ARGs	antibiotic resistance genes
LPS	lipopolysaccharides
PG	peptidoglycan
STEC	Shiga toxin-producing Escherichia coli
HUS	hemolytic-uremic syndrome
IBD	inflammatory bowel disease
Zot	Zonula occludens toxins
BSIs	bloodstream infections
CRISPR-Cas	clustered regularly interspersed short palindromic repeats-CRISPR-associated proteins
SaPI1	Staphylococcus aureus pathogenicity island-1
VG	virulent gene
APEC	avian pathogenic E. coli
OMV	outer membrane vesicles
ESKAPE pathogens	Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.
eDNA	extracellular DNA