The health of the microbial ecosystem of forest soil is crucial to sustainable forest management. The complex and vital interactions that occur between species of microorganisms in the forest soil are essential to maintain proper nutrient balance and recycling in the soil that ultimately leads to a healthier forest. This research aimed to develop tools to monitor the overall health of the microbial communities in the soil and how microbial ecosystems are affected by human and natural disturbances. The output of tools could then be used, for example, to monitor the effectiveness of management policies designed to sustain forest resources. Two computer programs were created (and are available for free) for extraction of defined validated target regions common to most sequence reads, detection of artificial sequences consisting of noise and, facilitation of data analysis by detecting and reorienting reverse complementary 16S rRNA gene sequences. The results from the project provide a functional window into the effects of timber harvesting on soil microbiota. Data analysis showed significant differences in transport, detoxification and organic matter degradation pathways between treatments, for example complete organic matter removal or severe soil compaction versus unlogged control sites. These analyses provide the first metagenomic characterization of microbial catabolism in forest soil.