Page 6 - Microorganism Species Analysis

DNA Sequencer DNA Sequencer
Genome Information
Microorganism Solutions Microorganism Solutions

Identification of Bacteria by Gene Analysis Data
The identification of microorganisms by gene analysis has become the general method in recent years. The Japanese
Pharmacopoeia shows a method of sequence analysis of part (approx. 300 bases) of bacterial 16S ribosomal DNA (rDNA). Gene Analysis of Changes in Microorganism Communities During Water Treatment
However, in practice it may not be possible to clearly distinguish between extremely closely related types using sequence
The treatment of factory effluent has been attracting greater attention in recent years as one approach to corporate Microorganism Species Observation of
information for only about 300 bases, and multiple types of bacteria can be identified as identical. It is believed that sequence
environmental management. Shimadzu installed and operates a wastewater treatment system that uses aeration. The
analysis of the entire 16S rDNA (approx. 1,500 bases) is required for accurate identification of bacteria by gene analysis.
example below shows the evaluation of changes in bacteria flora detected before and after the treatment process.
Sequence decoding with a general DNA sequencer is adequate for a restricted number of samples, such as colonies of
Observation of
specific bacteria produced by separation and cultivation. However, the throughput of a general DNA sequencer is too low to
conduct large-scale gene analysis, such as for the currently topical metagenome analysis that identifies microorganisms in Effluent from part washing Defoamer Defoamer
Microorganism Species
entire bacteria colonies. The DeNOVA-5000HT, which allows low-cost, long-chain decoding of multiple samples, is ideal for
such analysis. Treated wastewater
Kitchen effluent
Constant Primary Secondary
volume treatment treatment
pump tank tank
Washing
Features of Microorganism Community Analysis Systems Using wastewater Compressor
tank
the DeNOVA-5000HT High-Throughput BioMEMS DNA Sequencer Microorganism Species Identification of
The DeNOVA-5000HT can decode long-chain sequences of 800 bases or more with high statistical reliability (QV >
30 (99.9% reliability)). It covers the entire 16S rDNA (approx. 1,500 bases) with two sequence reactions and Feed pump
Identification of
decoding from both termini. Drain outlet
Compressed air
The DeNOVA-5000HT can continuously analyze 384 samples over 24 hours to decode more than 4 Mb per day. Raw water
Microorganism Species
The DeNOVA-5000HT has an especially high capacity for decoding long chains, which are not handled well by other tank ( indicates special nozzles)
genome sequencer systems.
Fig. 1 Schematic Diagram of Wastewater Treatment System
BioSpec-nano is a specialized spectrophotometer for routine laboratory needs for nucleic acid research. It can
analyze samples of 1 to 2 µL. To start the analysis, simply drop the sample on to the target and click a button. Test and research flow
MultiNA uses reusable microchips to achieve automated, high-sensitivity analysis of nucleic acid samples, such as 1. Take constant-volume wastewater samples at each stage before, during, and after treatment and extract the DNA
PCR amplified fragments and restriction enzyme digestion fragments. It allows high-performance, automated from microorganisms in wastewater.
analysis of up to 120 analyses at 80 sec minimum cycle time. 2. Amplify the 16S rDNA gene by PCR. Create a 16S rDNA library by gene cloning. Specific Microorganisms Detection of
3. Conduct qualification and quantitation of the PCR amplification products using MultiNA or BioSpec-nano.
4. Use a DNA sequencer to decode the entire base sequence of the 16S rDNA gene (approx. 1,500 bases).
Detection of
5. Conduct BLAST searches based on the sequence data and verify against the bacteria 16S rDNA gene sequence
database to identify the bacteria type by sequence homology.
Specific Microorganisms
Table 1 shows the bacteria types detected or identified in wastewater before, during, and after treatment.
Decoded sequence information
Database search Multiple types of bacteria were detected in the wastewater environment, including several known environmental
(BLAST search) bacteria.
Gene analysis can easily capture changes in bacteria communities, such as significant increases in species during
water treatment by aeration.
Microorganism sequence database search Analysis of Microorganism-Derived
Sequence homology search Table 1 Number of Bacteria Detected in Wastewater Before, During, and After Water Treatment Components
Multiple alignment analysis
Treatment
Creation of genealogical tree
Components
BLAST Top HIT Before During After
DeNOVA-5000HT Ideonella sp. 6 8 3
High-Throughput BioMEMS DNA Sequencer Sphingomonas sp. 6 5 4
Rhodobacter sp. 4 4 2
Analysis of Microorganism-Derived
Asticcacaulis sp. 2 5 6
Sinorhizobium 2 3 4
Brevundimonas sp. 2 0 3
Diaphorobacter nitroreducens 0 4 1
Leadbetterella sp. 0 0 3
Brevundimonas diminuta 0 0 2
Uncultured Bacterium PSB-M-1 0 2 0 Other Applications
Uncultured Bacterium A0640 0 2 0
Uncultured Bacterium 054 E02 B DI P58 2 0 0
Uncultured Bacterium LP B54 4 3 0
Other Applications
BioSpec-nano MCE-202 MultiNA Uncultured Bacterium HP1B26 3 2 0
Life Science Spectrophotometer Microchip Electrophoresis System MultiNA Microchips and Reagent Kits Uncultured Bacterium 17 18 21
for DNA/RNA Analysis Other species 9 5 11
6 7