Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H2S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.

Gut microbiota dysbiosis has been linked to many heath disorders including hepatitis C virus (HCV) infection. However, profiles of the gut microbiota alterations in HCV are inconsistent in the literature and are affected by the treatment regimens. Using samples collected prior to treatment from newly diagnosed patients, we characterized the gut microbiota structure in HCV patients as compared to healthy controls. Treatment-naive HCV microbiota showed increased diversity, an increased abundance of Prevotella, Succinivibrio, Catenibacterium, Megasphaera, and Ruminococcaceae, and a lower abundance of Bacteroides, Dialister, Bilophila, Streptococcus, parabacteroides, Enterobacteriaceae, Erysipelotrichaceae, Rikenellaceae, and Alistipes. Predicted community metagenomic functions showed a depletion of carbohydrate and lipid metabolism in HCV microbiota along with perturbations of amino acid metabolism. Receiver-operating characteristic analysis identified five disease-specific operational taxonomic units (OTUs) as potential biomarkers of HCV infections. Collectively, our findings reveal the alteration of gut microbiota in treatment naive HCV patients and suggest that gut microbiota may hold diagnostic promise in HCV infection.

Over the past decade, gut microbiota dysbiosis has been linked to many health disorders; however, the detailed mechanism of this correlation remains unclear. Gut microbiota can communicate with the host through immunological or metabolic signalling. Recently, microbiota-released extracellular vesicles (MEVs) have emerged as significant mediators in the intercellular signalling mechanism that could be an integral part of microbiota-host communications. MEVs are small membrane-bound vesicles that encase a broad spectrum of biologically active compounds (i.e., proteins, mRNA, miRNA, DNA, carbohydrates, and lipids), thus mediating the horizontal transfer of their cargo across intra- and intercellular space. In this study, we provide a comprehensive and in-depth discussion of the biogenesis of microbial-derived EVs, their classification and routes of production, as well as their role in inter-bacterial and inter-kingdom signaling.

Behavior and mood disorders have been linked to gut microbiota dysbiosis through the “microbiota-gut-brain axis”. Microbiota-targeting interventions are promising therapeutic modalities to restore or even maintain normal microbiome composition and activity in these disorders. Here, we test the impact of a commercial synbiotic formulation on gut microbiota composition and metabolic activity. We employed an ex-vivo continuous fermentation model that simulates the proximal colon to assess the effect of this formulation on microbiota structure and functionality as compared to no treatment control and microcrystalline cellulose as a dietary fiber control. The test formulation did not alter the diversity of gut microbiota over 48 h of treatment. However, it induced the enrichment of Lactobacillus, Collinsella and Erysipelotrichaceae. The test formulation significantly increased the level of microbiota-generated butyrate within 12 h of treatment as compared to 24 h required by microcrystalline cellulose to boost its production. The test formulation did not lead to a significant change in amino acid profiles. These results provide evidence of potential benefits related to synbiotic effects and general gut health and support the potential of this food formulation as a therapeutic dietary intervention in mood and behavior disorders.

The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the gut and the liver. A major cause of liver disorders is hepatitis C virus (HCV) infection that has been illustrated to be associated with gut microbiota dysbiosis at different stages of the disease progression. This dysbiosis may start a cycle of inflammation and metabolic disturbance that impacts the gut and liver health and contributes to the disease progression. This review discusses the latest literature addressing this interplay between the gut microbiota and the liver in HCV infection from both directions. Additionally, we highlight the contribution of gut microbiota to the metabolism of antivirals used in HCV treatment regimens and the impact of these medications on the microbiota composition. This review sheds light on the potential of the gut microbiota manipulation as an alternative therapeutic approach to control the liver complications post HCV infection.

Microbiota-gut-brain axis is an evident pathway of host-microbiota crosstalk that is linked to multiple brain disorders. Microbiota released extracellular vesicles (MEVs) has emerged as a key player in intercellular signaling in host microbiome communications. However, their role in gut-brain axis signaling is poorly investigated. Here, we performed a deep multi-omics profiling of MEVs content generated ex vivo and from stool samples in order to get some insights on their role in gut-brain-axis signaling. Metabolomics profiling identified a wide array of metabolites embedded in MEVs, including lipids, carbohydrates, amino acids, vitamins, and organic acids. Interestingly, many neurotransmitter-related compounds were detected inside MEVs, including arachidonyl-dopamine (NADA), gabapentin, glutamate and N-acylethanolamines. Next, we aimed to identify commensal microbes with psychobiotic activity. We isolated 58 Bacteroides strains assigned to four genera, 11 species, and 4 new species based on 16S rDNA sequencing. We performed whole genome sequencing of 18 representative isolates, followed by a comparative analysis of the structure of polysaccharide utilization loci (PUL) and glutamate decarboxylase (GAD), a genetic system involved in GABA production. Quantifying GABA was done using competitive ELISA, wherein three isolates (B. finegoldii, B. faecis, and B. caccae) showed high GABA production (4.5-7 mM range) in supernatant whereas 2.2 to 4 uM GABA concentration was detected inside microvesicles extracted using ultracentrifugation. To test the biodistribution of MEVs from the gut to other parts of the body, CACO-2, RIN-14 B, and hCMEC/D3 cells showed a capacity to internalize labeled MEVs through an endocytic mechanism. Additionally, MEVs exhibited a dose dependent paracellular transport through CACO-2 intestinal cells and hCMEC/D3 brain endothelial cells. In vivo results showed biodistribution of MEVs to liver, stomach and spleen. Overall, our results reveal the capabilities of MEVs to cross the intestinal and blood brain barriers to deliver their cargoes of neuroactive molecules to the brain as a new signaling mechanism in microbiota-gut-brain axis communications.

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