Microbial diversity describes the number of different species of microbes present and their distribution. The study of microbial community diversity and the interrelationship between different microbial communities helps in fully understanding their contribution to the environment as well as in the discovery of new organisms and genes that are valuable to biotechnology.
The members of microbial communities tend to rely on the changes in the environment, such as availability of resources, temperature, solute concentration, and pressure. With modern techniques such as rank abundance curve, microbial taxonomy & species identification, and Venn diagram, the diversity of microbial communities can be analyzed and unveiled.
Rank abundance curve (RAC) is a computational measure of relative species abundance, species richness, and species evenness. The construction method is to count the number of sequences contained in each OTU in a single sample and sort the OTUs according to the abundance (number of sequences contained) from large to small. It is presented as a graph showing the abundance rank (x-axis) and the relative abundance (y-axis). RACs provide essential information that supports species richness and community complexity.
The rarefaction curve is to randomly select a certain number of individuals from the sample, and count the number of species represented by these individuals. The curve is composed of the number of individuals and species and when the curve tends to be flat, it indicates that the sequencing data volume is reasonable.
Microbial taxonomy deals with the identification, classification, and nomenclature of microorganisms. Microbiologists sort the sequences into each OTU according to the similarity of their base composition. When performing taxonomic analysis, researchers compare each high-quality sequence with the SILVA database to find the specific information that is closest and has the credibility of more than 80%, following all sequences in each OTU are compared to find out the specific information of the closest ancestors with different sequences in the same OTU.
Shannon Diversity Index reflects the level of microbial diversity in a sample or community. When the curve tends to be flat, it indicates that the sequencing data volume is large enough to reflect most of the microbial information in the sample. Analytical tools used in the Shannon diversity index include mothur software, R language tool, and other related tools.
In the microbial population analysis, for data with fewer groups (≤5), researchers can draw a Venn diagram to statistically analyze the species and numbers of unique or common species among different sample groups, and visually display the similarity and overlap of species composition among sample groups. In the Venn diagram, the number in each petal represents the number of species unique to the corresponding group, and the sum of the numbers in each circle represents the total number of species in the group. In general, an OTU with a similar level of 97% is selected for analysis.
With the aid of these useful visualization tools, microbial researchers can quickly and accurately analyze microbial community diversity and predict how communities will respond to novel environmental conditions. In addition, microbial diversity study can also provide insights into the treatment of human diseases as the microbiome plays a vital role in human health and homeostasis.