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Next Generation Sequencing (NGS) in Microbiology

The field of microbiology includes the subcategories virology, mycology, parasitology and bacteriology. Important areas for applied microbiology are medicine, pharmaceutical and biotechnological industry, agriculture, environment, food safety and animal health.

This overview is focusing on bacteriology.  A major challenge is the detection and classification of bacteria in medicine. The NIH Humane Microbiome Project applies NGS in order to study the microbiome in human health.

Different commercial solutions for application of NGS in microbiology are listed under NGS Targeted Gene Panels for Microbiology.

The knowledge about the genome of the microorganisms and its expression regulations is the basis for the utilisation of microorganisms in biotechnological production.

NGS in Medical Microbiology

Microorganism are a major source for human diseases and cause of death. Each year hundreds of thousands humans die due to infections with multi-drug resistant pathogens. The overuse of antibiotics lead to the development of multi-drug resistant pathogens. In order to reduce these numbers and enable the right antibiotic treatments knowledge about the pathogens is important. The classification of bacteria, including the determination of potential resistances and pathogencity factors will be enabled by deep sequencing of samples from infected patients. This knowledge improves the efficiency of treatment strategies and enables effective monitoring programs.

There are numerous pathogens that are able to infect and replicate in different hosts like humans or animals, these pathogens are denoted zoonotic pathogens. Therefore, NGS application in pathogen diagnostics in human medicine is closely related to diagnostics in food safety and animal health.

NGS in Food Safety and Animal Health

More information about the role of NGS in microbiology of food safety and animal health is available in the corresponding articles.

NGS in Agricultural Microbiology 

Numerous microorgansims are known to infect plants. For agricultural microbiology applies the same as for the usage of NGS in food safety and animal health. Currently, the focus on NGS application in this area is on research, one example is the application of NGS in the study of "nuclear processes associated with plant immunity and pathogen susceptibility".

NGS in Pharmaceutical and Biotechnological Microbiology

In the pharmaceutical industry microorganisms are used for example in the production of antibiotics, enzymes, vitamins and vaccines.

In the industrial microbiology or biotechnology microorganisms are investigated for its applications in wastewater treatment or degradation of environmentally hazardous substances that occur during ecological calamities such as oil pollutions or other pollution from the chemical industry. In order to characterise or modify microorganisms for its application in biotechnology the particular knowledge about the genome and its regulation is a requirement. NGS analysis will help to provide these knowledge.

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