The main two questions that large microbiome studies typically address are “who’s there?” and “what are they doing?” The first question aims at screening what kind of organisms are present, and it provides a low-resolution, relative composition of the microbiome. The second question focuses on precisely characterizing microbial communities by sequencing their entire genome on and providing insights into their metabolic capabilities. While DNA sequencing has become relatively affordable, differences in cost still exist between targeted and shotgun approaches, thus making these strategies quite complementary and commonly used.
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