biostudies-literatureYang WBill & Melinda Gates FoundationBill & Melinda Gates FoundationNIAID NIH HHSNew England Biolabs, Inc.NIHNIH HHSgkaf226https://www.ebi.ac.uk/biostudies/studies/S-EPMC11954522biostudies-literatureUnknown53(6)Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence forNucleic acids researchProxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.PMC11954522R44 AI172703R44AI172703Yang WMangelson HAuch BLiachko IEttwiller LLuyten YReister ESisson ZRoberts RJfalseProxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for2025-01-01T00:00:00Z2025 Mar2026-04-18T03:13:28.984Z2025-07-12T03:04:16.466ZS-EPMC119545224015686810.1093/nar/gkaf226