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.
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.
On-demand webinar
Disentangling the complexity of soil communities with highly accurate long-read metagenome assembly
Understanding microbial diversity is crucial not only for conserving and maintaining ecosystems, but also for human and environmental health. However, many microorganisms, particularly of environmental samples such as soil, are difficult to culture and therefore largely unknown. Now, HiFi sequencing on the Revio system is allowing microbiologists to sequence near-to-complete microbes directly from the environment, without the need to culture, with metagenome sequencing and metagenome-assembled genomes (MAGs). 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.
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
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 sample* 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 <$5 per sample* 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 <$60 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 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
2024 Microbial Genomics SMRT Grant awardees
We are thrilled to announce and congratulate the winning proposals and finalists for awards for the 2024 Microbial Genomics SMRT Grant. While there were hundreds of submissions this year from all around the world, only a select few could be chosen. Congratulations to these innovative scientists leading the future of microbiome and metagenomics research. We look forward to what they will be able to accomplish with 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?
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.
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.
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 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.
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
ONSO HIGHLY ACCURATE SBB SHORT-READ SEQUENCING
Blog
Going beyond the “needle in a haystack” with Onso short-read sequencing
We’ve shown how the Onso system excels at needle-in-a-haystack applications, like liquid biopsy research. Now, explore how the exceptional accuracy of the Onso system extends beyond the proverbial haystack across diverse fields such as oncology, public health, and human genetics research.
Blog
Leveraging genomic surveillance in wastewater to protect public health
At PacBio, we are invigorated by the transformative potential of our high-accuracy short-read sequencing technology. The ability to leverage such advanced tools in wastewater surveillance represents a pivotal step forward in safeguarding public health.
Spotlight
Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants in Mycobacterium tuberculosis (Mtb)
SBB offers an extraordinary and highly accurate method for detecting minor populations of drug-resistant Mtb at as low as 0.001% frequency without needing complex error correction techniques like UMIs or SMOR. It also addresses the limitations of SBS by reducing error rates and simplifying the process, making it a critical tool for early detection of heteroresistance in Mtb, which is essential for tackling drug-resistant tuberculosis. Applied broadly, this capability offers advantages for detecting cancer cells in liquid biopsy samples with tumor-derived cell-free DNA and for other infectious disease applications such as wastewater detection.
Allender, C. J., et al. (2024). Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants. BMC genomics, 25(1), 789. https://doi.org/10.1186/s12864-024-10697-1