Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

Abstract

Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production.

Fig. 1.

RDP classification of the sequences at phylum and class levels. RDP classifier was used with a bootstrap cutoff of 50. Pooled sequence reads from all 10 pigs in each group were used. (A) RDP classification of the sequence reads from farm 1 at phylum level. (B) RDP classification of the sequence reads from farm 2 at phylum level. (C) RDP classification of the sequence reads from farm 1 at class level. (D) RDP classification of the sequence reads from farm 2 at class level.

Fig. 2.

Differentially abundant genera between tylosin and no-tylosin groups. Pigs in the tylosin groups received tylosin in their feed during the whole experimental period (10–22 wk of age), whereas pigs in the no-tylosin groups did not receive tylosin. The heat map was created using genus based results after normalization. Yellow indicates abundant genera and black indicates less abundant genera. Each column represents groups and each row indicates genus. F1 and F2 indicate farm 1 and farm 2, respectively, and T and NT represent each tylosin group and no-tylosin group. (A) Differentially abundant genera were indicated by arrows and color-coded. Genus names indicate by the color their relationship to the phylum level. (B) Twelve differentially abundant genera and unclassified genera.

Fig. 3.

Distribution of OTUs in the two treatment groups in farm 1. The heat map for farm 1 was created using OTUs with an OTU definition at a similarity cutoff of 95%. Each column represents groups and each row indicates OTUs. OTUs were sorted with the most abundant OTUs displayed at the top and the least abundant OTUs at the bottom. T and NT indicate tylosin and no-tylosin group, respectively, and numbers indicates weeks of age. Abundant OTUs were red color-coded and white blanks indicate missing OTUs.

Fig. 4.

Distribution of OTUs in the two treatment groups in the farm 2. The heat map for the farm 2 was created using OTUs with an OTU definition at a similarity cutoff of 93%. Each column represents groups and each row indicates OTUs. OTUs were sorted with the most abundant OTUs displayed at the top and the least abundant OTUs at the bottom. T and NT indicate tylosin and no-tylosin group, respectively, and numbers indicates weeks of age. Abundant OTUs were red color-coded and white blanks indicate missing OTUs.