Increasing attention is given to studies of the microbiomes of humans and other animals, given their importance in health and disease. The application of cultivation-independent genomics methods has revealed a diversity of little known and previously unknown organisms in mouth- and gut-associated consortia, as well as the mobile genetic elements that associate with all microbial community members. Among the bacterial groups are fascinating organisms such Melainabacteria (from a lineage sibling to Cyanobacteria) and three lineages of enigmatic Candidate Phyla Radiation (CPR) bacteria (Gracilibacteria, Absconditabacteria and Saccharibacteria) that are likely symbionts of bacterial and/or archaeal community members. Reconstruction of oral and gut-derived metagenomic sequences has brought to light phages whose genomes rival in size those of CPR bacteria (up to 660 kbp in length). Some of these phages are represented by manually curated, complete genomes. A subset of the phages use an alternative genetic code in which a stop codon has been reassigned to code for an amino acid, yet they replicate in bacteria that use the normal genetic code. In combination, these studies reveal novel aspects of human and animal microbiology, including phage-bacteria interactions that may have important health implications.