Abstract
Trillions of microbes exist in the human body, particularly the gastrointestinal tract, coevolved with the host in a mutually beneficial relationship. The main role of the intestinal microbiome is the fermentation of non-digestible substrates and increased growth of beneficial microbes that produce key antimicrobial metabolites such as short-chain fatty acids, etc., to inhibit the growth of pathogenic microbes besides other functions. Intestinal microbiota can prevent pathogen colonization through the mechanism of colonization resistance. A wide range of resistomes are present in both beneficial and pathogenic microbes. Giving antibiotic exposure to the intestinal microbiome (both beneficial and hostile) can trigger a resistome response, affecting colonization resistance. The following review provides a mechanistic overview of the intestinal microbiome and the impacts of antibiotic therapy on pathogen colonization and diseases. Further, we also discuss the epidemiology of immunocompromised patients who are at high risk for nosocomial infections, colonization and decolonization of multi-drug resistant organisms in the intestine, and the direct and indirect mechanisms that govern colonization resistance to the pathogens.
Highlights
Phylum Bacteroidetes comprises aerobic, anaerobic, non-spore-forming, Gram-negative, rod-shaped bacteria that colonize the intestine
The increased prevalence of Proteobacteria in the microbial community can be diagnosed as dysbiosis and diseases [7]
Pathogenic E. coli strains and Klebsiella are found in low abundance in the Enterobacteriaceae family of Proteobacteria
Summary
Intestinal microbes are stable under physiological conditions, but antibiotics administration, nutrients availability, physical stress, and host factors can all cause dysbiosis in the microbiota (Figure 1). Dysbiosis is characterized by a reduction in the diversity of microbes and the normal function of the intestinal microbiota in maintaining host wellness. It may cause loss of specific microbial populations that dysregulate the production of antimicrobial peptides or metabolites against pathogen colonization [8,9]. Antibiotic activity and intestinal absorption determine how antibiotics affect the composition of the microbiota and host susceptibility. These key factors, among others, can be considered when selecting antibiotics and determining their effects on the intestinal microbiota
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