Amoxicillin Increased Functional Pathway Genes and Beta-Lactam Resistance Genes by Pathogens Bloomed in Intestinal Microbiota Using a Simulator of the Human Intestinal Microbial Ecosystem.

Lei Liu,Daqing Mao,Huai Lin,Hongmei Qi,Qing Wang,Siyi Wang,Ranjit Das,Yingang Xue,Yi Luo,Jing Yang

doi:10.3389/fmicb.2020.01213

Abstract

Antibiotics are frequently used to treat bacterial infections; however, they affect not only the target pathogen but also commensal gut bacteria. They may cause the dysbiosis of human intestinal microbiota and consequent metabolic alterations, as well as the spreading of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). In vitro experiments by simulator of the human intestinal microbial ecosystem (SHIME) can clarify the direct effects of antibiotics on different regions of the human intestinal microbiota, allowing complex human microbiota to be stably maintained in the absence of host cells. However, there are very few articles added the antibiotics into this in vitro model to observe the effects of antibiotics on the human intestinal microbiota. To date, no studies have focused on the correlations between the bloomed pathogens caused by amoxicillin (AMX) exposure and increased functional pathway genes as well as ARGs. This study investigated the influence of 600 mg day–1 AMX on human intestinal microbiota using SHIME. The impact of AMX on the composition and function of the human intestinal microbiota was revealed by 16S rRNA gene sequencing and high-throughput quantitative PCR. The results suggested that: (i) AMX treatment has tremendous influence on the overall taxonomic composition of the gut microbiota by increasing the relative abundance of Klebsiella [linear discriminant analysis (LDA) score = 5.26] and Bacteroides uniformis (LDA score = 4.75), as well as taxonomic diversity (Simpson, P = 0.067, T-test; Shannon, P = 0.061, T-test), and decreasing the members of Parabacteroides (LDA score = 4.18), Bifidobacterium (LDA score = 4.06), and Phascolarctobacterium (LDA score = 3.95); (ii) AMX exposure significantly enhanced the functional pathway genes and beta-lactam resistance genes, and the bloomed pathogens were strongly correlated with the metabolic and immune system diseases gene numbers (R = 0.98, P < 0.001) or bl2_len and bl2be_shv2 abundance (R = 0.94, P < 0.001); (iii) the changes caused by AMX were “SHIME-compartment” different with more significant alteration in ascending colon, and the effects were permanent, which could not be restored after 2-week AMX discontinuance. Overall results demonstrated negative side-effects of AMX, which should be considered for AMX prescription.

Highlights

Human intestinal microbiota co-exists in symbiosis with human beings and comprises with about 150 times more genes than the human genome, which makes intestinal microbiota become “another” genome of human beings (Qin et al, 2010)
The effects of 600 mg day−1 AMX treatment on the gut bacterial community were revealed by the 16S rRNA gene sequencing of fecal samples collected from three different vessels designated as ascending, transverse, and descending colon
The simulator of the human intestinal microbial ecosystem (SHIME) model was stably operated in this study because the predominant phyla of Bacteriodetes, Proteobacteria, Synergistetes, and Firmicutes in the gut microbiome was previously demonstrated Yu et al (2016)

Summary

Introduction

Human intestinal microbiota co-exists in symbiosis with human beings and comprises with about 150 times more genes than the human genome, which makes intestinal microbiota become “another” genome of human beings (Qin et al, 2010). Human intestinal microbiota has been demonstrated to provide numerous important functions for the human health, including fermentation of indigestible dietary polysaccharides, synthesis of essential amino acids, and vitamins, modulation of the immune function and protection from the pathogens, as well as metabolism of the xenobiotic drugs (Chow et al, 2010; Yatsunenko et al, 2012; Cabreiro et al, 2013). Both human and veterinary antibiotics were detected in the collective gut of the Chinese population through our previous research (Wang et al, 2020). No studies have suggested the bloom of K. pneumoniae caused by AMX exposure contributed to the increase of functional pathway genes and beta-lactam resistance genes

Methods

Results

Conclusion