Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children

Abstract

The gut microbiome represents an important reservoir of antibiotic resistance genes (ARGs). Effective methods are urgently needed for managing the gut resistome to fight against the antibiotic resistance threat. In this study, we show that a gut microbiota-targeted dietary intervention, which shifts the dominant fermentation of gut bacteria from protein to carbohydrate, significantly diminished the gut resistome and alleviated metabolic syndrome in obese children. Of the non-redundant metagenomic gene catalog of ~2 × 106 microbial genes, 399 ARGs were identified in 131 gene types and conferred resistance to 47 antibiotics. Both the richness and diversity of the gut resistome were significantly reduced after the intervention. A total of 201 of the 399 ARGs were carried in 120 co-abundance gene groups (CAGs) directly binned from the gene catalog across both pre-and post-intervention samples. The intervention significantly reduced several CAGs in Klebsiella, Enterobacter and Escherichia, which were the major hubs for multiple resistance gene types. Thus, dietary intervention may become a potentially effective method for diminishing the gut resistome.

Microbiome as a tool and a target in the effort to address antimicrobial resistance

“…The mechanisms of colonization resistance include nutrient competition and direct bactericidal activity, immune stimulation, and various aspects of metabolic activity (120)(121)(122). Diet shifts may be associated with decreases in the types of organisms that often carry ARGs (123). When further elucidated, these mechanisms are likely to provide good leads for informed interventions to counter the burden of AMR.…”

Potential Elimination of Human Gut Resistome by Exploiting the Benefits of Functional Foods

“…As the pipeline of research into antimicrobial agent, with a few exceptions, seems to dry up, dietary interventions are under active consideration for the time being. In Wu et al (2016) showed in their study that a gut microbiota-targeted dietary intervention in obese children managed not only to alter the composition and functionality of the intestinal microbiome but, furthermore, to remarkably decrease their gut resistome. The diet that they had previously implemented (Zhang et al, 2015) included whole grains, traditional Chinese medicinal foods, and prebiotics (WTP diet), and with a genome-centric metagenomic approach, this resulted in a reduction of body weight and inflammation parameters.…”

“…The diet that they had previously implemented (Zhang et al, 2015) included whole grains, traditional Chinese medicinal foods, and prebiotics (WTP diet), and with a genome-centric metagenomic approach, this resulted in a reduction of body weight and inflammation parameters. According to their data, other than weight loss and health improvements, they reported a decrease of the resistome richness, a reduction in the AR gene members, and the diminution of multiple-resistance AR gene carriers (reduced 69%), showcasing a possible novel perspective for the issue (Wu et al, 2016). Another important notion in this study is that, because of the diet type (high carbohydrate), Bifidobacterium was augmented and had few or no ARgenes, whereas the decreased bacteria resembled a minefield with their great burden combined with the final reduction of the resistome.…”

“…It's becoming more than obvious that the gut resistome might be receptive to probiotic and prebiotic supplementation. The preferable result of this manipulation would be the elimination or even the uprooting of Multi-Drug Resistant (MDR) strains and restoration of dysbiosis and gut resilience (Wu et al, 2016;MacPherson et al, 2018).…”

Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis

“…Therefore, how to regulate the gut microbiota of obese individuals by diet [11,12], drugs, or probiotics and prebiotics [13], attracts scienti c attention.…”