At least 6 highly diverse clades of Saccharibacteria inhabit the human oral cavity. However, all oral Saccharibacteria strains with currently available complete genome sequences or cultured isolates belong to clade G1, leaving clades G2 through G6 poorly understood. Here, a complete genome sequence of JB001, a clade G6 (“
Candidatus
Nanogingivalaceae”) Saccharibacteria strain, is reported.