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Substitution by Inosine at the 3′-Ultimate and Penultimate Positions of 16S rRNA Gene Universal Primers

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Abstract

Universal 16S rRNA gene primers (8F and 518R) bearing inosine substitutions at either the 3′-ultimate or the 3′-ultimate and penultimate base positions were exploited for the first time to study the bacterial community associated with coral polymicrobial Black Band Disease (BBD). Inosine-modified universal primer pairs display some shifting in the composition of 16S rRNA gene libraries, as well as expanding the observed diversity of a BBD bacterial community at the family/class level. Possible explanations for the observed shifts are discussed. These results thus point to the need for adopting multiple approaches in designing 16S rRNA universal primers for PCR amplification and subsequent construction of 16S rRNA gene libraries or pyrosequencing in the exploration of complex microbial communities.

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Acknowledgment

This investigation was supported by a grant (1167/07) from the Israel Science Foundation and by Levi Eshkol scholarships (to N.S. and O.H.S.) from the Israeli Ministry of Science, Culture and Sports.

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Authors and Affiliations

  1. Department of Biotechnology Engineering, Ben-Gurion University of the Negev, PO Box 653, Be’er Sheva, 84105, Israel

    Eitan Ben-Dov, Nachshon Siboni, Orr H. Shapiro, Luba Arotsker & Ariel Kushmaro

  2. Achva Academic College, MP Shikmim, 79800, Israel

    Eitan Ben-Dov

  3. National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Be’er-Sheva, 84105, Israel

    Ariel Kushmaro

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  1. Eitan Ben-Dov
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  2. Nachshon Siboni
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  3. Orr H. Shapiro
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  4. Luba Arotsker
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  5. Ariel Kushmaro
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Correspondence to Ariel Kushmaro.

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Ben-Dov, E., Siboni, N., Shapiro, O.H. et al. Substitution by Inosine at the 3′-Ultimate and Penultimate Positions of 16S rRNA Gene Universal Primers. Microb Ecol 61, 1–6 (2011). https://doi.org/10.1007/s00248-010-9718-2

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  • DOI: https://doi.org/10.1007/s00248-010-9718-2

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