Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves.
Milk containing antibiotics is used as cost-effective feed for calves, which may lead to antibiotic residues-associated food safety problems. This study aims to investigate the influence of antibiotics on rumen microbes. Through metagenomic sequencing, the rumen microbial communities of calves fed with pasteurized milk containing antibiotics (B1), milk containing antibiotics (B2) and fresh milk (B3) were explored. Each milk group included calves in 2 (T1), 3 (T2) and 6 (T3) months of age. Using FastQC software and SOAPdenovo 2, the filtered data, respectively, were performed with quality control and sequence splicing. Following KEGG annotation was conducted for the uploaded sequences using KAAS software. Using R software, both species abundance analysis and differential abundance analysis were performed. In the B1 samples, the species abundance of Bacteroidetes gradually decreased along with the extension of feeding time, while that of Fibrobacteres gradually increased. The species abundances of Proteobacteria (p value = 0.01) and Spirochaetes (p value = 0.03) had significant differences among T1, T2 and T3 samples. Meanwhile, only the species abundance of Spirochaetes (p value = 0.04) had significant difference among B1, B2 and B3 samples. Cell cycle involving GSK3β, CDK2 and CDK7 was significantly enriched for the differentially expressed genes in the T1 versus T2 and T1 versus T3 comparison groups. Milk containing antibiotics might have a great influence on these rumen microbes and lead to antibiotic residues-associated food safety problems. Furthermore, GSK3β, CDK2 and CDK7 in rumen bacteria might affect milk fat metabolism in early growth stages of calves.
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Wei
W
Li
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Yunsheng
Y
Han
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Xue
X
Yuan
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Guan
G
Wang
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Zhibo
Z
Wang
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Qiqi
Q
Pan
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China.
Yan
Y
Gao
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China. yongliqiu12@sina.com.
Yongli
Y
Qu
D000821:Animal Feed / Q000032:analysis; D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics; D044822:Biodiversity; D002417:Cattle; D000069196:Gastrointestinal Microbiome / Q000187:drug effects*; D016680:Genome, Bacterial / Q000235:genetics*; D056186:Metagenomics; D008892:Milk / Q000737:chemistry*; D011156:Population Density; D012417:Rumen / Q000382:microbiology*
D000900:Anti-Bacterial Agents
Abundance analysis; Differential analysis; Milk containing antibiotics; Newborn calf; Rumen microbial community