Prokaryotic Diversity Analysis

Overview

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.

Our Advantages:

Extensive experience.
Targeted region sequencing, enabling a rapid and efficient workflow.
More than 70% of our team is PhD and Masters-level scientists.
Advanced sequencing platforms.

Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Introduction to Our Prokaryotic Diversity Analysis

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).

Prokaryotic Diversity Analysis Workflow

Bioinformatics Analysis

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
	VPA
	Network analysis

Sample Requirement

1.8 < OD_260/280 < 2.0, OD_260/230 ≥ 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.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.