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Study

Study Name: Swine fecal microbial communities from Iowa, USA, under antibiotic and non-antibiotic feed

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Biosamples

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Biosamples: 4 Seq. Projects: 4
STUDY NAME
GOLD Study ID Gs0045367
Study Name Swine fecal microbial communities from Iowa, USA, under antibiotic and non-antibiotic feed
Other Names Fecal microbiome of Swine under antibiotic and non-antibiotic feed
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 367
Legacy GOLD ID Gm00215
Added By torey looft on 2009-06-18
Last Modified By Michelle Isbandi on 2014-05-13
STUDY DESCRIPTION
PI torey looft
Description 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.
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GOLD CLASSIFICATION
Ecosystem Host-associated
Ecosystem Category Mammals
Ecosystem Type Digestive system
Ecosystem Subtype Large intestine
Specific Ecosystem Fecal
Metagenomic Study Yes
STUDY COMPOSITION
Number of Biosamples 4
Number of Organisms 0
Number of Seq Projects 4
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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