ANALYSIS

Data from individual HOMIM signals are translated to a “bar code” format and normalized by comparing individual signal intensities to the average of signals from universal probes (Fig. 1).

Figure 1: Bacterial profile map or "bar code" of clinical samples from a single mouth. (A) Bacterial profiles of over 200 bacterial species comparing 10 samples from a single mouth. (B) Magnified from (A) illustrating dendrogram of cluster analysis and partial list of bacterial species tested. Band intensities represent relative bacterial proportions.

The bands correspond to presence or absence and band intensities are scored as 0, 1+, 2+, 3+, 4+ or 5+. These data will be available to clients as Excel tables. For details, see "Data Analysis Procedure of the HOMIM online tool." Thus, more intense bands reflect higher proportions of a given species. Differences or similarities in profiles can readily be seen. Samples are subsequently subjected to cluster analysis (Dr. George Chen). The dendrogram of the cluster analysis (top of figure) is shown more clearly in Figure 1B. The cluster program sorts the profiles into the appropriate clusters. It is noteworthy in this analysis of sites from a single mouth that samples 4 and 5, which clustered tightly together, were samples from the left side of the tongue and the right side of the tongue, illustrating the level of reproducibility with the assay.  These data are what you would expect to see.

Consequently, bacterial profiles of 100's of HOMIMs of clinical samples can be readily analyzed as shown in Figure 2.

Figure 2: Bacterial profiles of 461 bacterial taxa (representing about 300 species) comparing subgingival plaque from 105 healthy sites in periodontally healthy subjects (n=20) to 154 diseased sites from periodontally diseased subjects (n=47). Differences in profiles can be seen at a glance. (Courtesy of AP Colombo)

The data from Fig. 2 can be analyzed further using several statistical methods to determine specific bacterial associations (for examples, see Colombo et al. 2009; Preza et al. 2009a; 2009b). To examine the relationships of entire microbial profiles with respect to site characteristics (e.g., health and disease, pocket depth), we used correspondence analysis (CA) as shown in the graph in Fig. 3 below.

Figure 3: Correspondence analysis of subgingival plaque bacterial communities in health and disease. Each symbol represents one community from one site. Communities that are closer together have more similar HOMIM profiles. In this plot, the healthy sites from healthy subjects (green circles) are distinct from healthy and diseased sites in diseased subjects (red symbols). (Courtesy of Dr. Vanja Klepac-Ceraj)