Abstract
We applied a high-throughput sequencing platform, Ion PGM, for viral detection in fecal samples from adult cows collected in Hokkaido, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.25 ml of fecal specimens (N = 8), and more than 5 μg of cDNA was synthesized. Unbiased high-throughput sequencing using the 318 v2 semiconductor chip of these eight samples yielded 57–580 K (average: 270 K, after data analysis) reads in a single run. As a result, viral genome sequences were detected in each specimen. In addition to bacteriophage, mammal- and insect-derived viruses, partial genome sequences of plant, algal, and protozoal viruses were detected. Thus, this metagenomic analysis of fecal specimens could be useful to comprehensively understand viral populations of the intestine and food sources in animals.
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Acknowledgement
We thank Ms. Yuka Tanaka and Ms. Misa Sato (Kyoto Prefectural University of Medicine, Kyoto, Japan) for technical assistance.
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Motooka, D., Nakamura, S., Hagiwara, K., Nakaya, T. (2015). Viral Detection by High-Throughput Sequencing. In: Uyeda, I., Masuta, C. (eds) Plant Virology Protocols. Methods in Molecular Biology, vol 1236. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1743-3_11
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DOI: https://doi.org/10.1007/978-1-4939-1743-3_11
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