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Microbial Single-Cell Sequencing


The microbial single-cell sequencing platform at CD Genomics has a strong capability to explore the microbial world at single-cell resolution, generating complete view of the genome by utilizing the next generation sequencing technology or PacBio SMRT technology. Combined with metagnomics, this platform can better characterize microbial communities functionally and phylogenetically on spatial and temporal scales.

Our Advantages:
  • Cloud-based platform for bioinformatics analysis.
  • Targeted region sequencing, enabling a rapid and efficient workflow.
  • Extensive experience.
  • Both Illumina PE250/300 and PacBio systems are availableMore than 70% of our team is PhD and Masters-level scientists.
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After a long period of understanding and cooperation, we believe that service and quality will be immediately sought.

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Introduction to our microbial single-cell sequencing

Over the past decade, microbial single-cell sequencing has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental or medical samples. Since metagenome assemblies often collapse due to strain heterogeneity, microbial single-cell sequencing that has the ability to capture it, provides a powerful complement to shotgun metagnomics in microbial community studies. Microbial single-cell sequencing, with implications for microbial ecology, evolutionary biology, biotechnology and human health, continues on its exciting trajectory.

The rise of microbial single-cell sequencing primarily relies on the technical breakthrough in single-cell isolation, whole-genome amplification, and high-throughput sequencing. With decades of genomics experience, we have established validated, high-throughput, and automated experimental and bioinformatic workflow for microbial single-cell sequencing. Based on our microbial single-cell sequencing, we can perform microbial single-cell sequencing at whole-genome scale or by targeting 16S/18S or customer-designated molecular markers. The qualified sequences generated by Illumina or PacBio SMRT sequencing platforms can be assembled de novo or guided by a reference genome, further for advanced bioinformatics analysis.

Our microbial single-cell sequencing platform enables us to assess the genomic content of an environmental or clinical sample at the single-cell level, identify novel metabolic networks in microbial communities, study genomic variability within microbial populations, acknowledge the genomes from the rare biosphere, decipher the mode of the phage–host interaction, and capture physical cell–cell associations between microorganisms in the environment. Therefore, microbial single-cell sequencing has been widely used for scientific research, environmental protection, clinical and industrial applications.

Microbial single-cell sequencing workflow

Bioinformatics analysis

Our bioinformatics analysis includes four parts: read quality control, library quality control, assembly, and downstream bioinformatics analysis. We can tailor this bioinformatics pipeline to meet your requirements.

Steps Descriptions
Read quality control Remove contaminants, Trim or filter low-quality sequences and adapters
Library quality control

• Library quality control by tools such as Cross Block Assembly

• Assembly by tools such as SPAdes and IDBA-UD

• Assembly quality control by tools such as ProDeGe, Acdc, and Anvi’o

• Genome quality check by tools such as CheckM and Anvi’o

Downstream bioinformatics analysis

Once a single-cell genome is determined, it can be placed into a larger evolutionary, ecological, and functional context.

• Assess intra- and inter-phylum-level relationships of microbial lineages

• Quantify abundance patterns across temporal and spatial gradients

• Determine genetic heterogeneity within microbial populations

• Decipher the mode of the phage–host interaction

Sample requirement

Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, q-PCR data, statistic data, and your designated bioinformatics report.

Solutions

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