What is a microbe? In practice, the term microbe is used to describe living things invisible to the human eye, that is, generally less than about 0.2 mm. The terms microbe, microorganism, bacteria, germ, and even bug are often used interchangeably by nonscientists to describe these small organisms. Microbiologists have specific names for the various microbes, which include Bacteria, Archaea and some members of the Eukarya. The first two groups (domains), although unlike in many ways, share a type of cellular organization known as prokaryotic. They lack membrane-enclosed organelles, such as mitochondria, chloroplasts and, most notably, a nucleus. The genomes of Bacteria and Archaea typically contain little non-coding DNA and range in size from 0.5 to 10 million base pairs. By contrast, members of life’s third domain, Eukarya, which comprises animals, plants, fungi, algae, and protozoa have larger genomes with substantially more non-coding DNA. Some eukaryotes are also too small to be seen individually except under a microscope and thus have been traditionally studied by microbiologists. Included among these small eukaryotes are many fungi, such as baker’s yeast and the human pathogen Candida, and many of the algae and protozoa (harmless paramecia, for instance, and the malaria parasite Plasmodium). Viruses, although arguably not alive, in that they can replicate only inside cells and have no metabolism or cell structure of their own, are also encompassed in the science of microbiology. In this report, we address primarily metagenomics projects that focus on Bacteria, Archaea and viruses. Because of their larger genomes, microbial eukaryotes have received less attention, a situation which should be remedied as sequencing becomes less expensive and bioinformatic methods become more powerful.