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Microbial Single-Cell Genome Sequencing

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Recent advancement in single-cell sequencing based technologies has allowed us to decipher the genetic code and genomic variation of uncultured microorganisms. Traditional 16S/18S/ITS sequencing and metagenomics have limited capability as they may only provide the average results, neglecting the outliers. We provide microbial single-cell genome sequencing to reveal the heterogeneity of microbial populations.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Streamlined single-cell sorting and lysis, whole genome amplification, barcoded library generation and multiplexing sequencing.
  • The most advanced microbial single-cell sequencing technologies and bioinformatics tools.
Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Introduction to our microbial single-cell genome sequencing

Single-cell sequencing methods has led to a paradigm shift in the field of microbial genomics, away from microbial population analysis and toward comprehensive studies of individual microorganisms. We provide single-cell genome sequencing to decipher the diversity of microorganisms. The workflow of this service generally includes single-cell preparation, cell lysis, single-cell genome amplification, library construction and whole-genome sequencing. Depending on the type of samples, we utilize advanced flow-assisted cell sorting (FACS), laser-capture-microdissection, micromanipulation or microfluidic platform to perform single-cell isolation. The isolated cells are subsequently lysed and each genome is amplified through whole-genome amplification (WGA) methods (multiple-displacement-amplification (MDA) or MALBAC). After WGA, the amplified DNA is used to create libraries for Illumina sequencing.

Microbial single-cell genome sequencing can be used to discover low-abundance microbial members, reveal phylogenetic relationships, infer microbial evolution and explore potential biosynthetic/metabolism processes. It has been applied to a wide range of fields such as scientific research, epidemiology, human health and drug development.

Microbial single-cell genome sequencing workflow

Bioinformatics Analysis

Our bioinformatics analyses generally include read quality control, genome assembly, genome quality control and comparative genomics analysis. Our bioinformatics analysis pipeline is flexible to your needs. Please feel free to contact us.

Bioinformatics Analysis Details
Read Quality Control Read quality assessment, sequence trimming and filtering using tools like Trim and Quality Filter
Genome Assembly Genome assembly using tools like SPAdes and IDBA-UD
Genome Quality Control Assessing the quality and continuity of assembled genome using tools like CheckM and Anvi'o
Comparative Genomics Analysis Phylogenetic analysis, variant calling (SNP/InDel/SV) and annotation, developmental genetics, virus-host interaction, etc.

Sample requirement

    1. Cells: single cells or a small number of cells stored in a PCR tube, containing 4 uL 1xPBS, along with negative control.
    2. DNA: 1.8 < OD260/280 < 2.2.
    3. No contamination. Please transport samples along with enough dry ice.

Sampling kits: we provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: raw sequencing data, assembled and annotated sequences, quality-control dashboard and the customized bioinformatics report.


  1. Wang Y, Navin N E. Advances and applications of single-cell sequencing technologies. Molecular cell, 2015, 58(4): 598-609.
  2. Bowers R M, Doud D F R, Woyke T. Analysis of single-cell genome sequences of bacteria and archaea. Emerging Topics in Life Sciences, 2017, 1(3): 249-255.
* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.

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