摘要
      Carbadox是一种喹喔啉二氮氧化物抗生素，在美国有超过40％的幼猪在饲喂，已证明在体外诱导噬菌体DNA转导;然而，carbadox对猪微生物组功能的影响知之甚少。我们研究了carbadox对猪肠道微生物基因表达（粪便metatranscriptome）和噬菌体种群动态（粪便dsDNA viromes）的体内纵向影响。利用FIGfam（异功能同系物序列）和SEED子系统数据库对微生物宏基因组，转录组和virome序列进行分类推理和基因功能注释。当比较微生物FIGfam注释的beta多样性时，在carbadox引入后2天，对照和carbadox群落是不同的。这种效应是由与carbadox有关的微生物呼吸作用，碳水化合物利用和RNA代谢相关的FIGfamn（n = 66）的较低表达引起的（q <0.1），表明某些种群内具有抑菌或杀菌作用。有趣的是，在加入carbadox后2天（q≤0.07），carbadox处理引起与噬菌体溶解循环的所有阶段相关的更大表达，表明carbadox介导的噬菌体诱导和噬菌体DNA重组。在饲料中连续7天使用carbadox后可降低这些影响，表明有急性影响。另外，病毒包括一些编码四环素，氨基糖苷和β-内酰胺抗生素耐药性的基因，但是这些基因的频率没有随着时间的推移或治疗变化。结果显示由于施用卡巴多，猪肠道细菌生长代谢，前噬菌体诱导以及细菌适体基因的潜在转导均有所下降。

      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.

http://mbio.asm.org/content/8/4/e00709-17.short