Sequencing Platform |
Illuminia MiSeq ™, NextSeq2000 ™ |
Read Length |
2 x 300 bp, Unique Dual Indexing (UDI) |
Target Regions |
V1-V2, V1-V3, V3-V4, V3, V4, V4-V5, V5-V6, V6-V8, ITS2, 18S
Others available upon request
|
Accepted Sample Types |
Extracted Genomic DNA, or raw samples |
DNA Extraction |
ZymoBIOMICS 96 Magbead DNA (D4308)
ZymoBIOMICS DNA Miniprep (D4300)
|
Library Prep |
Quick-16S NGS Library Prep (D6400)
Quick-16S Plus NGS Library Prep (D6421)
|
Plastid rRNA Blockers |
PNA PCR Blockers
Blocks amplification of the V4 region of chloroplast and mitochondrial rRNA genes
|
Absolute Quantification |
Quantification of absolute 16S or ITS gene copy number using qPCR with library preparation primers |
Quality Control |
A positive control for DNA extraction (ZymoBIOMICS Microbial Community Standard, D6300) and a positive control for library preparation (ZymoBIOMICS Microbial Community DNA Standard, D6305) are included in each project as a quality control. Results are reported in the final project report. Negative extraction controls and negative qPCR controls are also monitored with real time PCR and can be analyzed upon request. |
Sequencing Analysis |
Amplicon Sequence Variant (ASV) based analysis with DADA2 and Qiime 1.9 to provide higher accuracy and better resolution of data. |
Reference Database |
As publicly available databases (e.g. Greengenes, UNITE) contain a multitude of errors, inconsistent annotations, and poor sequence quality, we utilized an in-house curated reference database. |
Data Visualization |
Absolute abundance boxplot, taxa abundance barplot, taxa abundance heatmap, ASV abundance heatmap, alpha diversity boxplot and rarefaction curves, beta diversity 3D Emperor plot, Taxa2ASV decomposer |
Statistical Analysis |
LEfSe analysis uncovers taxa/traits that are differentially distributed among defined sample groups. |
Data Storage |
Raw sequencing data and analysis report are stored for up to 3 months |