Metagenomic Sequencing Analysis of the Effects of Colistin Sulfate on the Pig Gut Microbiome

Abstract

The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease. However, despite its promise, using metagenomic sequencing to explore the effects of colistin on gut microbiome composition in pig has not been reported. Herein, we evaluated the roles of colistin in gut microbiome modulation in pigs. Metagenomic analysis demonstrated that overall microbial diversity was higher in the colistin group compared with the control group. Antibiotic Resistance Genes Database analysis demonstrated that following colistin treatment, expression levels of tsnr, ant6ia, tetq, oleb, norm, ant3ia, and mexh were significantly upregulated, indicating that colistin may induce transformation of antibiotic resistance genes. Colistin also affected the microbiome distribution patterns at both genus and phylum levels. In addition, at the species level, colistin significantly reduced the abundance of Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea and enhanced the abundance of Treponema succinifaciens and Acidaminococcus fermentans compared to the control group. Gene Ontology analysis demonstrated that following treatment with colistin, metabolic process, cellular process, and single-organism process were the dominant affected terms. Kyoto Encyclopedia of Genes and Genomes analysis showed that oxidative phosphorylation, protein processing in endoplasmic reticulum, various types of N-glycan biosynthesis, protein processing in endoplasmic reticulum, pathogenic Escherichia coli infection, and mitogen-activated protein kinase signaling pathway–yeast were the dominant signaling pathways in the colistin group. Overall, our results suggested that colistin affects microbial diversity and may modulate gut microbiome composition in pig, potentially providing novel strategy or antibiotic rationalization pertinent to human and animal health.

Effect of feeding raw potato starch on the composition dynamics of the piglet intestinal microbiome

“…We speculated that RPS could improve intestinal homeostasis and thereby support growth performance by preventing diarrhea in weaned and growing pigs. Recently developed metagenomics technologies yield high-quality and high-throughput sequencing results, which can facilitate the analysis of the composition, abundance, and function of porcine intestinal microbial communities [ 11 , 15 ], and have enabled the investigation of the effect of RPS on animal and human gut microbiota [ 11 , 14 , 16 – 18 ]. Therefore, the aim of the present study was to investigate the effects of two different concentrations of RPS feeds on growth performance, SCFA production, and the composition of intestinal microbial communities of weaned piglets.…”

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

“…To determine how widely distributed the species/strains represented by the MAGs in the present study are among pigs from other studies in different geolocations, the presence and relative abundance of these MAGs within publicly available swine gut metagenomic data sets was assessed. These metagenomic sequences were from 626 fecal and cecal content samples within nine studies representing 13 different counties ( 14 – 22 ) (Table S6). On average, 45.5% ± 0.4% SEM of these metagenomic sequences mapped to one of the MAGs from the present study (Table S7).…”

Dissecting the Effect of Berberine on the Intestinal Microbiome in the Weaned Piglets by Metagenomic Sequencing

“…The microbes in the gut are more numerous than the body’s other organs. The complexity of the environment and microorganisms results in less rigorous data analysis using traditional methods; however, the development of metagenomics and high-throughput sequencing technology has promoted the study of gut microbes considerably ( Walker et al, 2014 ; Guo et al, 2021 ). In the present study, a major part of raw data (>99%) contributed to the clean data, and the Q20 (%) was more than 96% in the gut microbiomes of the control and berberine groups.…”