Managing the Microbiome: How the Gut Influences Development and Disease

Abstract

The microbiome lies at the forefront of scientific research, as researchers work to uncover its mysterious influence on human development and disease. This paper reviews how the microbiome is studied, how researchers can improve its study, and what clinical applications microbiome research might yield. For this review, we analyzed studies concerning the role of the microbiome in disease and early development, the common methodologies by which the microbiome is researched in the lab, and modern clinical treatments for dysbiosis and their possible future applications. We found that the gut microbiome is essential for proper development of various physiological systems and that gut dysbiosis is a clear factor in the etiology of various diseases. Furthermore, we found that germ-free animal models and microbiome manipulation techniques are inadequate, reducing the efficacy of microbiome research. Nonetheless, research continues to show the significance of microbiome manipulation in the clinical treatment of disease, having shown great promise in the prevention and treatment of dysbiosis. Though the clinical applications of microbiome manipulation are currently limited, the significance of dysbiosis in the etiology of a wide array of diseases indicates the significance of this research and highlights the need for more effective research methods concerning the microbiome.

The Gut-Liver Axis in Cholestatic Liver Diseases

“…Reduced diversity prepares the ground for pathobionts to overgrow commensals and induce diseases. Clostridioides difficile infection presents the prototype disease of this mechanism [204]. For PSC, a small pilot trial including ten patients with PSC-IBD could demonstrate improved diversity after fecal microbiome transplantation and a decrease in alkaline phosphatase of more than 50% in 3 patients [205].…”

First Metabolic Insights into Ex Vivo Cryptosporidium parvum-Infected Bovine Small Intestinal Explants Studied under Physioxic Conditions

“…Interestingly, low oxygen concentrations promote the growth of distinct bacteria (e.g., γ-Proteobacteria, Vibrionaceae, and Pseudomonadales) [67], thereby influencing indole production [68]. Similarly, it is well known that intestinal microbiomes influence the outcome of several gut infections [44][45][46][47]. This phenomenon was also confirmed for Cryptosporidium infections [4,17].…”

“…In vivo, the life cycle of C. parvum occurs in the small intestine-a unique biological niche with a complex, highly structured, and multispecies-composed (i.e., micro-and macrobiota) consortium, which is known to influence intestinal host innate immune reactions, as previously demonstrated [4,[44][45][46][47]. This compartment not only promotes nutrient absorption (interestingly, monosaccharide absorption takes place in the ileum, which is also parasitized by C. parvum), but also acts as a physical barrier by forming part of the host innate immune system to combat invasive pathogens.…”

Microbiota, Bacterial Carbonic Anhydrases, and Modulators of Their Activity: Links to Human Diseases?

“…The recent increase of microbiome studies sheds light on its contributing impact on etiology and the progression of many diseases. A microbiota imbalance, named “dysbiosis,” can cause significant effects on the host [ 16 ]. Understanding the link between illness and dysbiosis could let researchers sufficiently define the development of an increasing number of human diseases and discover innovative treatments, modulating the microbiota composition to restore its eubiosis status and so the host health.…”