Collateral effects of antibiotics on mammalian gut microbiomes

Abstract

Antibiotics are an essential component of the modern lifestyle. They improve our lives by treating disease, preventing disease, and in the case of agricultural animals by improving feed efficiency. However, antibiotic usage is not without collateral effects. The development and spread of antibiotic resistance is the most notorious concern associated with antibiotic use. New technologies have enabled the study of how the microbiota responds to the antibiotic disturbance, including how the community recovers after the antibiotic is removed. One common theme in studies of antibiotic effects is a rapid increase in Escherichia coli followed by a gradual decline. Increases in E. coli are also associated with systemic host stresses, and may be an indicator of ecosystem disturbances of the intestinal microbiota. Moreover, recent studies have shown additional effects mediated by antibiotics on the gut microbiota, such as the stimulation of gene transfer among gut bacteria and the reduction of immune responses in peripheral organs. Querying the microbiota after antibiotic treatment has led to intriguing hypotheses regarding predicting or mitigating unfavorable treatment outcomes. Here we explore the varied effects of antibiotics on human and animal microbiotas.

Impact of the Use of β-Lactam Antimicrobials on the Emergence of Escherichia coli Isolates Resistant to Cephalosporins under Standard Pig-Rearing Conditions

“…to overgrow high-prevalence strains during enrichment (16). Additionally, weaning poses enough stress that it may contribute to E. coli overgrowth in pigs (17,18). On the other hand, in some cases, PFGE results suggest that some of the clones were shared among piglets of the same pen (for example, the litters from sows numbers 25 and 11) (see Table S1 in the supplemental material), indicating a common source within the pen.…”

“…Several studies have demonstrated a short-lived increase in the E. coli population after antimicrobial treatment or a stressful event. Since the sows were far from these events, they may carry undetectable amounts of CR E. coli (17,18), and the limitations of the bacteriological techniques did not allow their detection. Hence, the farm was cleaned and depopulated during the 6 months prior to the study; incorrect cleaning and disinfection of the premises may play a role in the persistence of these organisms.…”

Gut microbiota, healthy ageing and age-associated intestinal diseases: Drosphila intestine as a good model

“…The bacteria community shift that can cause gut pathology in the ageing fly intestine was not examined in the literature (2), the causal relationship between dysbiosis and dysplasia is clearly established in many publications. The dysbiosis of the gut microbiota, characterized by the expansion of opportunistic pathogens such as E. coli, can lead to dysplasia in mammals and invertebrates (12). Likewise, dysbiosis of the intestinal microfora, characterized by an expansion of the Gammaproteobacteria, is strongly correlated to intestinal barrier dysfunction with ageing in Drosophila.…”

Probiotics or antibiotics: future challenges in medicine

“…the 16S rRNA gene sequence) for making taxonomic assignments. For example, 16S rRNA gene sequence analysis of the entire community illustrated that most bacterial taxa in the gut were influenced by the administration of ciprofloxacin to humans, leading to diversity, evenness and decreased richness (Dethlefsen et al, 2008;Looft & Allen, 2012).…”