Metagenomics is a robust, interdisciplinary approach for studying microbial community composition, function, and dynamics. It typically involves a core of molecular biology, microbiology, ecology, statistics, and computational biology. Exciting outcomes anticipated from these studies include unraveling of complex interactions that characterize the ecological milieu of microbial communities. Diverse habitats from which metagenomes have been reported include human guts, caterpillar guts, thermal vents in oceans, ore deposits, polar caps, and even soils that adhere to plant roots. Knowledge generated from metagenomic projects has tremendous potential to benefit human health, agriculture, and ecosystem functions. This article provides a brief history of technical advances in metagenomics, including DNA sequencing methods, and some case studies. A specific example is provided of microbial metagenomes found at the roots of native grass species (family Poaceae) that can grow on degraded lands undergoing revegetation.