title: Substitution by inosine at the 3'-ultimate and penultimate positions of 16S rRNA gene universal primers.
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.
authors.affiliation: Department of Biotechnology Engineering, Ben-Gurion University of the Negev, PO Box 653, Be'er Sheva, 84105, Israel.
authors.forename: Eitan
authors.initials: E
authors.lastname: Ben-Dov
authors.forename: Nachshon
authors.initials: N
authors.lastname: Siboni
authors.forename: Orr H
authors.initials: OH
authors.lastname: Shapiro
authors.forename: Luba
authors.initials: L
authors.lastname: Arotsker
authors.forename: Ariel
authors.initials: A
authors.lastname: Kushmaro
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000382:microbiology; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics*; D004463:Ecology / Q000379:methods*; D015723:Gene Library; D005821:Genetic Techniques; D007288:Inosine / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D007288:Inosine