Microbial Epigenomics

Microbial DNA contains three major types of methylation: N4-methylcytosine (4mC), 5-methylcytosine (5mC) and N6-methyladenine (6mA). With advanced DNA sequencing technologies, we can analyze the frequency and distribution of methylated residues in microbial genomes to fully understand their functions.

Our Advantages:
  • Provide robust, cost-efficient solutions for microbial epigenomics research.
  • Advanced sequencing platforms: Illumina HiSeq, Nanopore, and PacBio systems are available to satisfy diverse sequencing requirements.
  • Extensive experience in handling diverse types of samples.
  • Strong expertise in bioinformatics analysis. We can customize the bioinformatics pipeline to meet your specific needs.
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Introduction to Our Microbial Epigenomics Platform

DNA methylation plays an important role in the regulation of gene expression, virulence, and pathogen-host interactions. Our integrated microbial epigenomics platform, utilizing advanced epigenomic techniques including restriction enzyme digest sequencing, bisulfite sequencing, and ChIP-Seq, single-molecule real-time sequencing (SMRT), and nanopore-based sequencing, can detect the diverse forms of DNA methylation at a genome-wide scale and enables a more complete understanding of microbial epigenomes. Not only do we provide the full set of methylated positions and targeted motifs, we also offer a complete map of the methyl transferase (MTase) enzymes and restriction-modification (RM) systems responsible for each methylated motif.

DNA methylation also contributes to cellular differentiation and development of organisms, which is crucial to understand gene expression and silencing in the development of cancer and other diseases. Microbial epigenomics provides insight into important tumorigenic pathways and enables us to find the molecular markers in multiple biological processes and understand underlying mechanisms associated with complex diseases. Microbial epigenomics analysis can be used in many areas of research, including cell cycle control, DNA repair, developmental biology, cancer research, and discovery of potential biomarkers and drug targets.

Microbial Epigenomics Analysis Workflow

Bioinformatics Analysis

Our bioinformatics analysis of microbial epigenomics mainly includes three parts: methylation, structural variation, and SNPs. We are flexible to your needs.

Bioinformatics steps for comprehensive characterization of a microbial epigenome (Beaulaurier et al. 2019)Figure 1. Bioinformatics steps for comprehensive characterization of a microbial epigenome (Beaulaurier et al. 2019).

Sample Requirement

Sampling kits: We provide a complete range of MicroCollect™ microbial sampling kits for clients, in order to recovery microorganisms from the oral cavity, saliva, urine, and stool.

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


  1. John Beaulaurier, et al. Deciphering bacterial epigenomes using modern sequencing technologies. Nature Reviews. 2019, 20:157-163.
  2. Satoshi Hiraoka et al. Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature Communications. 2019, 10(59):1-10.
  3. Le Zhang, et al. Bioinformatics analysis of metagenomics data of biogas-producing microbial communities in anaerobic digesters: A review. Renewable and Sustainable Energy Reviews. 2018, 1364-0321.
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