biostudies-literatureUnknown54(1)Rutjens SCephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg^-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg^-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four differeVeterinary research45https://www.ebi.ac.uk/biostudies/studies/S-EPMC10242799biostudies-literatureCefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur.PMC10242799Sauer JRutjens SCroubels SVereecke NDevreese MfalseCefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur.Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg^-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg^-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four differe2023-01-01T00:00:00Z2023 Jun2026-05-29T06:35:31.631Z2025-04-22T14:01:06.26ZS-EPMC102427993728070810.1186/s13567-023-01176-8