Applications of 16S/18S/ITS Amplicon Sequencing

16S/18S/ITS amplicon sequencing has now been a well-established method. Due to its low cost, shorter cycle and low quality requirement of the sample, 16S/18S/ITS amplicon sequencing is widely used in the study of microorganisms.

16S/18S/ITS amplicon sequencing reveals the species of microorganisms in environmental samples and their differences, relative abundance, population structure and evolutionary relationships. It plays an important role in the research of microorganisms and human health, agriculture and animal husbandry, environmental detection and treatment, and utilization of microorganism resources.


  • Intestine

The number of intestinal microorganisms is more than 10 times that of human body's own cells, which plays an extremely important role in metabolism, growth, immunity and disease emergence. Many research results show that intestinal microorganisms are directly related to the pathogenesis of various diseases, such as cancer, obesity and neurodegenerative diseases. Main research directions of intestinal microorganisms at present are as follow:

i. Differences in intestinal flora between disease group and healthy group.
ii. Study the intestinal flora of drug or dietary intervention groups.
iii. Intestinal flora of the same population in different growth stages.
iv. Study the intestinal flora of a group during the development of a disease.
v. Study microorganisms in multiple body parts of the same group.

  • Reproductive tract

The microorganisms in reproductive tract are important for women's health, reproductive function and infant's birth. 16S/18S/ITS amplicon sequencing can obtain the information of most microorganisms in the genital tract. Through bioinformatics/statistical analysis, a large number of data are processed and analyzed to find the microbial community composition related to environmental factors (antibiotic use, bacterial inflammation, etc.) in the genital tract.

  • Oral cavity and respiratory tract

Oral cavity is an important ecological area for human microorganisms to colonize and survive. Oral cavity microorganisms include not only bacteria, but also fungi, viruses, spirochetes and archaea. Under normal circumstances, the close and complex interactions between oral microbial communities and hosts maintain the health of the host, and breaking this ecological balance will lead to disease. Oral diseases such as dental caries, periodontal disease and oral cancer seriously affect human life and health.

The microorganism colonized in the respiratory tract and human body are always in a dynamic ecological balance, which plays an important role in maintaining human health and is closely related to the development of various upper respiratory diseases.

Analysis of oral and respiratory tract microbial diversity with 16S/18S/ITS amplicon sequencing is able to obtain a precise analysis of microbial diversity, community structure, species relationship, and increase people's understanding of relationships among oral health, respiratory tract health and disease-related microorganisms.

  • Skin

The main function of skin is to act as a physical barrier to protect the body from foreign organisms or toxic substances. At the same time, skin is also a part of human body in contact with the external environment, so various microorganisms might affect us, including bacteria, fungi, viruses and so on. Once the balance between the microbiome and the skin surface tissue is broken, it will lead to skin diseases or infections. 16S/18S/ITS amplicon sequencing systematically analyzes the community of skin microflora and their functions, allows people to better understanding the health, disease and infection of skin, makes the structure characteristics of skin microbiome and its relationship with skin tissue and environment clear.

In addition, 16S/18S/ITS amplicon sequencing can also be used for microbiological safety detection of food and medicine.

Agriculture and animal husbandry

  • Interaction between rhizosphere microorganisms and plants

The rhizosphere microorganisms survive in root interior, root periphery and soil. Microorganisms in and around the roots are vital for plant growth, production, carbon fixation and phytoremediation. 16S/18S/ITS amplicon sequencing makes it easier to reveal the interaction between rhizosphere microorganisms and plants.

  • Fertilization treatment

Microbial fertilizer is a kind of biological agent that contains living microorganisms and increases plant yield or improves quality in use. It helps people develop microbial fertilizers which can repair soil, improve fertilizer utilization rate and enhance plant resistance.

  • Continuous cropping obstacle

Continuous cropping obstacle refers to the phenomenon of plant growth weakening, yield decreasing and quality declining even under normal cultivation and management conditions when the same crop or related crop is continuously planted in the same soil. As a result of continuous cropping, a special soil environment is formed, it inhibits the growth and reproduction of beneficial microorganisms such as nitrogen-fixing bacteria, rhizobia, photosynthetic bacteria, actinomycetes, ammonifying bacteria, nitrifying bacteria, mycorrhizal fungi, and so on, while harmful microorganisms proliferate in large numbers and change the soil microflora. 16S/18S/ITS amplicon sequencing enables people to understand the structure of microbial communities in these soils, to make full use of the parasitic, killing or competitive action of some beneficial bacteria to reduce the number of pathogenic bacteria in soil and prevent the spread of disease.

  • Analysis of gastrointestinal microbial diversity

Good gastrointestinal function is essential for maintaining animal health and ensuring productive potential. Animal gastrointestinal tract microorganisms mainly include bacteria, fungi, protozoa and so on. The gastrointestinal tract provides a stable environment for these microorganisms, which convert feedstuffs into vital substances for animals through complex biochemical reactions. The gastrointestinal microorganism has a complex relationship of competition and collaboration, and this dynamic balance in the animal maintains the normal growth of the organism. 16S/18S/ITS amplicon sequencing can detect the microbial community structure in the gastrointestinal tract and assess the health and nutritional status of the host.


  • Water

The number and kinds of microorganisms in the water are enormous. By 16S/18S/ITS amplicon sequencing, people could analyze the population structure and diversity of microorganisms (including prokaryotic microorganisms and eukaryotic microorganisms) in the water (including river water, lake water, glacial meltwater, seawater), and study their dynamic changes. It can provide reliable basis for better acquainting with the microbial composition of water source, optimizing the community structure and regulating the community function, and also provide help for sewage treatment.

  • Air

The atmospheric microbial biosphere is a microbial ecosystem closely related to other environmental biospheres. It is also a biosphere that directly affects human respiratory system and skin. With the wide application of 16S/18S/ITS amplicon sequencing, the microbial diversity and the community structure of air microorganisms have been gradually recognized.

  • Petroleum degradation

With the development of the petroleum industry, a large amount of crude oil and its processed products enter the soil and water. Oil pollution has become a prominent problem in the protection of ecological environment. Compared with physical and chemical methods, bioremediation is considered to be the most economical, efficient and environmentally friendly method. 16S/18S/ITS amplicon sequencing can help researchers discover more and better practical microorganisms. And by adding beneficial microorganisms, oil can be efficiently removed without causing eutrophication.

  • Special / extreme environment

There are many extreme environments in nature, such as glaciers, craters, deep seas and so on. These places are not suitable for the survival of human beings and other animals and plants, but there are a large number of microorganisms living in these circumstances. Extreme microorganisms include thermophilic bacteria, psychrophilic bacteria, halophilic bacteria, acidophilic bacteria, alkalophilic bacteria, barotropic bacteria, and extreme anaerobic bacteria. Because of the special living environment, the complexity of microorganisms and the difference of their functions have great value of scientific research, and the application prospect of their metabolites as products is immeasurable.

At CD Genomics, we are dedicated to providing reliable microbial diversity analysis services, including 16S/18S/ITS amplicon sequencing, full-length 16S/18S/ITS amplicon sequencing, and metagenomic shotgun sequencing.


  1. Edwards, J., Johnson, C., Santosmedellín, C., Lurie, E., Podishetty, N. K., & Bhatnagar, S., et al. (2015) ‘Structure, variation, and assembly of the root-associated microbiomes of rice’, Proceedings of the National Academy of Sciences of the United States of America, 112(8), E911.
  2. Pei, H., Xu, H., Wang, J., Jin, Y., Xiao, H. D., & Ma, C., et al. (2017) ‘16s rrna gene amplicon sequencing reveals significant changes in microbial compositions during cyanobacteria-laden drinking water sludge storage’, Environmental Science & Technology, 51(21), 12774.
  3. Liang, S., Gliniewicz, K., Mendessoares, H., Settles, M. L., Forney, L. J., & Coats, E. R., et al. (2015) ‘Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures’, Bioresource Technology, 179, 268-274.
  4. Neumann, A. P., Mccormick, C. A., & Suen, G. (2017) ‘Fibrobacter communities in the gastrointestinal tracts of diverse hindgut - fermenting herbivores are distinct from those of the rumen’, Environmental Microbiology, 19(9).
  5. Tito, R. Y., Cypers, H., Joossens, M., Varkas, G., Van, P. L., & Glorieus, E., et al. (2016) ‘Brief report: dialister as a microbial marker of disease activity in spondyloarthritis’, Arthritis & Rheumatology, 69(1), 114.
  6. Montoya-Porras, L. M., Omar, T. C., Juan, F. A., Herrera, X. C. M., & Cadavid-Restrepo, G. E. (2017) ‘16s rrna gene amplicon sequencing reveals dominance of actinobacteria in rhodnius pallescens, compared to triatoma maculata, midgut microbiota in natural populations of vector insects from colombia’. Acta Tropica, 178, 327-32.
  7. Moon, J., Jang, Y., Kim, N., Park, W. B., Park, K. I., & Lee, S. T., et al. (2018) ‘Diagnosis of haemophilus influenzae pneumonia by nanopore 16s amplicon sequencing of sputum’, Emerging Infectious Diseases, 24(10).
For Research Use Only. Not for use in diagnostic procedures.
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