Abstract
In the twenty first century, the changing epidemiology of inflammatory bowel disease (IBD) globally with increasing disease incidence across many countries relates to the altered gut microbiota, due to a combinatorial effect of environmental factors, human immune responses and genetics. IBD is a gastrointestinal disease associated with a gut microbial dysbiosis, including an expansion of facultative anaerobic bacteria of the family Enterobacteriaceae. Advances in high-throughput sequencing enable us to entangle the gut microbiota in human health and IBD beyond the gut bacterial microbiota, expanding insights into the mycobiota, virobiota and helminthes. Caudovirales (viruses) and Basidiomycota, Ascomycota, and Candida albicans (fungi) are revealed to be increased in IBD. The deconvolution of the gut microbiota in IBD lays the basis for unveiling the roles of these various gut microbiota components in IBD pathogenesis and being conductive to instructing on future IBD diagnosis and therapeutics. Here we comprehensively elucidate the alterations in the gut microbiota in IBD, discuss the effect of diets in the gut microbiota in relation to IBD, and illustrate the potential of manipulation of gut microbiota for IBD therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in IBD.
Highlights
Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative disease (UC), are proposed to result from an inappropriate immune response to the gut microbes in a genetically susceptible host
This study showed that rectal mucosa-associated microbiome profiling offered a feasible biomarker for the diagnosis of CD at the early stage of disease
Mice transplanted with microbiota from humans on a typical unrestricted American diet (AMER) responded incompletely to plant-rich, calorierestricted diet with optimized nutrient intake (CRON), while those transplanted with microbiota from CRON-consuming individuals responded strongly to both CRON and AMER diets (Griffin et al, 2017)
Summary
Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative disease (UC), are proposed to result from an inappropriate immune response to the gut microbes in a genetically susceptible host. It is a chronic inflammatory disorder of the intestinal tract of an unknown cause. Due to the expansion in application of high-throughput deep sequencing technology in the past decade, we are able to gradually unveiling the role of the microbiome in development of IBD. These findings have improved our knowledge on the functional mechanisms of the microbiome in the pathogenesis of IBD. We discuss the role of the gut microbiota, including the bacterial microbiota, mycobiota and virobiota in the development of IBD as well as microbiotabased therapeutic approaches in the treatment of IBD
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