BackgroundSeagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.ResultsThe metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular,Shigella sonnei,Escherichia albertii,Klebsiella pneumonia,Salmonella entericaandShigella flexneriwere the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such asadeL,evgS,tetA,PmrF, andevgAaccumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded toEnterobacteriaceaeandCampylobacteriaceaebacterial hosts respectively.Caliciviridae,CoronaviridaeandPicornaviridaewere the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs ofGammacoronavirusandDeltacoronavirushad highly similarity with somecoronavirusreferences.ConclusionsIn general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09379-1.