Analysis of community composition determined using different recovery and sequencing strategies. A) Results of analysis of Subjects 3 and 7 are shown comparing sequencing using 454/Roche GS FLX versus Titanium, and use of different variable region primers. To characterize the Titanium sequencing method, 295,946 454 Titanium sequence reads were used (Additional File 2). The 454 GS FXL reads are from the samples in Additional File 1. The percentages of different bacterial families are compared in bar graphs. "Seq. Method" indicates GS FLX ("X") or Titanium ("T"). The families present are indicated in the key beside the graphs. "Var. Region" indicates the 16S rRNA gene region amplified by each primer set (sequences used are in Additional File 4). The * indicates slightly different versions of the primers used as specified in Additional File 4. B) Percentages of sequences assigned for each primer set as a function of taxonomic level. C) Summary of regions amplified and regions sequenced for each primer set. Gray indicates the regions amplified, dark gray indicates the regions sequenced, light gray indicates regions amplified but not sequenced.