DNA sequence analysis is the process of comparing and phylogenetically analyzing the DNA sequences obtained with standard nucleic acid sequences to identify microbial species by means of a decision criterion. Common DNA sequence analyses include 16S rDNA, 26S rDNA, ITS rDNA, housekeeping gene sequences and whole genome sequences, etc., which can be used for the identification of microorganisms such as bacteria, yeasts and filamentous fungi (moulds).

16S rDNA sequence analysis

16S rDNA is the most commonly used marker gene in bacterial phylogenetic taxonomy research. It contains both highly conserved regions and moderately conserved and highly variable regions, which is suitable for the study of the taxonomic relationships of various bacteria types with different evolutionary distances. 16S rDNA sequence analysis is a common method for the identification of bacteria at genera and species level.

House-keeping gene sequence analysis

House-keeping genes are genes that are stably expressed within the cell and maintain minimal cellular function. House-keeping gene sequence analysis can be used to determine the taxonomic units of microorganisms, especially when identification by rDNA is difficult.

ITS rDNA sequence analysis

ITS (internal transcribed space), ITS1 is located between 18S and 5.8S rDNA, and ITS2 is located between 5.8S and 28S rDNA. ITS1 and ITS2 are often collectively referred to as ITS, and the 5.8S rDNA gene is located between ITS1 and ITS2. The ITS rDNA sequence is a moderately conserved region, exhibiting relative intra-species consistency and more pronounced inter-species variation. Because ITS rDNA sequence fragments are short and easy to analyze，ITS rDNA sequence analysis has been widely used in the phylogeny of fungi between different species or similar genus.

Whole genome sequence analysis

Whole genome sequence is the base composition of all genetic material in cells of organisms. The whole genome sequence of microorganisms can be obtained by high-throughput sequencing technology, and it can be further used for species identification, strain typing, function mining and safety evaluation and other analyses. With the rapid development of sequencing technology and the decreasing cost of sequencing, the application of whole genome sequence analysis has become more and more widespread. In recent years, whole genome sequence analysis has been successively introduced into the regulations and guidelines in the fields of food, medicine, feed and other fields. Compared with traditional microbial identification methods, whole genome sequence analysis has significant advantages in resolution and accuracy, and it has become one of the routine techniques in molecular biology laboratories.