Project Name Swine fecal viromes with and without in-feed antibiotics 
Domain (1) bacteria
Investigators (1)
Institution NADC/USDA
Project Code CAM_P_0000909
Project Type metagenome
Publications (1)


Antibiotics are a cost-effective tool for improving feed-efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two in-feed antibiotics (carbadox and ASP250 [chlortetracycline, sulfamethazine, and penicillin]) on swine intestinal phage metagenomes (viromes). We also monitored the bacterial communities using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of phage integrase-encoding genes was significantly increased in the medicated versus non-medicated viromes, demonstrating the induction of prophages with antibiotic treatment. Phage-bacteria population dynamics were also examined. We observed a decrease in the relative abundance of Streptococcus bacteria (prey) when Streptococcus phages (predators) were abundant, supporting the kill-the-winner ecological model of population dynamics in the swine fecal microbiome. The data show that gut ecosystem dynamics are influenced by phages, and that prophage induction is a collateral effect of in-feed antibiotics.


No assemblies.


Sample Name PI Desc
RL1_NonmedDay0_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL2_SubtherDay0_virome NA pooled feces from 6 pigs of like treatment and time - pre-subtherapeutic amounts of carbadox in feed
RL3_NonmedDay14_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL4_SubtherDay14_virome NA pooled feces from 6 pigs of like treatment and time - 14 days of subtherapeutic carbadox in feed
RL5_TherDay0_virome NA pooled feces from 6 pigs of like treatment and time - pre-therapeutic amounts of carbadox in feed
RL6_NonmedDay17_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL7_1_TherDay3_virome NA pooled feces from 6 pigs of like treatment and time - 3 days of therapeutic amounts of carbadox in feed
RL8_1_NonmedDay42_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL9_1_TherDay28_virome NA pooled feces from 6 pigs of like treatment and time - 21 day sof therapeutic amounts of carbadox in feed
RL7_2_NonmedDay56_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL8_2_ASP250Day0_virome NA pooled feces from 6 pigs of like treatment and time - pre-ASP250 in feed
RL9_2_NonmedDay64_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL10_ASP250Day8_virome NA pooled feces from 6 pigs of like treatment and time - 8 days of ASP250 in feed
RL11_NonmedDay70_virome NA pooled feces from 6 pigs of like treatment and time - nonmedicated feed
RL12_ASP250Day14_virome NA pooled feces from 6 pigs of like treatment and time - 14 days of ASP250 in feed