Microbes touch every part of our lives. They’re what make up the beneficial communities living in our guts and the pathogens that drive major public health crises. If you’re a scientist trying to track antimicrobial resistance (AMR), assemble genomes from a complex wastewater sample, or run strain-level surveillance of emerging infectious diseases its obviosu that the need for high-resolution microbial data at scale is only continuing to grow.
Historically, researchers have worked under the assumption of a tradeoff. You could have long, highly accurate reads, but at a premium cost, or you could scale up affordably, but risk incomplete assemblies and lower resolution.
Now, there’s no need for 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.
Scalable, cost-effective solutions for every microbial genomics application
HiFi sequencing supports the full range of microbial genomics applications, with solutions that scale to fit different inputs, budgets, and project goals:
Whole genome sequencing of isolates — Generate complete, closed microbial genomes, including plasmids, for strain tracking, reference genome building, and antimicrobial resistance research.
Shotgun metagenomics — Characterize microbial communities across human, environmental, and clinical research samples, and assemble metagenome-assembled genomes (MAGs) that capture even low-abundance species.
Full-length 16S rRNA profiling — Go beyond genus-level identification with strain-resolved profiles, and multiplex hundreds to thousands of samples per SMRT Cell.
To help right-size projects, HiFi solutions are available for:
- Low input, high complexity studies
- High-throughput, low-cost studies
- Low-throughput, cost-effective projects
When paired with new library preparation strategies, ranging from low-input Ampli-Fi protocols to high-multiplexed prep kits, labs can right-size their workflows to meet both their scientific goals and financial realities.
How to choose the right library prep for your microbial genomics study
Selecting the right library prep is key to optimizing your results. PacBio offers a range of solutions, including through trusted compatible partners, each designed for specific input types, throughput needs, and budgets.
For whole genome sequencing of isolates and metagenomes:
For 16S rRNA gene sequencing:
Microbial genomics applications library preparation solutions for PacBio HiFi sequencing.
These prep options give researchers flexibility to match workflow to project needs without sacrificing accuracy. No matter your research goals, sample type, or budget, there is a HiFi library prep solution designed for you.
How do different library prep options compare for metagenome and isolate WGS?
With the recent introduction of the Ampli-Fi protocol, researchers now have more flexibility for challenging microbial studies. Ampli-Fi supports sequencing from as little as 1 ng of DNA, opening doors for challenging inputs that would otherwise make library prep difficult.
But how does Ampli-Fi compare to mainstay SMRTbell libraries, the PCR-free library prep solution that consistently delivers?
The short answer: Both yield outstanding results. Ampli-Fi shines when working with particularly difficult samples like those with low biomass, degraded DNA, or contaminants. Meanwhile, PCR-free SMRTbell prep delivers exceptional accuracy for reference-grade genomes and retains native methylation information. Together, they give researchers the confidence that, no matter the sample or study type, there’s a HiFi-ready prep that will work.
Putting it to the test, a head-to-head comparison of MAGs from the ATCC MSA-1003 mock community shows consistently impressive performance between the two library prep methods across assembly tools and sequencing platforms.
Metagenome-assembled genomes from 3 metagenome assemblers (hifiasm-meta, metaFlye, and metaMDBG) of ATCC MSA-1003 mock community with Ampli-Fi protocol sequenced on the Revio and Vega systems and standard PCR-free SMRTbell library prep sequenced on the Revio system. There were no evident differences in MAGs between the two library prep approaches.
Likewise, for isolate assembly, Ampli-Fi holds its own. Sequencing of Cronobacter sakazakii, a pathogenic bacteria primarily affecting infants, generates complete genomes across replicates, demonstrating reliable HiFi performance.
Microbial isolate assembly results using the Ampli-Fi protocol sequenced on the Vega system for Cronobacter sakazakii strain 2001-10-01. All assemblies are nearly perfect, with only a single missing contig due to size selection.
Explore the data yourself
To take a look firsthand, the PacBio datasets page provides access to assemblies and performance summaries generated from real microbial projects, spanning isolates, metagenomes, and 16S profiling.
These datasets serve as a clear demonstration of what HiFi can deliver: complete assemblies, high-quality MAGs, and strain-resolved community profiles that hold up across different sample types and study designs. These are not controlled test cases, but examples of HiFi sequencing in action, showing what you can expect in your own work.
For those who want to dig deeper, we also maintain well-documented open-source pipelines on GitHub. These resources are available for anyone to use, adapt, and improve, encouraging collaboration that pushes microbial genomics forward.
Shaping the future of microbial genomics
Microbial genomics is no longer bound by tradeoffs. PacBio HiFi sequencing offers a path to uncompromised microbial genomics—high accuracy, complete assemblies, and affordability at every scale.
For public health labs, that means scaling pathogen surveillance without blowing your budget. For academic researchers, it means generating reference-quality data you can trust. For food safety and industrial microbiology, it means clarity and confidence in every result.
With HiFi sequencing, you can stop choosing between cost and accuracy. Whatever your project, there’s a HiFi solution for you.
Visit PacBio microbial genomics resources to explore performance data, download protocols, and request a consult from a HiFi sequencing expert.