Two key issues for microarray hybridization of microbial communities are specificity and sensitivity since environmental communities can have such vast diversities. Both of these conditions can be improved at various stages of microarray design, construction, target preparation, or hybridization. During probe design, determining the best criteria for probe design, such as using experimentally determined design criteria (He et al., 2005b; Liebich et al., 2006) can improve specificity, thus decreasing the number of false positives . Probe length also affects specificity and sensitivity; longer probes are more sensitive, but less specific (Denef et al., 2003; He et al., 2005a) .