Long-read sequencing enables species-level resolution and drives functional insights with full-length 16S sequencing and 10 kb HiFi reads for metagenome profiling and assembly.

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Explore metagenomics with confidence

Highly accurate long reads – HiFi reads – with single-molecule resolution are ideal for full-length 16S rRNA sequencing, shotgun metagenomic profiling, and metagenome assembly, so that you can:

  • Determine community composition at the species or strain-level with competitively priced full-length 16S sequencing
  • Identify 6-8 full-length genes in every HiFi read with efficient, cost-effective metagenomic profiling
  • Generate up to 45 high-quality (HQ) metagenome-assembled genomes (MAGs) for up to 4 multiplexed human fecal samples or up to 110 HQ MAGs for 1 sample per SMRT Cell 8M on the Sequel II or IIe system
  • Leverage epigenomic data to associate contigs and plasmids from closely related strains

Microbial sequencing methods

HiFi metagenomics sees performance enhancements across the board

Shotgun metagenomics with PacBio highly accurate long-read sequencing (aka HiFi sequencing) has been the premier approach for generating microbial datasets that are both very high quality and stunningly complete. Now, the Revio system offers faster and more cost-effective long-read sequencing for metagenomics researchers, allowing for more high-quality and complete microbial datasets and access to new frontiers of discovery.

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Metagenomic Datasets

Application Dataset Data type PacBio system
Metagenomic profiling and assembly HiFi reads Sequel II system
Metagenomic profiling and assembly HiFi reads Sequel II system
Full-length 16S sequencing HiFi reads Sequel II system



Accurate and flexible HiFi solutions for metagenomics and microbiome sequencing allow researchers to study microbes and microbial communities in high resolution without the need for culturing. The exceptional accuracy and long read lengths of HiFi sequencing gives scientists the flexibility and high resolution they need.

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Can microbial communities turn plastic waste into sustainable food?

Before being awarded a PacBio SMRT Grant in 2021, the researchers only had short-read data on the microbial communities used to digest and flexibly convert plastics. This left the team with an incomplete picture of the composition and collective functional capabilities of their bacterial consortia. So, to fill this information gap and advance their process design they utilized PacBio long-read metagenomics to successfully capture, and close metagenome-assembled genomes for strains found within their experimental microbial communities.

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Strain-level identification of bacterial communities with the exceptional accuracy of PacBio full-length 16S sequencing

Using DADA2 software, all copies of the 16S housekeeping gene can be recovered from microbial communities. 16S sequence variants from the same strain appear in the data in integer ratios that reflect their copy number in each genome. In some cases, for example E. coli O157:H7 in the Zymo mock community, this high-resolution information can be used to unambiguously identify not only the species but the strain present. Explore this research further:

Callahan, B. J.,  et al. (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research.

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On-demand webinar


Topics covered include:

  • The importance of high accuracy and long read length for making microbial genomics discoveries that stand out
  • The latest PacBio innovations, including Revio data, that have the potential to revolutionize quality, capacity, and cost-effectiveness in microbial community profiling and MAG assembly
  • Exciting new capabilities developed by Zymo Research tailored specifically for the HiFi microbiome and metagenomics community

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  • Learn the recent advances by PacBio in shotgun metagenomics that are leading to improved results, capacity, and cost effectiveness in microbial community profiling and MAG assembly
  • Understand the importance of both high accuracy and long reads for metagenomics
  • Hear how hifiasm-meta can be utilized to obtain more HQ, complete, circular, single contig MAGs with PacBio HiFi shotgun metagenomics data

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Both read length and accuracy matter for metagenome assembly and functional profiling

Comparing analysis results using HiFi data from a sheep fecal sample to results using lower accuracy subreads from the same data set show the impact of improving accuracy on assembly contiguity, MAG recovery and gene discovery. In the figure, the more contiguous HiFi assembly enabled recovery of 25% more complete biosynthetic gene clusters (BCGs) than noisy CLR long reads. Explore this research further:

Bickhart, D.M. et al. (2022). Generation of lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.. Nature Biotechnology, 0.1038/s41587-021-01130-z

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Application brief

Microbiome and metagenome sequencing with HiFi reads

Highly accurate long reads – HiFi reads – with single-molecule resolution make Single
Molecule, Real-Time (SMRT) sequencing ideal for full-length 16S rRNA sequencing,
metagenome profiling, and metagenome assembly.

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Application brief

BugSeq taxonomic and functional profiling with HiFi metagenomics

HiFi metagenome profiling provides more (and richer) functional information and precise species classifications.

  • Each HiFi read typically has an average of eight intact genes per read, providing richer information about genes that co-occur in a single microbe, and may be co-expressed
  • 80-90% of HiFi reads have at least one functional annotation, and typically average four, whereas only ~1/3 of short reads can be annotated even once
  • HiFi reads can assign taxonomy with high precision and recall

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BugSeq Bioinformatics, a leading provider of infectious disease bioinformatic solutions, has joined the PacBio Compatible program as a PacBio partner. Combined with the high quality, long reads of the PacBio HiFi platform, BugSeq enables recovery of complete microbial genomes, strain-level profiling, and detection of antimicrobial resistance mutations from metagenomic samples.

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Microbiome blog

Digest HiFi microbiome and metagenomics research with Publications at a Glance

If you are interested in seeing how PacBio technology is making an impact in current metagenomics and microbiome research, our new Publications at a Glance are an effortless and convenient way to access the latest PacBio-driven discoveries from the community.

This first Publications at a Glance series is comprised of a single-page document (written by PacBio scientists) that delivers busy researchers a quick and easy-to-digest summary of important peer-reviewed articles in microbiome and metagenomics research. Each one highlights key findings from the featured publication, shows how PacBio technology contributed to the findings, and outlines implications for future studies.

Access publications at a glance

Workflow: from DNA to resolved microbial communities

*Read lengths, reads/data per SMRT Cell 8M and other sequencing performance results vary based on sample quality/type and insert size.

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Library preparation

Prepare targeted sequences or shotgun libraries to characterize your microbial community.

Explore recommendations for all SMRT sequencing applications

Extract DNA using the commercially available kit of your choice

Full-length 16S sequencing

Shotgun metagenomic profiling and metagenome assembly


Use PacBio HiFi long-read sequencing systems for affordable, high-quality metagenomic sequencing*

Full-length 16S sequencing

  • With 1.6 kb HiFi reads generate up to 3.5 million >Q20 reads with a 10-hour movie collection time
  • Resolve up to 192 communities per SMRT Cell 8M

Metagenome profiling

  • With 10 kb HiFi reads generate up to 3 million >Q20 reads with a 30-hour movie collection time
  • Profile up to 48 communities per SMRT Cell 8M for taxonomic or functional profiling

Metagenome assembly

  • With 10 kb HiFi reads generate up to 3 million >Q20 reads with a 30-hour movie collection time
  • Multiplex up to 4 samples per SMRT Cell 8M to generate high-quality MAGs

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Data analysis

Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet.

Full-length 16S sequencing

Metagenome profiling

Metagenome assembly

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