Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome

Antimicrobial resistance, especially the emergence of multidrug-resistant human pathogens, remains a serious public health crisis across the globe. The human gut microbiome regulates essential human functions including digestion, energy metabolism, brain function, and immunity by modulating multiple endocrine, neural, and immune pathways of the host. Increasing evidence shows adverse effects of antibiotics on the community structure and functions of healthy gut microbiomes. Short-term antibiotic treatment is able to change the richness and diversity of species into a long-term dysbiotic state. The colonization of invading pathogens is encouraged because of decreased competitive exclusion. Furthermore, the accumulation of antimicrobial resistant genes in the gut microbiome (gut resistome) facilitates the emergence of multidrug-resistant nosocomial pathogens. In this study, the adverse effects of antibiotics on the gut microbiome are highlighted in terms of dysbiosis and the accumulation of resistance genes. In light of evidence of such adverse impacts, several epidemiological studies have been conducted on traditional culture techniques and 16S rRNA metagenomics to assess the compositional and functional changes occurring in the gut microbiome after exposure to antibiotics. They have failed to agree on specific antibiotic-associated microbiome and its functional redundancy subsequent to exposure to antibiotics. This mini-review describes the composition and role of a healthy microbiome to understand and appraise the value of gut microbiome and summarizes the current understanding of adverse effects of antibiotics on it.