Microbial Gene Fragment Analysis

Overview

Traditional microbial inspection methods (such as culture) cannot give a comprehensive qualitative and quantitative view of the microbes, the interaction among microbes and microbes with the environment. Microbial fragment analysis emerged as a method of microbial analysis using differences in gene fragment size or marker fluorescence. It is widely used in the analysis of microbial communities in the fields of medicine, environment, and agricultural research. Generating species-specific and fluorescence labeled 16S ribosomal DNA (rDNA) fragments by terminal restriction fragment length polymorphism (T-RFLP) technology is a suitable tool to overcome the problems of many other methods.

Our Advantages:

Sensitivity - Fragments that vary from only one base pair only are precisely sized
Capacity to perform loads of specimens of DNA fragments in a day
Flexibly conducted custom bioinformatics analysis according to clients' requirements.
Validated and automated experimental process

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Introduction to Our Microbial Gene Fragment Analysis Service

The determination of static or dynamic balances among microorganisms is of fast-growing interest. The generation of species-specific and fluorescently labeled 16S ribosomal DNA (rDNA) fragments by the terminal restriction fragment length polymorphism (T-RFLP) technique is a suitable tool that meets the criteria. For the separation of these fragments, technologies include capillary gel electrophoresis and polyacrylamide gel electrophoresis.

CD Genomics provides T-RFLP technology to fragment microbial genes, the digested amplicons are separated by polyacrylamide gel electrophoresis or by running it in capillary gel electrophoresis. Our microbial gene fragment analysis is multiplexing, allowing the assessment of more than 20 loci in a single reaction, and fragments that vary from only one base pair only are precisely sized. The automated workflows for the analysis of loads of specimens of DNA fragments within a short period.

Microbial Gene Fragment Analysis Workflow

Analysis Content

We have a standard pipeline for microbial gene fragment analysis, which covers raw data handling and in-depth data mining.

PIPELINE	DETAILS
T-RFLP profiles of SSU RNA genes	primer choice enzyme choice electrophoresis method
Distinguish signal from noise	percentage threshold variable percentage threshold standardization to the smallest total peak area statistically significant deviation from mean signal
Alignment of profiles	fixed detection window pre-defined fragment size range hierarchical clustering
Identifying community members	APLAUS TRUFFLER PAT
Visualizing relationships	Principal component analyss (PCA) Multidemnsional scaling (MDS) Self organizing maps (SOM) Additive main effects and multiplicative interactions (AMMI)
Identify groups	Cluster analysis with clustering criteria Model-based approaches
Linking community changes to environmental differences	Canonical correspondence analysis (CCA) Redundancy analysis (RDA)

Sample Requirement

1. Specimens from human, animal, natural and industrial environments, as well as DNA and PCR products.
2. 1.8 < OD_260/280 < 2.0, OD_260/230 ≥ 1.8, no degradation or contamination.

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

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