Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome.

One hundred and twenty pigs were used to evaluate the effects of different dietary lysine levels on the growth performance, apparent nutrient digestibility, and abundance of cationic amino acid transporter messenger RNA (mRNA) in the small intestine of finishing pigs. Pigs received a low lysine diet (LL, 0.60% lysine), moderate lysine diet (ML, 0.80% lysine) or a high lysine diet (HL, 1.00% lysine) for 28 days. A digestion test was carried out during the third week. Although the apparent nutrient digestibility in pigs fed experimental diets were different (P < 0.05) and the highest when pigs were fed ML diet, diets did not change the growth performance. In the duodenum, mRNA abundance of PepT-1, as detected by real-time RT-PCR, was reduced in the LL diet (P < 0.05). A greater abundance of b(0,+) AT and PepT-1 mRNA was associated with the ML diet (P < 0.05) in the jejunum and ileum, respectively. In the ileum, the HL diet had a lower abundance of CAT-1 mRNA compared with other diets. These results showed that the finishing pigs would gain better nutrient digestibility when the dietary lysine content was 0.80%, and dietary lysine levels influenced the expression of cationic amino acid transporter mRNA in the small intestine of finishing pigs.

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