MICROBIAL GENOMICS SOLUTIONS
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.
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.
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.
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.
Webinar
Unlocking human microbiome clarity with PacBio HiFi sequencing
Join a live rebroadcast of this popular session on PacBio HiFi sequencing for human microbiome research, followed by a new live Q&A with PacBio microbial genomics expert Jeremy Wilkinson, PhD.
In this session, you’ll hear how PacBio HiFi sequencing supports full-length 16S and shotgun metagenomics approaches for human microbiome research, helping researchers resolve species- and strain-level variation, uncover novel taxa, generate more complete MAGs, and improve pathway and functional annotation in complex microbial communities.
Blog
HOW HIFI METAGENOMIC SEQUENCING IS POWERING AI-DRIVEN DISCOVERY WITH BASECAMP RESEARCH
Basecamp Research’s recent selection of PacBio HiFi sequencing to support its Trillion Gene Atlas initiative highlights an important shift in biological AI: the future will not be shaped by model scale alone, but by the quality, completeness, and context of the underlying data.
Microbiome + metagenomics
Characterize, assemble, and gain a better understanding of microbial communities and metagenomics.
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 highly accurate long-read and short-read sequencing can provide.
Microbial genomics within reach and at scale with PacBio HiFi sequencing
Automated end-to-end workflows from extraction to analysis and optimized kits drive greater throughput for HiFi microbial sequencing at lower costs.
Microbial whole genome sequencing
Obtain reference-grade high accuracy, closed chromosomes and plasmids with methylation signatures using the seqWell LongPlex multiplexing kit or the HiFi plex prep kit 96 and an end-to-end scalable workflow. Identify strain and functional characteristics, antimicrobial resistance (AMR) genes, and mobile vectors, all for as low as ~$25 USD/sample* with the ability to multiplex up to 384 libraries/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 as low as ~$3/sample* at >30k average reads per sample.† PacBio Github analysis completes a seamless workflow.
Viral sequencing
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. Use an amplicon or target enrichment approach for <$5/sample* or de novo assemble large viral genomes.
Shotgun metagenome sequencing
Achieve richer functional information and profile species with high precision and recall with the seqWell LongPlex multiplexing kit or the HiFi plex prep kit 96 and PacBio GitHub workflows for analysis. Prep and sequence for as low as ~$32/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 Vega 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 within reach and at scale enabled by HiFi systems
Microbial genomics applications with PacBio HiFi systems
Long-read sequencing myths: debunked. Microbiology
Curious about what HiFi accuracy can actually do for your microbiology and metagenomics research? Chances are, it’s much more than you think. Imagine pinpointing community composition down to the species or strain level, capturing complete 16S rRNA sequences, or producing hundreds of top-notch metagenome-assembled genomes (MAGs)—just for starters.
This is part five of our six-part myth-busting series, where we dispel common myths and misconceptions about PacBio sequencing in microbial genomics applications.
Smrt Grant
2025 MICROBIOME SMRT GRANT AWARDEES
We are thrilled to announce the winners of the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics. This year’s program received hundreds of amazing proposals from researchers around the globe, each one on the pursuit to learn even more from the microbiome. With so many groundbreaking ideas, we couldn’t stop at just one awardee, so we picked four! Join us in congratulating these bold scientists who are charting the future of human microbiome and metagenomics research. We can’t wait to see the discoveries they’ll uncover with the power of high-accuracy, long-read HiFi sequencing.
MICROBIAL GENOMICS IN ACTION
WEBINAR
Kinnex kits enable full-length 16S and RNA sequencing at scale
When new sequencing instruments are released, great leaps in genomics capabilities follow. But did you know that for some applications like 16S microbiome research, gene annotation, or cancer transcriptomics, “new-instrument-level” performance can be achieved with something as simple as an off-the-shelf kit?
HOW HIFI SEQUENCING ACHIEVES SCALABLE MICROBIAL GENOMICS WITHOUT COMPROMISE
PacBio HiFi sequencing combines accuracy, throughput, and cost-effectiveness in a way that removes the need to sacrifice one thing for another. HiFi microbial sequencing is becoming the method of choice for microbial researchers because it delivers clear, complete genomes and flexible workflows that match the needs and budgets of projects ranging from a handful of isolates to thousands of complex metagenomes.
Disentangling the complexity of soil communities with highly accurate long-read metagenome assembly
In this webinar, discover how MAGs are now more obtainable than ever before with highly accurate long-read sequencing. Learn how HiFi reads allow for more and higher quality MAGs than other technologies both across and within species at the strain level, and hear about two studies utilizing HiFi shotgun metagenome sequencing on soil samples to better characterize the microbes within these diverse ecosystems.
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.
EXPLORE
Did you know we have a comprehensive library of reports, papers, and videos related to microbial genomics?
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.
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.
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?
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.
VIRUS SEQUENCING
Explore how scientists are using HiFi sequencing to understand viral evolution and host-pathogen dynamics.
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.
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.
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
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.
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