16S/18S/ITS amplicon sequencing is a commonly used method for studying taxonomic composition, phylogenetic structure and relative abundance of species in a microbial community. In brief, the hypervariable regions (V3 and V4) of 16s rDNA in prokaryote, while in case of eukaryote the hypervariable regions (V1-V9) of 18s rDNA or the ITS region are amplified by PCR. Then the amplicons are sequenced on high-throughput sequencing platform. Data analysis of these unique hypervariable regions is able to reveal the differences in composition and abundance of bacteria, fungi and archaea across environmental samples. This method thus plays a crucial role in studying the composition and dynamic changes of microbiomes in complex water, soil or fecal matter samples.
Technique Highlights
— Study of microbial communities without prior culturing
— High-throughout method generates high volume sequence data with low cost
— High accuracy without sample bias
— Assessing community sample in situ objectively reflects the diversity and dynamics of the community.
— Ability to identify novel microbes and novel genes in environmental community samples
Sample Requirement
Sample type: Genomic DNA
Sample quantity: DNA >= 5 ug; concentration >= 100 ng/ul
Sample purity: OD260/280 = 1.7~2.0
Sample without severe degradation
Schematic workflow from sample preparation to bioinformatics data analysis
Service Workflow
Deliverables
a. Sequencing data QC
b. Reads assembling assembling, obtain unique tags
c. OTU generation and statistic analysis
d. Species assignment and abundance statistics
e. OTU and species abundance heatmap
f. Alpha diversity analysis
g. Beta diversity analysis
h. PCA analysis
i. PCoA analysis
j. UPGMA
k. Inter-group significance of variance analysis
l. Phylogenetic tree generation
