biostudies-literatureGao JOcean Negative Carbon Emissions (ONCE) ProgramMOST | National Natural Science Foundation of China (NSFC)e0077024https://www.ebi.ac.uk/biostudies/studies/S-EPMC11656776biostudies-literatureUnknown9(12)16S rRNA gene sequencing is the gold standard for identifying microbial diversity in environmental communities. The Illumina short-read platform is widely used in marine environment studies due to its cost-effectiveness and high accuracy, but its limited read length restricts taxonomic identification mainly to genus or family levels. Recently, the PacBio long-read sequencing platform was developed. This method has exceptional base-level resolution exceeding 99%, thereby effectively mitigating the challenges associated with high error rates commonly observed in long-read sequencing technologies. However, few studies have compared the PacBio long-read and Illumina short-read platforms in marine deep-sea sediments. Here, the PacBio long-read and Illumina short-read platforms were compared witmSphereImproved resolution of microbial diversity in deep-sea surface sediments using PacBio long-read 16S rRNA gene sequencing.PMC1165677642188102, 42293292Cai RJiao NSa BLeung EL-HGao JChen XYan YLiu DWang ZDeng WYan WfalseImproved resolution of microbial diversity in deep-sea surface sediments using PacBio long-read 16S rRNA gene sequencing.16S rRNA gene sequencing is the gold standard for identifying microbial diversity in environmental communities. The Illumina short-read platform is widely used in marine environment studies due to its cost-effectiveness and high accuracy, but its limited read length restricts taxonomic identification mainly to genus or family levels. Recently, the PacBio long-read sequencing platform was developed. This method has exceptional base-level resolution exceeding 99%, thereby effectively mitigating the challenges associated with high error rates commonly observed in long-read sequencing technologies. However, few studies have compared the PacBio long-read and Illumina short-read platforms in marine deep-sea sediments. Here, the PacBio long-read and Illumina short-read platforms were compared wit2024-01-01T00:00:00Z2024 Dec2025-04-22T10:38:21.49Z2025-04-05T23:41:44.767ZS-EPMC116567763953067310.1128/msphere.00770-24