Metagenomics
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.
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.
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 |
Brochure
SETTING NEW STANDARDS IN METAGENOMICS AND MICROBIOME SEQUENCING
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.
Blog
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.
Spotlight
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.
On-demand webinar
METAGENOME ASSEMBLY AND CHARACTERIZATION OF A POOLED HUMAN FECAL REFERENCE
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
ON-DEMAND WEBINAR
HIFI METAGENOMICS: MORE SAMPLES, MORE SPECIES, MORE MAGS
- 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
Spotlight
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
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.
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
BUGSEQ JOINS PACBIO COMPATIBLE PRODUCTS, ENABLES LEADING ACCURACY INFECTIOUS DISEASE ANALYSIS FOR LONG READS
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.
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.
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.
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
- Follow full-length 16S rRNA protocol with recommended primers
- Or use Intus Biosciences
Shotgun metagenomic profiling and metagenome assembly
- Create ~10-15 kb libraries for HiFi metagenomics
- Protocol: Preparing whole genome and metagenome libraries using SMRTbell prep kit 3.0
Sequencing
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
Data analysis
Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet.
Full-length 16S sequencing
- Use circular consensus sequencing analysis to produce HiFi reads through multiple observations of single circularized templates
- Analyze 16S data with either DADA2, QIIME 2, microbiomehelper, One Codex, EZBiome, or with our GitHub-posted pipeline
Metagenome profiling
- Use HiFi sequencing to study metagenome compositions and functions using Sourmash, DIAMOND and MEGAN-LR with our Github-posted pipeline or with BugSeq, a PacBio Compatible Partner.
Metagenome assembly
- De novo assemble metagenomes to high consensus accuracies >99.999% with hifiasm-meta , metaFlye, or HiCanu
- Bin high-quality MAGs from HiFi assemblies with our streamlined GitHub-posted pipeline using minimap2, MetaBAT2, CheckM, and GTDB-Tk
- Utilize epigenetic signatures to improve shotgun metagenomic analysis