Culture-independent analysis of the midgut microbial community Under the learn more limitations posed by working with a rare endemic and protected species with minimum sampling allowed, we analyzed three specimens from which separate clone libraries of 16S rRNA gene amplicons were generated and 87 clones screened. Sequences from the three different guts are labeled with the suffixes A, B, and C, respectively, on Table 2. At this resolution level the number of Dotur-defined species was 29 and the Chao1 estimator [48]

predicted a total number of species of 51,7. We also calculated the estimated FK228 coverage by applying the Good’s index [49] which, at species level, resulted 81.6 %. In order to check with an independent method whether the sampling size had been truly effective in yielding an adequate representation of the community, we compared the cluster analysis dendrogram obtained with the first 46 clones screened (Additional file 1: Material S1 and Additional file 2: Material S2) with those generated with

the whole set of 87 (Figures 4 and 5), from whose comparison it can be observed that the community structure was already fully delineated from selleck the first stepwise subset of randomly selected clones. Further, considering the phylum rank as a more functional assessment of population diversity we run rarefaction curves with OTUs defined at a phylum level similarity threshold (81%). The result obtained indicated a saturating curve and is shown in the supplementary Additional file 3: Figure S3. Figure 4 Maximum likelihood tree of 16S rRNA gene clone sequences recovered of the midgut of Cansiliella servadeii affiliated with gram-positive bacteria. The sequences of GenBank dataset showing the closest

similarity levels have been added. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap ID-8 value shown next to the branches. Only values greater than 50 are indicated. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). Figure 5 Maximum likelihood tree of 16S rRNA gene clone sequences recovered of the midgut of Cansiliella servadeii affiliated with Proteobacteria and Bacteriodetes. Sequences from GenBank dataset showing the closest similarity levels have been added. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. Only values higher than 50 are indicated. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option).