Microbial sequencing methods

Advancing our understanding of the microbial world through discovery-based research entails comprehensive analysis of microbial genomes, their interactions, communities, and environments in which they live.

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See what is possible

Single Molecule, Real-Time (SMRT) sequencing on the PacBio systems provides a deeper understanding of microbes and microbial communities by giving scientists the ability to:

Solutions Guide

A new standard in pathogen genomics

Detect, track, and characterize pathogens to a new standard of completeness and precision. PacBio® solutions offer exceptional accuracy and long read lengths to support a wide range of pathogen surveillance applications.

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Application brief


  • Generate closed chromosomes and plasmids from even the most repeat-dense and GC-rich genomes easily, affordably, and at high throughput
  • Identify ever-evolving genes associated with toxicity, virulence, and antimicrobial resistance
  • Precisely identify strains, serotypes, and plasmids to track pathogen outbreaks in human, plant, and animal species, through food systems, hospitals, and communities
  • Comprehensively characterize microbes to facilitate scientific breakthroughs and discovery

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The genome of a novel Streptomyces anulatus strain isolated from a Chinese medicinal herb was sequenced with PacBio and fully assembled to reveal 52 putative biosynthetic gene clusters, including numerous with significant differences from known clusters. Growth under diverse conditions produced two novel compounds, with more potential yet to be unlocked.

Liu, et. al. (2022). Exploration of diverse secondary metabolites from Streptomyces sp. YINM00001, using genome mining and one strain many compounds approach. Front Microbiol.

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Figure 2: The new PacBio bioinformatics pipeline increased the number of high quality MAGs in each of the four human fecal samples sequenced.


Obtain more species and MAGs from HiFi shotgun metagenomics data with updated pipelines

Microbial and metagenomics enthusiasts rejoice: newly optimized bioinformatics pipelines are enabling scientists to detect even more species and assemble more single contig metagenomes using HiFi sequencing than ever before – with up to 9-fold increases in some cases.

Due to the continuous advances, improved results, and cost-effectiveness of PacBio HiFi long-read sequencing, it is an increasingly popular tool for metagenomic analysis of complex microbial communities.

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Despite its importance as a clinical target, only 4 herpes simplex virus type 2 strains have complete genomes due to dense repeats and ~70% GC content. Here, scientists report the complete de novo assembly and annotation of an additional strain commonly used in research, HSV-2 strain G.

Chang, W. et. al. (2022). Complete genome sequence of herpes simplex virus 2 strain G. Viruses 14(3), 536; https://doi.org/10.3390/v14030536.


Cost-effective microbiome and metagenomic HiFi sequencing with PacBio service providers

Full-length 16S and shotgun metagenome HiFi sequencing with certified PacBio service providers can deliver remarkably affordable microbiome and metagenomic data with explanatory power that is second to none.

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