Applications of Microbial Whole Genome Sequencing

Microorganisms widely exist in nature and are closely related to human life and production. They are generally divided into fungi, actinomycetes, bacteria, spirulina, rickettsia, chlamydia, mycoplasma and viruses. Microbial whole genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing the entire microbial genome is important for construction of accurate reference genomes, microbial identification, and other comparative genomic studies. Comparative genomic analysis based on whole genome sequencing plays an irreplaceable role in studying pathogenic mechanisms of pathogenic microorganism, evolution of pathogenic genes and screening of novel, efficient drug targets. Microbial whole genome sequencing can be widely used in various fields.


Pathogenic microorganism includes all kinds of microorganisms that cause human diseases, food corruption, animal infection in animal husbandry and breeding industry, and plant diseases. Researches focus on disease-related genes, regulatory and interaction systems, metabolic systems, genetic variation, laboratory diagnosis and specific prevention, drug resistance genes, virulence genes and so on. Specifically, microbial whole genome sequencing can be applied to:

  • Diagnosis and identification of pathogens
  • Epidemiological investigation and tracing
  • Rapid identification of pathogen character
  • Analysis and prediction of disease prevalence
  • Vaccine variation monitoring and efficacy evaluation
  • Surveillance of foodborne pathogens
  • Drug targets discovery


Whole genome sequencing of microorganisms in food and bioinformatics analysis of data can help people predict genes that play an important role in the fermentation process or product quality, providing information about the metabolic pathways of microorganisms and their interaction with the environment. Microbial whole genome sequencing opens up the possibility of modifying microorganisms to make them more efficient in the production of vinegar, liquor, yogurt, and many other fermentation processes.


Microorganism in agriculture involves planting and breeding, processing of agricultural products, agricultural biotechnology, agricultural ecology and other research and application. Microbial whole genome sequencing can make people have a better understanding of agriculture microbe from genomic level, and the subsequent studies on genome structure and function lay an important foundation for agromicrobiology in the field below:

  • Establish agricultural microbial gene bank
  • Soil microorganism (including root microorganism)
  • Plant nutrition
  • Biological nitrogen fixation
  • Microbial pesticide
  • Microbial fertilizer
  • Feed additive
  • Biogas fermentation

Environment & Industry

The microorganism is one of the important factors to maintain the energy and material circulation in the ecosystem, it plays an important role in the degradation of various pollutants and harmful substances, and has great application value in energy production and renewable utilization. Some environmental microorganisms can adapt to special environments, such as high temperature, low temperature, high pressure, acid, alkali, heavy metal, and high substrate concentration.

Microbial whole genome sequencing allows people to know about the secrets of these microorganisms' adaptation to extreme environments, and provides a lot of assistance in pollution control, environmental protection, oil exploitation, preservation and transportation of food and medicine, biofuel, fermentation industry and many other fields in environment and industry.

At CD Genomics, our expert team with extensive experience can help you fully understand microbial communities and take advantage of them. For this purpose, we provide the following services:

16S/18S/ITS Amplicon Sequencing
Metagenomic Shotgun Sequencing
Viral Metagenomic Sequencing
Metatranscriptomic Sequencing
Microbial Whole Genome Sequencing
Viral Genome Sequencing


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  4. Bennett GM, Moran NA (2013) ‘Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect’, Genome Biol Evol, 5:1675–1688.
For Research Use Only. Not for use in diagnostic procedures.
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