Metaproteomic analysis of gut resistome in the cecal microbiota of fattening pigs raised without antibiotics

Abstract

Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (controls, CTRL). The top three relative abundant microbials in both groups were Escherichia coli, Ruminococcus and Lactobacillus, followed by Bacteroides and Bifidobacterium. E. coli, Lactobacillus and Bacteroides were found to be increased in the CTRL group, whereas Ruminococcus and Clostridium were greater in the ABF group. The highest abundance of antibiotic resistance proteins (>10 log2 expression levels, ELs) was tetracycline resistance (TetR) and aminoglycoside resistance (AMGR) proteins found in Bacteroides with a significant increase in the CTRL group. High TetR (5.32 ELs) was found in Ruminococcus in the CTRL group although pigs in both groups have never received tetracycline, possibly reflecting the influence of environments in farms. In E. coli, AMGR and β-Lactamase family were observed in both groups (3-6 ELs), whereas multidrug resistance proteins were significantly expressed in the CTRL group (~3 ELs). In the ABF group, CRISPR-associated endonucleases Cas1 and Cas9, functioned to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, with 8.6 and 4.15 ELs, respectively. In conclusion, this study demonstrated that CRISPR-associated endonucleases were markedly observed in the ABF group, whereas higher levels of TetR, AMGR and multidrug resistance proteins were markedly observed in dominant bacterial species in the CTRL group.