Targeted Single-Cell Sequencing

Recent advancement in single-cell sequencing based technologies allow the assignment of functional roles to members of mixed microbiome samples. We use targeted single-cell sequencing to isolate individual cells from samples for genome sequencing and apply to targeted studies of microorganisms causing diseases or found in natural environment.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Streamlined single-cell sorting and lysis, PCR screening, and whole genome sequencing.
  • The most advanced microbial single-cell sequencing technologies and methods.
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Introduction to our targeted single-cell sequencing

Microorganisms found in the natural environment can significantly affect the ecosystem. The human body can also be viewed as an environment inhabited by a collection of diverse microorganisms, which play a critical role in determining a person's health condition. Single-cell genomics of mixed microbiome samples has greatly accelerated the human microbiome research, and it provides access to individual microbial genomes without the requirement of microbial cultivation. It has led to the discovery of microorganisms with novel metabolic features, or even an alternative genetic code. To better determine which cells are to be sequenced, targeted cell capture is becoming a highly attractive alternative for studying environmental microbes and human microbiome.

There are several methods for identity-based targeting of populations, such as FACS, PCR screening and function-driven or activity-driven approaches. For example, PCR screening of amplified single cell genomes by targeting marker genes (e.g. 16S/18S rRNAs or customer-specified protein-coding genes) enables individual cell analysis in complex environmental samples. Antibodies are also generally used to isolate cells of interest based on cell-surface markers. We can design the optimal targeted call capture scheme for your specific microbial single-cell sequencing projects.

Targeted single-cell sequencing workflow

Bioinformatics Analysis

Our bioinformatics analyses generally include Data preprocessing, genome assembly, genome quality control and comparative genomics analysis, which can be customized to your specific needs. Please feel free to contact us.

Bioinformatics Analysis Details
Data Pre-processing 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, etc.

Sample requirement

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, PCR screening results, assembled and annotated sequences, quality-control dashboard, and the customized bioinformatics report.


  1. Woyke T, Doud D F R, Schulz F. The trajectory of microbial single-cell sequencing. Nature Methods, 2017, 14(11): 1045.
  2. Tolonen A C, Xavier R J. Dissecting the human microbiome with single-cell genomics. Genome medicine, 2017, 9(1): 56.
  3. 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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