Ultra deep sequencing, discovery of novel viruses. A summer South Dakota time-point (August 5, 2009) was selected for deep sequencing due to high Nosema load and the presence of several common honey bee viruses, including ABPV, BQCV and SBV. All expected microbes (Nosema ceranae, Crithidia mellificae) and viruses were detected [ABPV (39,352 reads aligned by BlastN evalue,1610 27 ), BQCV (2,868 reads) and SBV (4,414 reads)]. In addition, we detected Spiroplasma sequences (70,407 reads) consistent with the presence of both Spiroplasma apis and S. melliferum (66 reads and 44 reads aligning to the RNA PolB gene of each, respectively).