UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitatingmicrobes belong to phylum-level divisions forwhich there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA(opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibriumwith the canonicalGGN glycine codons, displaying strainspecific variation across the human population. SR1 encodes a divergent tRNA_UCA^Gly with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA_UCA^Gly with glycine in vitro with similar activity comparedwith normal tRNA _UCC^Gly. Coexpression of SR1 glycyltRNA synthetase and tRNA_UCA^Gly in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an inframe TGA codon. Comparative genomic analysis with HumanMicrobiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.