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 antibiotics in feed (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 viromes of medicated swine over that in the viromes of nonmedicated swine, demonstrating the induction of prophages with antibiotic treatment. Phage-bacterium 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.

Serpulina hyodysenteriae B204 cells treated with mitomycin (20 g of mitomycin/ml of culture broth) lysed and released bacteriophages. Bacteriophage particles, precipitated by using polyethylene glycol and purified by CsCl density gradient ultracentrifugation, had a buoyant density of 1.375 g/cm 3 and consisted of a head (45-nm diameter) and an ultrastructurally simple (noncontractile) tail (64 by 9 nm) composed of at least 13 proteins with molecular masses ranging between 13 and 101 kDa. The purified bacteriophage has been designated VSH-1 (VSH for virus of S. hyodysenteriae). VSH-1 was incapable of lytic growth on any of five intestinal spirochete strains, representing three Serpulina species. VSH-1 nucleic acid was determined to be approximately 7.5 kb in size and to be linear, double-stranded DNA based on differential staining with acridine orange, DNase I sensitivity, electrophoretic mobility, and contour length as measured by electron microscopy. Phage DNA digested by the restriction enzymes SspI, AseI, EcoRV, and AflII gave electrophoretic banding patterns nearly identical to those of digested chromosomal DNA from S. hyodysenteriae. Additionally, VSH-1 DNA fragments hybridized with probes complementary to S. hyodysenteriae chromosomal genes nox and flaA1. When purified bacteriophages induced from cultures of S. hyodysenteriae A203 (⌬flaA1 593-762::cat) were added to growing cells of strain A216 (⌬nox 438-760::kan), transductants (Cm r Km r ) were obtained at a frequency of 1.5 ؋ 10 ؊6 per phage particle (enumerated by electron microscopy). These findings indicate that induced VSH-1 virions package DNA of S. hyodysenteriae and are capable of transferring host genes between cells of that spirochete. To our knowledge, this is the first report of genetic transduction of a spirochete.Natural gene transfer mechanisms (conjugative plasmids and transducing bacteriophages) have not been demonstrated for spirochetes. Indirect evidence of lateral gene transfer has been obtained for Borrelia spp. (16). The existence of DNAfilled membrane vesicles on the surfaces of Borrelia burgdorferi cells has been reported, although their possible role in gene transfer is unknown (7). In addition, several extrachromosomal elements have been identified in B. burgdorferi, and an extrachromosomal plasmid of 2.6 kb has been isolated from Treponema denticola and characterized (10,25). In cultures of various spirochetes, bacteriophages have been observed free, attached to cells, or within cells as noted previously (9). Three lytic phages of Leptospira biflexa have been isolated and characterized (24). However, to our knowledge, there is no evidence that these three phages play a role in gene transfer.The spirochete Serpulina hyodysenteriae causes swine dysentery, an enteric disease producing a severe mucohemorrhagic diarrhea in infected swine (8). Potential genetic transfer elements for S. hyodysenteriae have been identified. Ritchie and colleagues observed bacteriophages with the same morphology in 18 different cultures of S. hyodysente...

VSH-1 is a mitomycin C-inducible prophage of the anaerobic spirochete Brachyspira hyodysenteriae. Purified VSH-1 virions are noninfectious, contain random 7.5-kb fragments of the bacterial genome, and mediate generalized transduction of B. hyodysenteriae cells. In order to identify and sequence genes of this novel gene transfer agent (GTA), proteins associated either with VSH-1 capsids or with tails were purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal amino acid sequences of 11 proteins were determined. Degenerate PCR primers were designed from the amino acid sequences and used to amplify several VSH-1 genes from B. hyodysenteriae strain B204 DNA. A clone library of B. hyodysenteriae B204 DNA was subsequently screened by Southern hybridization methods and used to identify and sequence overlapping DNA inserts containing additional VSH-1 genes. VSH-1 genes spanned 16.3 kb of the B. hyodysenteriae Brachyspira hyodysenteriae is an anaerobic spirochete and the etiologic agent of swine dysentery, a severe, mucohemorrhagic intestinal disease afflicting animals in the postweaning period of growth (20). B. hyodysenteriae cells contain a defective prophage, VSH-1, which is induced when mitomycin C is added to cultures of growing cells (27). This prophage has been purified and characterized previously (28). VSH-1 particles resemble virions in morphology but, with a head diameter of 45 nm and a tail length of 64 nm, are substantially smaller.VSH-1 virions contain random 7.5-kb fragments of host genomic DNA (28), making it difficult to identify VSH-1 genes. Purified virions are "noninfectious," that is, they do not lyse spirochete cells when added to cultures of B. hyodysenteriae or of other Brachyspira species. VSH-1 transfers bacterial genes between B. hyodysenteriae cells (28, 52) and has likely contributed to the recombinant population structure of B. hyodysenteriae (55). This generalized transduction activity of VSH-1 is useful for constructing B. hyodysenteriae mutant strains (35).VSH-1 is the first natural gene transfer mechanism to be described for a spirochete.The ability to recognize VSH-1-specific genes would be a major advance for investigating intracellular and intercellular activities of VSH-1 and for evaluating its ecological significance to its host bacterium. To overcome the inability to identify distinct VSH-1 genes carried by virions, structural protein genes were identified from the sequences of VSH-1 head and tail proteins. Genes for endolysin and holin proteins, proteins enabling the release of bacteriophage from bacterial cells, were discovered during nucleotide sequence analyses. Recombinant endolysin was shown to degrade peptidoglycan. Based on its genome and biological properties, VSH-1 resembles prophagelike gene transfer agents (GTA) reported for other bacteria (3,32,37,46,56). MATERIALS AND METHODSSeparation of VSH-1 whole virions and tailless heads. VSH-1 particles were harvested from B. hyodysenteriae strain B204 cultures (400 ml) in NT broth 7 to 8 h after...