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Single Microbe Genome Sequencing Service

Creative Biolabs' Single Microbe Genome Sequencing Service

At Creative Biolabs, we offer a distinguished Single Microbe Genome Sequencing Service, harnessing our expertise in single-cell genome sequencing to elucidate complex microbial ecosystems. Our service amplifies genomic DNA from lysed cells, followed by high-throughput sequencing to unveil cellular population disparities and evolutionary relationships. Our advanced Single Cell Genomics Platform facilitates a nuanced exploration of microbial genomes at a single-cell level, aiding in investigating microbial behavior and interactions within ecosystems. By employing various single-cell omics strategies, we provide a holistic view of microbial dynamics, advancing microbial research into the era of single-cell analysis, thereby enhancing understanding of microbial ecosystems and their implications on human health and the environment.

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Currently, elucidating strain-level information of microbial communities poses quite a challenge. If high-quality genomes at the strain level from microbial communities could be decoded, it would greatly assist in understanding microbial behaviors and their impacts on hosts.

Shortcomings of Existing Technologies

Disadvantages of existing single microbe genome sequencing technologies.Fig.1 Disadvantages of existing single microbe genome sequencing technologies.

Technical Principle

To address the aforementioned issues, research teams from Harvard University and Massachusetts Institute of Technology developed a high-throughput single-cell microbial genomic sequencing technology, with the following experimental principles:

  1. Utilizing droplet microfluidics technology, the research teams encapsulated thousands of microbes individually within droplets;
  2. Within each droplet, microbes were lysed and DNA was released;
  3. Whole genome amplification was performed, the amplified DNA was fragmented and adapters were attached, subsequently within droplets, DNA was labeled using tags with specific sequences;
  4. All DNA within droplets was pooled and library sequencing was conducted.

Experiment workflow.Fig.2 Experiment workflow1.

Bioinformatics Analysis Principle

As the DNA tags marking the contents within droplets are unique for each droplet, sequencing results can be segregated according to DNA tags, obtaining genomic information of individual microbes within each droplet. Collections of sequencing sequences with the same barcode are termed as a single amplified genome (SAG). For complex microbial communities, where the reference genomes of most microbes are generally unknown, a single SAG typically covers less than 50% of the whole genome and cannot be directly used as a reference genome. This poses a unique challenge for single-cell genomic analysis of microbial communities. To obtain high-quality reference genomes of microbial communities, the research teams developed a general bioinformatics analysis workflow:

  1. By extracting and comparing genomic signature information from each single-cell, single-cell microbes from the same species within samples were identified, and then assembled together to construct species-level reference genomes;
  2. Further, individual microbial genomes were compared with reference genomes to identify single-cell microbes from different strains, and genome assembly was performed. Through this method, genomes of various different species and different strains within species in the samples can be obtained.

Bioinformatics analysis workflowFig.3 Bioinformatics analysis workflow1.

Technical Advantages

  • High-throughput Detection:
    • Tens of thousands of individual microbial genomes can be obtained at once
    • No culturing required
  • New Species, New Strains:
    • Discovering new species, new strains; compensating for the resolution deficiency of metagenomics
  • Good Genome Assembly Quality:
    • Genome quality comparable to isolated culture;
    • Supports functional gene/metabolic pathway research
  • Exploring Inter-strain Relationships:
    • Analyzing horizontal gene transfer
    • Studying host-phage association

Application Fields

Applications of our Single Microbe Genome Sequencing Service.Fig.4 Applications of our Single Microbe Genome Sequencing Service.

Technical Parameters

Service Type Sample Requirements Sequencing Strategy Data Requirement per sample
Single Microbe Genome Sequencing
  • Sample Type: Fresh human, environmental, agricultural and pastoral microbiome samples (add final concentration of 25% glycerol, shake well), -80°C preservation, dry ice transport; High-throughput single-cell microbial genomic sequencing
  • Sample State: Cell viability >90%;
  • Sample Requirement Quantity: Cell number ≥2×106 cells/sample; Cell concentration ≥2×107 cells/mL; Cell size: Diameter <10um
Illumina PE150 6000 cells, 150G raw data

Table.1 Technical Parameters for Single Microbe Genome Sequencing Service


  1. Zheng, Wenshan, et al. "High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome." Science 376.6597 (2022): eabm1483.
! ! For Research Use Only. Not for diagnostic or therapeutic purposes.