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Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves

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Abstract

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.

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Acknowledgements

This study was funded by National Natural Science Foundation of China (Grant Number 31340031); Synergetic Innovation Center of Food Safety and Nutrition, National Key Technologies R&D Program (Grant Numbers 2012BAD12B05-1 and 2012BAD12B02).

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Authors and Affiliations

  1. College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Street, Daqing, 163319, Heilongjiang, China

    Wei Li, Yunsheng Han, Xue Yuan, Guan Wang, Zhibo Wang, Qiqi Pan, Yan Gao & Yongli Qu

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  1. Wei Li
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  2. Yunsheng Han
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  3. Xue Yuan
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  4. Guan Wang
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  7. Yan Gao
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  8. Yongli Qu
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Correspondence to Yongli Qu.

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Communicated by Yusuf Akhter.

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Li, W., Han, Y., Yuan, X. et al. Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves. Arch Microbiol 199, 433–443 (2017). https://doi.org/10.1007/s00203-016-1311-8

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  • DOI: https://doi.org/10.1007/s00203-016-1311-8

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