The MD 257 template for amplicon generation was based on the total RNA fraction depleted of poly(A) + RNA (see ''Preparation of genomic DNA, total RNA, poly(A)+RNA and cDNA''). The supernatant was cleared of small RNA molecules using the MEGAclear Kit (Applied Biosystems, Ambion, CA) and depleted of host ribosomal RNA performing two cycles of the MICROBEnrich (Applied Biosystems, Ambion, CA) protocol. Subsequent depletion of bacterial ribosomal RNA yielded an RNA sample enriched for bacterial transcripts (MICROBExpress, Applied Biosystems, Ambion, CA), which was subjected to cDNA synthesis (Just cDNA Double-Stranded cDNA Synthesis Kit, Stratagene, CA) after elimination of residual contaminating genomic DNA using the Turbo DNA-free Kit (Applied Biosystems, Ambion, CA).