Amplicon Sequencing for Microbiome Research: Introduction, Advantages, and Applications
The identification of microbial groups is an important step in understanding the interrelationship of microorganisms in a community. It is done to determine all present microbial taxa and their relative abundance, and as well their phylogenetic relationships. One of the methods used to establish phylogenetic relationships is by sequencing common genes. One of the easiest genes to be sequenced are DNA barcodes or short sequences of housekeeping genes which are highly conserved in all species and contains high levels of variability enough to identify organisms up to the species level. For microorganisms, common DNA barcodes are the 16S and 18S ribosomal RNA sequences and the Internal Transcribed Spacer (ITS) genes which are commonly used to classify bacteria, archaea, and fungi.
Microbial amplicon sequencing by Next Generation Sequencing (NGS) technologies made it easy to use these housekeeping genes to identify microorganisms. This method has been widely used for the rapid diagnosis of bacteria in clinical, environmental, and industrial samples. Rapid pathogen identification aids in providing clinical diagnosis and selecting appropriate antibiotic treatment. It is also used in routine identification of bacteria in clinical laboratories to retrieve clinically relevant information to determine the role of microorganisms in disease, health, pathogenicity, epidemiology, etc. Amplicon-based NGS has also shown its potential application in virus detection. In the recent emergence of the COVID-19, amplicon sequencing has been used to design rapid testing kits that confirm the presence of the virus in clinical respiratory samples.
Another application of 16S, 18S, and ITS sequencing is for microbial community profiling. An example of this is in determining microbial communities that contribute to soil enrichment in order to select the best soil type for agricultural application depending on the crop to be planted. rRNA gene amplicons show their potential in analyzing water quality by identifying dominant microbial groups present in the water at a particular time which can be used to detect contamination, such as by fecal microorganisms.
Also, in determining animal gut microbiota, this sequencing technology has proven its effectivity to properly profile microbial members of the gut microbiota of animals and humans and to detect variations in the members and their abundance that could aid in disease diagnosis.
In terms of food, profiling of bacterial communities that are known to contaminate food is essential to determine appropriate food preparation and processing techniques in order to prevent contamination of food. Common processing of food, such as fermentation, pasteurization, and preservation, are designed depending on the knowledge of common food pathogens that contaminate food.
Profiling microbial communities and microbiomes are beneficial in understanding key processes happening in the environment. Establishing phylogenetic relationships can also help in comprehending the behavior of microbial groups and predict their evolutionary tendencies. 16S, 18S, and ITS amplicon sequencing provide a rapid and accurate method of microbial classification that can be useful for microbial profiling studies.
About CD Genomics
CD Genomics has become one of the top providers in genomic research, devoting to providing reliable services to pharmaceutical and biotech companies as well as academia and government agencies. CD Genomics MicrobioSeq division is further developed with the mission to accelerate the entire microbiome industry toward breakthrough discoveries. Through years of efforts, CD Genomics MicrobioSeq has been an internationally leading provider of microbial sampling products, microbial testing services, microbial genomics services, and integrated bioinformatics services for hospitals, food, diagnostics, pharma, agriculture, biotechnology, and research institutes.
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