Menu

Microbial genomics

See the microbial world in high resolution

Connect with a PacBio scientist

MICROBIAL GENOMICS SOLUTIONS

white public health icon

PUBLIC HEALTH + SURVEILLANCE

Protect public health with comprehensive genomic surveillance solutions that deliver the complete information you need for accurate characterization and tracking of all pathogens circulating in the community.

Learn more

microbiology infectious disease white icon

INFECTIOUS DISEASE + MICROBIOLOGY RESEARCH

Advance human health with new insights into the viruses, bacteria, and protozoa that cause infectious disease. Reveal the biology of host-pathogen dynamics, drug resistance, and immune escape.

Learn more

white industrial microbiology icon

DISCOVERY AND INDUSTRIAL MICROBIOLOGY

Address the global need for novel therapeutics, environmental remediation, and efficient chemical production by mining even the most difficult to sequence microbial genomes and complex microbial communities.

Learn more

plant animal microbiology icon

PLANT AND ANIMAL MICROBIOLOGY

Explore the biology of microbial symbionts, pathogens, microbiomes and phytobiomes and the roles they play in crop yields, livestock health, and the preservation of wild animals and natural habitats.

Learn more

Microbiome + metagenomics

Characterize, assemble, and gain a better understanding of microbial communities and metagenomics.

Learn more

SETTING A NEW STANDARD FOR MICROBIAL SEQUENCING

Microbes account for most of the diversity of life on our planet, yet fewer than 1% have been identified. To understand this ever-evolving world, scientists need the unbiased, accurate, and comprehensive information that only PacBio long-read sequencing can provide.

Targeted - amplicon Targeted - enrichment Whole genome sequencing Metagenome sequencing
COVID-19 and virus sequencing
Microbiology research
Infectious disease research
Industrial microbiology
Plant + animal microbiology
Healthcare associated infections
Foodbourne pathogens
Microbiome

Webinar

MORE SAMPLES, LOWER COSTS, LESS TIME: NEW PACBIO HIFI PREP KITS + MICROBIAL WGS AND ANTI-MICROBIAL RESISTANCE

Learn how the HiFi plex prep kit 96 allows users to sequence small genomes at similar costs to short-read prep workflows, all while making high-quality sequencing more accessible by eliminating common bottlenecks related to cost, time, and labor.

Register now

Microbial genomics at scale with PacBio HiFi sequencing

Microbial genomics with PacBio long-read HiFi sequencing is accurate, scalable, and cost-effective

Automated end-to-end workflows and product enhancements drive cost-effective and scalable HiFi microbial sequencing

View application brief

 

Microbial whole genome sequencing

With HiFi plex prep kit 96 and an end-to-end scalable workflow from extraction to analysis, obtain reference-grade high accuracy, closed chromosomes and plasmids plus methylation signatures and identify strain and functional characteristics, AMR genes, and mobile vectors, all for <$50 USD per sample* with the ability to multiplex up to 384 libraries per SMRT Cell.

Full-length 16S / ITS sequencing

Sequence the entire gene to enable more species- and strain-level taxonomy. Pairing full-length 16S with the Kinnex 16S rRNA kit enables more samples per SMRT Cell (up to a 1,536-plex) and/or more reads per sample for <$5 per amplicon* at >30k average reads per sample. Analyze with the PacBio GitHub workflow.

Viral sequencing

Using an amplicon or target enrichment approach, sequence entire genes or genomes to deconvolute complex viral mixtures into quasispecies and unique haplotypes, identify and quantify minor variants linked to resistance or immunology, and track the evolution and phylogeny of viral populations, for <$10 per amplicon* or de novo assemble large viral genomes.

Shotgun metagenome sequencing

With the HiFi plex prep kit 96 and PacBio GitHub workflows for analysis, achieve richer functional information and profile species with high precision and recall for <$50 per sample* or sequence deeper and recover many high-quality metagenome-assembled genomes (HQ MAGs) and many circular, single-contig MAGs, even at lower coverage.

* Prices, listed in USD, are approximate and may vary by region. Pricing includes library and sequencing reagents run on a Sequel® II/IIe or Revio™ system and does not include instrument amortization, other reagents, or DNA extraction.
† Reads per sample and number of samples per SMRT Cell and other sequencing performance results vary based on sample quality/type and insert size.

Microbial genomics at scale enabled by the Revio system

HiFi sequencing on the Revio system with supporting products, Kinnex 16S rRNA and HiFi plex prep kits, brings higher throughput and lower costs for microbial genomics applications.

 

$995 USD per SMRT Cell for sequencing1

Four independent sequencing stages that generate 90 Gb per SMRT Cell for multi-application runs

Simultaneous epigenetic information from native DNA sequencing applications

SMRT Cell 1 SMRT Cell 2 SMRT Cell 3 SMRT Cell 4
Microbial isolate whole genome sequencing Viral targeted sequencing Kinnex full-length 16S sequencing Shotgun metagenome sequencing
Application Samples per SMRT Cell Samples per Revio run with 4 SMRT Cells Estimated samples per year2
Microbial de novo assembly3 384 1,536 ~499,200
Targeted amplicon sequencing4 ≥1,000 ≥4,000 ~2.6M for 1 – 5 kb
~1.3M for 5+ kb
Kinnex 16S rRNA 1,536 6,144 ~2M
Shotgun metagenomic profiling 96 384 ~124,800
Shotgun metagenomic assembly 12 48 ~15,600
1. US list price is $995 for sequencing reagents for one Revio SMRT Cell, which has an expected yield of 90 Gb, equivalent to a 30× human genome. 2. Estimated samples per year calculated by assuming 1,300 SMRT Cells per year for each Revio system run using 4 SMRT Cells, 365 days in a year, and 90% utilization. Annual throughput is based on 1,300 Revio SMRT Cells. All sample throughputs are estimates per Revio run using 1 or 4 SMRT Cells. Coverage may vary based on sample quality, library quality, and fragment lengths. 3. Currently available SMRTbell® barcoded adapter plates contains 384 SMRTbell barcoded adapters. Microbial de novo assembly assumes microbes with ~1.2 Gb of total genome size per SMRT Cell. 4. Amplicon sequencing assumes 12-hour movie time for 1–5 kb, 24-hour movie time for 5+ kb, and >50× per sample.

MICROBIAL GENOMICS IN ACTION

photo of romaine lettuce in field

Thwart food-borne contaminants with the exceptional accuracy of HiFi sequencing

HiFi sequencing delivers the highly accurate and comprehensive microbial sequence data possible to give food safety and public health professionals the clarity they need to better understand contaminants and make informed and timely decisions.

Read the blog

Abstract image representing metagenomics

METAGENOME ASSEMBLY AND CHARACTERIZATION OF A POOLED HUMAN FECAL REFERENCE

Discover how high accuracy and long read length are important for making microbial genomics discoveries that stand out based upon the latest PacBio innovations and Revio data that have the potential to revolutionize quality, capacity, and cost-effectiveness in microbial community profiling and MAG assembly. Hear about exciting new capabilities developed by Zymo Research tailored specifically for the HiFi microbiome and metagenomics community.

Watch webinar

Null

Meeting the threat of antimicrobial resistance with HiFi sequencing and artificial intelligence

After conducting a battery of technology comparisons, OpGen’s Ares Genetics has adopted PacBio HiFi microbial whole genome sequencing. The company believes the read length and high accuracy of HiFi data will enable it to develop a suite of cutting-edge AI solutions with potential to revolutionize the way we combat the spread of antimicrobial resistance.

Learn more

Sprite decoration

EXPLORE

Did you know we have a comprehensive library of reports, papers, and videos related to microbial genomics?

Explore resources

SHAPING THE FUTURE

FASTER AND MORE AFFORDABLE SEQUENCING WITH THE HIFI MICROBIAL HIGH-THROUGHPUT WORKFLOW

Highly-accurate HiFi reads produced by PacBio long-read sequencers — such as the Sequel IIe and Revio systems — enable researchers to access entirely new levels of contiguity, completeness, and accuracy when assembling genomes.

Read more

Simplified Revio and Vega system overlapping

Flexible and scalable HiFi sequencing for microbial genomics research

HiFi sequencing applications give researchers more complete and detailed information about microbial genomes, spurring new insights into host-pathogen dynamics, microbial evolution and adaptation, and critical traits including drug resistance, infectivity, and virulence.

Track the evolution of viral populations

Achieve accurate surveillance of viral populations in a host, within a community, or across geographic regions by phasing entire viral genes or genomes.

Resolve bacterial strains, serotypes, and plasmids

Track pathogen outbreaks in humans, plants, and animals through food systems, hospitals, and communities with affordable, high-throughput, high-quality whole genome sequencing.

Improve gene discovery

Obtain improved gene discovery with reliably closed highly accurate bacterial genomes.

Correlate specific species

Distinguish community composition at the strain level to correlate specific species to difference in metagenome function or systemic outcomes.

Connect metagenome community functions

Use closed and high-quality MAGs to align metagenome community functions to specific strains.

The power of HiFi Sequencing for metagenome assembly

One way to improve assembly completeness and contiguity is to use long-read sequencing. However, not all long reads are the same. Did you know that once read lengths are longer than most of the repeats in a genome or metagenome, incremental gains in raw read accuracy improve assemblies faster than higher coverage or even large gains in read length?

Learn more

APPLICATIONS TO FUEL MICROBIOLOGY AND INFECTIOUS DISEASE RESEARCH

MICROBIAL WHOLE GENOME SEQUENCING

Learn how affordable it is to upgrade your draft-quality microbial whole genome sequencing pipeline to consistently produce closed, reference-quality genomes.

Learn more

VIRUS SEQUENCING

Explore how scientists are using HiFi sequencing to understand viral evolution and host-pathogen dynamics.

Learn more

METAGENOME SEQUENCING AND ASSEMBLY

Overcome the challenge of distinguishing reads from closely related strains in a metagenome sample with long, highly accurate HiFi reads, yielding more and higher quality MAGs than what can be achieved with other technologies.

Learn more

BENEFITS OF MICROBIAL SEQUENCING

TRACK THE SPREAD AND TRAITS OF PATHOGENS

Scientists in commercial, academic, and government research teams are using highly accurate HiFi sequencing data to resolve variants of the SARS-CoV-2 virus that exist within one individual or across a cohort, which is critical to developing and maintaining effective diagnostics, vaccines, and therapeutics.

Learn more

Roundel image of older scientists working in lab for Accelerate discovery

ACCELERATE DISCOVERY AND ADVANCE RESEARCH

PacBio allows microbiology researchers to fully characterize microbial organisms, dissect complex microbial communities, and identify emerging pathogens with high accuracy, enabling scientists around the world to accelerate discovery, advance research, and protect human, animal, and environmental health.

Microbial whole genome sequencing best practices

Metagenomic sequencing best practices guide

IDENTIFY AND TRACK ANTIMICROBIAL RESISTANCE TO IMPROVE HUMAN HEALTH

Antimicrobial resistance (AMR) is a global health concern and is a significant threat to human and animal health. PacBio sequencing can identify strain characteristics, AMR genes, and mobile vectors mediating the spread of drug resistance.

Learn more

Roundel image of microbiome

CONNECTING THE MICROBIOME TO OUTCOMES IN HUMAN HEALTH

The microbiome comprises trillions of microorganisms living on and inside each of us. PacBio is helping scientists unravel the complex interplay between microbiomes and the full scope of its potential for treating disease and promoting health.

Revio metagenomics + Kinnex 16S data release demonstrate futuristic microbiome capabilities

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.