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Shirley, NY 11967
USA
Email: contact@cd-genomics.com

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 generating accurate reference genomes, for
microbial identification, and other comparative genomic studies. Comparative genomic analysis based
on whole genome sequencing plays an irreplaceable role in studying pathogenic mechanism 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.

Diseases

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

Foods

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, yoghourt, and many
other fermentation processes.

Agriculture

Microorganism in agriculture involves in 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
 45-1 Ramsey Road
Shirley, NY 11967
USA
Email: contact@cd-genomics.com

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

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.

References:

1. Abriouel, H., Lerma, L.L., Muñoz, M.D.C.C., Montoro, B.P., Kabisch, J., Pichner, R., Cho, G.S., Neve, H.,
Fusco, V., Franz, C.M., Gálvez, A. & Benomar, N. (2015) ‘The controversial nature of the Weissella genus:
technological and functional aspects versus whole genome analysis-based pathogenic potential for their
application in food and health’, Front. Microbiol., 6: 1997.

2. Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R,
Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D,
Sawanpanyalert P, Sobel J, Schlundt J (2012) ‘Integrating genome-based informatics to modernize global
disease monitoring, information sharing, and response’, Emerg Infect Dis, 18: e1.

3. Agren R, Liu L, Shoaie S, VongsangnakW, Nookaew I, Nielsen J (2013) ‘The RAVEN toolbox and its use for
generating a genome-scale metabolic model for Penicillium chrysogenum’, PLoS Comput Biol, 9:e1002980.

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.