Our prokaryotic diversity analysis platform based on 16S rRNA gene sequencing aims to characterize prokaryotic diversity productively and economically by utilizing the advanced next/third generation sequencing technology and other molecular biology methods. Our experienced experts employ this platform to assist our clients in meeting both scientific and regulatory requirements.
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Our integrated prokaryotic diversity analysis platform can be used for profiling of prokaryotic community in your samples utilizing diverse molecular biology techniques. The principle of our prokaryotic diversity detection platform is based on the role of 16S rRNA as the molecular marker in prokaryotes. 16S rRNA gene has nine conserved regions and nine hypervariable regions. Among them, V4-V5 region is the best choice for bacterial diversity analysis and annotation due to its high specificity and large amount of database information. The two sets of primers (519F/915R and 344F/915R) offer the highest resolution for archaebacterial diversity analysis. This platform enables both short-read 16S rRNA sequencing by Illumina HiSeq/Roche 454 instruments and full-length 16S rRNA sequencing by PacBio SMRT sequencing or Nanopore sequencing. The generated sequencing data are validated by Sanger sequencing and q-PCR with genus- and species-specific primers. qPCR can also be used to quantify microbial species.
Based on this platform, we provide comprehensive prokaryotic diversity analyses for bacteria, archaea, actinomycetes. Bacteria and archaea are found in a broad range of habitats, such as soils, water, marshlands, and human body. Archaea even survive in harsh environments. The insight into prokaryotic community structure is an efficient way to understand the role of prokaryotes played in environments or human body, hence making use of prokaryotes or their products. Therefore, prokaryotic diversity analysis has been applied in a variety of fields, including basic research (such as prokaryotic evolution and epidemiologic studies), agricultural practice, environmental protection, as well as pharmaceutical, food, healthcare, and other industries. Additionally, we also have eukaryotic diversity analysis platform for eukaryotic samples (such as fungi, algae, protozoa).
Our bioinformatics analysis includes species annotation, diversity analysis, evolutionary analysis, functional profiling, and correlation analysis. The detailed bioinformatics analysis package is outlined in the following table.
Table 1. Our bioinformatics analysis package for prokaryotic diversity detection.
|Bioinformatics analysis||Problems to be solved|
|Species annotation||OTU clustering, species annotation|
|Diversity analysis||α diversity||Species richness within a single microbial ecosystem|
|β diversity||Diversity in microbial community between different environments|
|Meta-analysis||Comparative studies of abundant features between datasets|
|Evolutionary analysis||Construction of phylogenetic tree|
|Functional analysis||Analysis of the Intestinal Microflora||Locate the gut bacteria, predict human disease, and provide disease treatment|
|PICRUSt||Predict functional profiles|
|FAPROTAX||Predict the process of biochemical cycles|
|Tax4fun||Predict functional profiles|
|FunGuild||Predict the ecological roles of eukaryotes|
|Correlation analysis||CCA||Study the relationships between microbes and environmental factors|
1.8 < OD260/280 < 2.0, OD260/230 ≥ 1.8, no degradation or contamination.
Illumina platform: DNA amount ≥ 300 ng, PCR Products ≥400 ng
PacBio platform: gDNA ≥100 ng, PCR Products ≥400 ng
Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, q-PCR data, statistic data, and your designated bioinformatics report.