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Recent advances in next generation sequencing technology and publicly available computing programs and servers have increased the accessibility and applications of microbial metagenomic analysis beyond traditional genomics and bioinformatic analysis. We propose that the advent of next generation sequencing technology and publicly available computing frameworks make environmental metagenomic monitoring a potential tool for environmental and public health research and decision-making. As technology advances, the future of public health monitoring will be steered towards metagenomic analysis. Result shows how environmental sampling processed by next generation sequencing technology and analyzed by publicly available computing frameworks can be utilized in the areas of public health surveillance, risk assessment, risk communication, policy development and research.