Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

Abstract

In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency, and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. Furthermore, there are concerns that antibiotic feed additives may expand the antibiotic resistome of feedlot cattle by enriching antimicrobial resistance genes in pathogenic and nonpathogenic bacteria in the gut microbiota. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and untreated animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level however treated cattle had reduced the abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachanospira in the gut of treated steers was reduced. This may impact the ability of these animals to exclude pathogens from the gut. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

Effects of brewers’ spent grain protein hydrolysates on gas production, ruminal fermentation characteristics, microbial protein synthesis and microbial community in an artificial rumen fed a high grain diet

“…Notwithstanding, the effects of BSG protein hydrolysates on ruminal microbiome are not fully understood. Meanwhile, our results revealed that monensin greatly reduced the diversity of FPA microbial community were in agreement with previous in vitro [46] and in vivo [47,48] studies.…”

“…However, the addition of antibiotics reduced (P < 0.05) the RA of Firmicutes and Bacteroidetes and enhanced (P < 0.05) the RA of Proteobacteria at the phylum level. For all treatments, phyla of Firmicutes, Bacteroidetes and Proteobacteria were the most predominant, accounting for approximately 90% of the microbial biomass in FPA, which was consistent with the sequencing results of liquid associated microbial community of in vitro [46] and in vivo studies [47,48]. This suggested that phyla of Firmicutes, Bacteroidetes and Proteobacteria were predominant in both the liquid and particle-associated ruminal microbiome.…”

“…The rumen microbial community is usually dominated by Prevotella at genus level when fed high grain diets [54]. Members of Prevotella are able to utilise various nutrients such as starch, proteins and noncellulosic polysaccharides [55,56], and to convert lactate into propionate to prevent accumulation of the former [48]. Moreover, as Prevotella are also H 2 -consuming bacteria in addition to Selenomonas [57], the reduced H 2 with FlaH and AlcH was likely due to the increased RA of genus Prevotella.…”

Host genetics affected the resistome and its expression patterns in the rumen of beef cattle raised without antibiotics used in humans

“…In addition, tetracycline, MLS, and aminoglycoside classes of resistance were also predominant in fecal samples of feedlot cattle raised without antibiotic [33], suggesting that the pro les of ARG are consistent in different locations of digestive tract of ruminants. We detected broader ARG pro les (12 classes and 62 individual ARGs) in the rumen of beef cattle not administered antimicrobials used in human medicine than previously reported by Thomas et al [12] who studied the beef cattle supplemented with tylosin. Based on the analysis of 5 ruminal samples in cattle supplemented with monensin and tylosin, Thomas et al [12] did not detect aminoglycoside or β-lactam resistance genes in any sample.…”

“…Numerous antimicrobial resistance genes (ARGs) encode for resistance to an array of antimicrobials [9] that bacteria produce to compete and survive within complex ecological systems [10]. Recent efforts have documented the rumen resistome, a vast reservoir of ARGs that could be acquired by human commensals and pathogens [11] in beef cattle [12][13][14], dairy cattle [14], and sheep [15], and revealed that ARGs can be affected by diet [13] or antibiotic treatment [12]. However, these studies only assessed ARGs at genomic level using metagenomics based on short-read sequencing [12,13,15] or long-read sequencing [14] and with a limited number of animals were involved.…”