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Variability in the relative human DNA content during metagenomic analysis of gut microbiota

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Abstract

The comparative study of seven different methods for extraction of total DNA from human feces has been carried out. All these methods are recommended in protocols for metagenomic analysis of human gut microbiota. The relative abundance of human DNA in such samples registered by shotgun sequencing on a SOLiD 4 genetic analyzer has been investigated. It was shown that either initial amount of feces or a method applied for total DNA extraction insignificantly influenced the final relative human DNA proportion, which did not exceed 1% in healthy people. Invariance of this parameter allows to consider the increased proportion of human DNA in metagenomic samples as a potential marker of inflammatory bowel diseases.

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References

  1. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M’Rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D., and Bork, P., Nature, 2011, vol. 473, pp. 174–180.

    Article  CAS  Google Scholar 

  2. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D.R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J.M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H.B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Jian, M., Zhou, Y., Li, Y., Zhang, X., Qin, N., Yang, H., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., and Ehrlich, S.D., Nature, 2010, vol. 464, pp. 59–65.

    Article  CAS  Google Scholar 

  3. Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., Peng, Y., Zhang, D., Jie, Z., Wu, W., Qin, Y., Xue, W., Li, J., Han, L., Lu, D., Wu, P., Dai, Y., Sun, X., Li, Z., Tang, A., Zhong, S., Li, X., Chen, W., Xu, R., Wang, M., Feng, Q., Gong, M., Yu, J., Zhang, Y., Zhang, M., Hansen, T., Sanchez, G., Raes, J., Falony, G., Okuda, S., Almeida, M., LeChatelier, E., Renault, P., Pons, N., Batto, J.M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Yang, H., Wang, J., Ehrlich, S.D., Nielsen, R., Pedersen, O., and Kristiansen, K., Nature, 2012, vol. 490, pp. 55–60.

    Article  CAS  Google Scholar 

  4. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R., and Gordon, J.I., Nature, 2009, vol. 457, pp. 480–484.

    Article  CAS  Google Scholar 

  5. Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., Heath, A.C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J.G., Lozupone, C.A., Lauber, C., Clemente, J.C., Knights, D., Knight, R., and Gordon, J.I., Nature, 2012, vol. 486, pp. 222–227.

    CAS  Google Scholar 

  6. Angelakis, E., Armougom, F., Million, M., and Raoult, D., Future Microbiol., 2012, vol. 7, pp. 91–109.

    Article  Google Scholar 

  7. Donatin, E. and Drancourt, M., BMC Res. Notes, 2012, vol. 5, p. 702.

    Article  CAS  Google Scholar 

  8. Gomez-Alvarez, V., Teal, T.K., and Schmidt, T.M., ISME J., 2009, vol. 3, pp. 1314–1317.

    Article  Google Scholar 

  9. Smith, B., Li, N., Andersen, A.S., Slotved, H.C., and Krogfelt, K.A., Open Microbiol. J., 2011, vol. 5, pp. 14–17.

    Article  CAS  Google Scholar 

  10. Yuan, S., Cohen, D.B., Ravel, J., Abdo, Z., and Forney, L.J., PLoS One, 2012, vol. 7, e33865.

    Article  Google Scholar 

  11. Wesolowska-Andersen, A., Bahl, M.I., Carvalho, V., Kristiansen, K., Sicheritz-Ponten, T., Gupta, R., and Licht, T.R., Microbiome, 2014, vol. 2, p. 19.

    Article  Google Scholar 

  12. Apajalahti, J.H., Sarkilahti, L.K., Maki, B.R., Heikkinen, J.P., Nurminen, P.H., and Holben, W.E., Appl. Environ. Microbiol., 1998, vol. 64, pp. 4084–4088.

    CAS  Google Scholar 

  13. Bahl, M.I., Bergstrom, A., and Licht, T.R., FEMS Microbiol. Lett., 2012, vol. 329, pp. 193–197.

    Article  CAS  Google Scholar 

  14. Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V.K., Srivastava, T.P., Taylor, T.D., Noguchi, H., Mori, H., Ogura, Y., Ehrlich, D.S., Itoh, K., Takagi, T., Sakaki, Y., Hayashi, T., and Hattori, M., DNA Res., 2007, vol. 14, pp. 169–181.

    Article  CAS  Google Scholar 

  15. Tyakht, A.V., Kostryukova, E.S., Popenko, A.S., Belenikin, M.S., Pavlenko, A.V., Larin, A.K., Karpova, I.Y., Selezneva, O.V., Semashko, T.A., Ospanova, E.A., Babenko, V.V., Maev, I.V., Cheremushkin, S.V., Kucheryavyy, Y.A., Shcherbakov, P.L., Grinevich, V.B., Efimov, O.I., Sas, E.I., Abdulkhakov, R.A., Abdulkhakov, S.R., Lyalyukova, E.A., Livzan, M.A., Vlassov, V.V., Sagdeev, R.Z., Tsukanov, V.V., Osipenko, M.F., Kozlova, I.V., Tkachev, A.V., Sergienko, V.I., Alexeev, D.G., and Govorun, V.M., Nat. Commun., 2013, vol. 4, p. 2469.

    Article  Google Scholar 

  16. Yang, J.L., Wang, M.S., Cheng, A.C., Pan, K.C., Li, C.F., and Deng, S.X., World J. Gastroenterol., 2008, vol. 14, pp. 2872–2876.

    CAS  Google Scholar 

  17. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L., Genome Biol., 2009, vol. 10, R25.

  18. Vereecke, L., Beyaert, R., and van Loo, G., Trends Mol. Med., 2011, vol. 17, pp. 584–593.

    Article  CAS  Google Scholar 

  19. Nechvatal, J.M., Ram, J.L., Basson, M.D., Namprachan, P., Niec, S.R., Badsha, K.Z., Matherly, L.H., Majumdar, A.P., and Kato, I., J. Microbiol. Methods, 2008, vol. 72, pp. 124–132.

    Article  CAS  Google Scholar 

  20. Zhang, B.W., Li, M., Ma, L.C., and Wei, F.W., Biochem. Genet., 2006, vol. 44, pp. 503–512.

    CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Physical-Chemical Medicine, ul. Malaya Pirogovskaya 1a, Moscow, 119435, Russia

    E. S. Kostryukova, I. Y. Karpova, A. K. Larin, A. C. Popenko, A. V. Tyaht & E. N. Ilina

  2. Kazan Federal University, Kazan, Russia

    E. S. Kostryukova, I. Y. Karpova & A. K. Larin

  3. Moscow Institute of Physics and Technology, Moscow, Russia

    E. S. Kostryukova

Authors
  1. E. S. Kostryukova
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  2. I. Y. Karpova
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  3. A. K. Larin
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  4. A. C. Popenko
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  5. A. V. Tyaht
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  6. E. N. Ilina
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Correspondence to E. S. Kostryukova.

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Original Russian Text © E.S. Kostryukova, I.Y. Karpova, A.K. Larin, A.C. Popenko, A.V. Tyaht, E.N. Ilina, 2015, published in Biomeditsinskaya Khimiya.

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Kostryukova, E.S., Karpova, I.Y., Larin, A.K. et al. Variability in the relative human DNA content during metagenomic analysis of gut microbiota. Biochem. Moscow Suppl. Ser. B 9, 290–295 (2015). https://doi.org/10.1134/S1990750815030038

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  • DOI: https://doi.org/10.1134/S1990750815030038

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