immune signals to influence the host’s metabolism and immunity. Gut bacteria are intricately connected with human health and disease state, with specific bacteria species driving the characteristic dysbiosis found in gastrointestinal conditions such as inflammatory bowel disease (IBD); thus, gut bacteria changes could be harnessed to improve IBD diagnosis, prognosis, and treatment. The advancement in next-generation sequencing techniques such as 16S rRNA and whole-genome shotgun sequencing has allowed the exploration of the complexity of the gut microbial ecosystem with high resolution. Current microbiome data is promising and appears to perform better in some studies than the currently used fecal inflammation biomarker, calprotectin, in predicting IBD from healthy controls and irritable bowel syndrome (IBS). This study reviews current data on the differential potential of gut bacteria within IBD cohorts, and between IBD and other gastrointestinal diseases.

Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria

“…The limited existing literature on the above highlighted taxa suggests some possible explanations for their dynamics. For instance, RF39 of Group 1, which has been shown to decrease in abundance in mouse models of colitis, [54][55][56][57][58][59][60][61][62][63][64][65] has also been described as having a reduced genome and as being metabolically dependent on other bacteria for some amino acids and vitamins. 66,67 Our data support the hypothesis that auxotrophic bacteria such as RF39 are less likely to survive harsh colitic environments, as has been suggested to occur in IBD patients.…”

“…These taxa should be further studied for their relevance to host health. 64 For instance, determining the shared metabolic characteristics of gut bacteria which persist, and/or thrive, in the inflamed gut could reveal how these taxa or their metabolism may be linked to the development of an inflammatory environment. Such taxa or metabolic activities could act as biomarkers, wherein changes in their presence could indicate the onset of a flare before overt symptoms manifest.…”

The gut‐lung axis and asthma susceptibility in early life

“…A growing body of evidence indicates that the events surrounding gut microbial colonization and composition may critically affect the development of diseases at locations outside of the gastrointestinal tract 15,16 . Particular diseases are associated with depletion or enrichment of particular intestinal bacterial clades, and an understanding of these changes could be help to identify potential therapeutic targets or early predictive markers for disease development 17–19 . Figure 1 provides examples of how significant differences in the relative abundance of certain early‐life microbiota have been associated with the development of diseases such as: obesity, 20 atopic dermatitis, 21 hypertension and cardiovascular disease (CVD), 22,23 Type 1 diabetes, 24 asthma, 25 and attention deficit hyperactivity disorder (ADHD) 26 .…”

“…15,16 Particular diseases are associated with depletion or enrichment of particular intestinal bacterial clades, and an understanding of these changes could be help to identify potential therapeutic targets or early predictive markers for disease development. [17][18][19] Figure 1 provides examples of how significant differences in the relative abundance of certain early-life microbiota have been associated with the development of diseases such as: obesity, 20 atopic dermatitis, 21 hypertension and cardiovascular disease (CVD), 22,23 Type 1 diabetes, 24 asthma, 25 and attention deficit hyperactivity disorder (ADHD). 26 In this review, we will use the term "gut-lung axis" to discuss how changes in gut microbial composition during early-life may have a significant impact on respiratory illnesses such as asthma.…”

The Role of Microbiota in Upper and Lower Gastrointestinal Functional Disorders

“…Beyond FGIDs, gut microbiota also plays a critical role in the pathogenesis of organic diseases of the digestive tract, such as inflammatory bowel diseases [30][31][32], eosinophilic esophagitis [33], and others [34], as well as in the development of post-surgical complications [35,36], which require endoscopic treatment [37][38][39][40][41]. Characterization of the microbiota may represent a future therapeutic approach for these conditions as well.…”