Pacific Biosciences (PACB) Status update summary

Advances in HiFi sequencing for microbial genomics

• HiFi sequencing delivers highly accurate, long reads, enabling comprehensive microbial genomics applications such as metagenomics, isolate assembly, epigenetics, and full-length gene sequencing, with competitive costs and improved throughput using new SPRQ-Nx chemistry.

• Applications include whole genome sequencing, full-length gene sequencing (16S, ITS, 18S), and shotgun metagenomics, providing high-resolution taxonomic and functional profiling down to strain level without the need for hybrid assembly.

• New library prep kits and protocols, such as HiFi Plex Prep, Ampli-Fi, SeqWell LongPlex, and Kinnex, allow for flexible, scalable, and cost-effective sample processing, increasing sample throughput and read depth.

Insights from recurrent UTI microbiome research

• Study of 70 women (controls and rUTI cases) using PacBio Kinnex technology revealed no major differences in vaginal microbiome community state types between groups, but specific Lactobacillus crispatus amplicon sequence variants (ASVs) were enriched in rUTI cases.

• Integration of high-throughput 16S sequencing and plate sweep metagenomics enabled strain-level resolution, identifying a subclade of L. crispatus associated with rUTI.

• Combining multi-omics approaches provided deeper insights into microbial diversity and potential drivers of rUTI susceptibility.

Advances in metapangenomics and childhood undernutrition

• Long-read sequencing (PacBio Revio) outperformed short-read and other long-read platforms (ONT) in generating high-quality, complete metagenome-assembled genomes (MAGs) at lower cost per MAG.

• Custom genome databases from long-read data significantly increased classification rates of microbial sequences, enabling detailed pangenome and microbial GWAS analyses.

• Microbial diversity and genome stability were linked to linear growth outcomes in children, with higher diversity and instability associated with poor growth.