SETTING NEW STANDARDS IN METAGENOMICSAND MICROBIOME SEQUENCING
HIGH-RESOLUTION SEQUENCING TO RESOLVE AND CHARACTERIZE COMPLEXMICROBIAL COMMUNITIESThe microbiome is the collection of trillions of microbes,
The outstanding accuracy and long read lengths of HiFi
including bacteria, fungi, and viruses, that live in, on, andsequencing gives scientists the flexibility and high resolution
1around us and the systems we depend on. Characterizing
they need to:the composition of microbial communities and exploring how• Comprehensively dissect entire microbial communities tothese microbes interact with each other in the human gut, instrain-level resolution without the need to culture
animals, on built environments, and in natural ecosystems• Characterize complex microbial communities to understandis central to understanding their role in human, animal, andtheir role in human, animal, and environmental healthenvironmental health. Accurate and flexible HiFi solutions formetagenomics and microbiome sequencing allow researchers • Identify and fully characterize novel species and better
assemble new genomes
to study microbes and microbial communities in highresolution without the need for culturing.

“With [PacBio], we can now sequence complete genomes of nearly all abundant bacteria in a microbiome.
Short-read studies rarely provided complete sequences of even a single microbe.”2— Mikhail Kolmogorov, National Cancer InstituteFull-length 16S
Reveal the true diversity of complex microbiomes with highly
accurate, species- and strain-level resolution

Shotgun metagenome profiling
Achieve taxonomic profiles with high precision and recall
and obtain rich functional information

Shotgun metagenome assembly
Recover far more high-quality metagenome assembled genomes(HQ MAGs) and more circular, single-contig MAGs, even at lower
coverage“HiFi reads allows us to generate a nearly complete picture of the metagenome, not just a fragmented assembly.
Like complete genomics, which is already being applied to rare disease diagnostics, complete metagenomics
may soon make its way into medicine and many other disciplines.”2— Pavel A. Pevzner, University of California San DiegoC Percent unclassified

050

100

Full-length 16S is the only way to resolve all clades in the human gut, without bias3• The proportion of 16S sequences from each bacterial genus that cannot be identified
at the species level varies significantly depending on which variable region is used
• Since the human gut can harbor a broad diversity of bacterial clades, only full-length
sequences (V1–V9) can provide unbiased resolution of all the species present

V4

V1–V9

HiFi data yields more high-quality MAGs than noisy long-read data, especially at
low coverage4• HiFi assembled complete MAGs for low relative abundant species and high-quality
bins revealed a substantial number of HiFi bins below 10× coverage compared to thenoisy long-read (pCLR) datasets• In >90% complete bins, the average coverage of the HiFi bins is lower than pCLR, andseveral HiFi bins have <1× average coverage as opposed to pCLR with none

“Such high-quality metagenome assemblies may fundamentally change the practice in metagenome analysis
and shed light on the biological and biomedical implications of microbial communities.”5— Xiaowen Feng, Dana-Farber Cancer Institute, Harvard Medical School
400

SRALRASRM
LRM

350

Number of taxa

300
250
200

Obtain more taxa with high precision from HiFi data for both amplicon andshotgun approaches6• After filtering out noise from short-read shotgun metagenomics (SRM), amplicon
approaches detected more unique taxa than shotgun metagenomics

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ment0Sample• Long-read amplicon (LRA) and shotgun metagenomics (LRM) detected more taxa
than both with short reads

With highly accurate HiFi reads, hifiasm-meta moves metagenome assembly evenfurther with more MAGs5• When evaluated on seven empirical datasets, hifiasm-meta reconstructed tens tohundreds of single-contig circular bacterial genomes per dataset• hifiasm-meta outperforms other metagenome assemblers with more complete
circular single-contig MAGs
Learn more about our applications: pacb.com/metagenomics
1. https://www.niehs.nih.gov/health/topics/science/microbiome/index.cfm
2. Baxt, J. (2022). Long-reads and powerful algorithms identify “invisible” microbes
3. Johnson, J. S., et al. (2019) Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications. 10(1), 5029
4. Bickhart, D. M., et al. (2022) Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature biotechnology.
0.1038/s41587-021-01130-z
5. Feng, X., et al. (2022) Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature methods. 10.1038/s41592-022-01478-3
6. Gehrig, J., et al. (2022) Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data.
Microbial Genomics, 8(3), 10.1099/mgen.0.000794
Research use only. Not for use in diagnostic procedures. © 2023 Pacific Biosciences of California, Inc. (“PacBio”). All rights reserved. Information in this document is subject to change without notice. PacBio
assumes no responsibility for any errors or omissions in this document. Certain notices, terms, conditions and/or use restrictions may pertain to your use of PacBio products and/or third-party products. Referto the applicable PacBio terms and conditions of sale and to the applicable license terms at pacb.com/license. Pacific Biosciences, the PacBio logo, PacBio, Circulomics, Omniome, SMRT, SMRTbell, Iso-Seq,Sequel, Nanobind, SBB, Revio, and Onso are trademarks of PacBio.

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