H.U.Group Research Institute G.K.

H.U.Group Research Institute's microbiome analysis services
(16S rDNA analysis by Next-generation sequencer)

Overview

We provide a service that extracts DNA from various biological samples and analyzes the bacterial 16S rDNA using Next-generation sequencer MiSeq. The DNA sequence information read by the next-generation sequencer is subjected to homology search and various information analyses to compare the microbiome of each sample. We send back a report that summarizes the results of microbiome analysis to the clients.

Our features

Process control utilizing in-house system

-We have originally developed Laboratory Information Management System called LIToMaS.
From sample reception to analysis, we are monitoring progress in real time on LIToMaS.

In-house pipeline and originally developed database

-In order to respond to the new informatics methods and update the latest information of the sequence database, we have been developing the pipeline and the originally developed database by in-house.

Validated workflow

-We are conducting various studies to verify the validity. The details are below.

• Performance evaluation of bacterial DNA extraction reagents for feces and saliva samples.
• Performance evaluation of Sample container and fixing solution.
• Examination of library amplification conditions.
• Performance test of automatic dispensing machine.
• Confirmation of simultaneous repeatability and daily difference repeatability.
• Definition and setting of detection sensitivity.

Quality control system

-We are performing quality checks at different four stages in progress. For example, we check the following items: Quality check of extracted DNA, Library amplification check, Sequence quality check, and other checks.

Adoption of DNA extraction control and sequence control

-By adopting the control of the DNA extraction process and the DNA amplification process, we are determining whether the test is successful before sequencing.

Literature survey report of characteristic bacteria

-A researcher with specialized knowledge will survey literature related to the identified bacteria.

Description of main services

• Purification of DNAs from a various specimens.
• Amplification of 16S rDNA V3-4 region and its barcode labeling.
• Obtaining the DNA sequence information by using Next-generation sequencer.
• Basic bioinformatics analysis.

  -Calculation of α diversity・β diversity
  Alpha diversity indicates species diversity in one sample. While, Beta diversity is species diversity differences between different samples.

  -Stacked bar graph
  Stacked bar graph shows the relative abundance of bacterial genus level in each sample.

  -Heat map
  Heat map shows the bacterial microbiome in the samples and the relative abundance for each genus.

• Advanced bioinformatics analysis.
  

  -Principal coordinate analysis (PCoA)
  PCoA plots show the data present in the beta diversity distance matrix. Generally it is shown as a two-dimensional plot.

  - Linear discriminant analysis effect size (LEfSe) LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848/).

End-to-End Service

Since we own various equipment such as MiSeq,NextSeq and PacBio, metagenome shotgun analysis, long read analysis, and other analysis (e.g.: determination of genome of the strain) are now available. From the planning of client's test to the informatics, and the subsequent data meaning, we are able to provide a custom service along with client's demand. Please feel free to contact us.

Request and Inquiry

If you have any questions or requests, please contact us via e-mail or inquiry form. A staff in charge will contact you later.