The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome

Abstract

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration.

The genera of bacteriophages and their receptors are the major determinants of host range

“…This study represents a novel holistic approach to identify the host range determinants of phages infecting Salmonella by correlating phage characteristics with the host ranges using a multivariate analysis. NMDS was previously applied to identify patterns among molecular fingerprinting data (Ramette, ) and in microbial ecology, as a valid instrument to identify clusters and correlations within microbial and viral communities (Mason et al ., ; Niederdorfer et al ., ; Wang et al ., ; Johnson et al ., ). Here we expanded the use of NMDS to investigate phage–host interaction and ecology of phages infecting Salmonella .…”

A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research

“…Low levels of antibiotics in feed have been used as growth promotors which also impact the microbiota around this critical weaning period and thereafter ( 40 ). Additionally, antibiotic resistance genes derived from phages within the pig microbiota pose a serious problem not only for pig health but also that of humans ( 41 ). Post-weaning diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) as well as Salmonella enterica serovar Typhimurium is a major cause of death of piglets.…”

Bacterial Whack-a-Mole: Reconsidering the Public Health Relevance of Using Carbadox in Food Animals

“…These reports have been accompanied by heated policy debates where stakeholders have sought to define antibiotic applications into categories, such as “necessary versus unnecessary” or “therapeutic versus nontherapeutic” and have tried to categorize antibiotics by their relative importance to human medicine ( 7 ). A recent mBio study by Johnson et al ( 8 ) investigating the impact of carbadox on the swine gut microbiome provides an important example of how even antimicrobial agents with no foreseeable utility in human medicine may pose a public health threat when used in food animals.…”