Microorganism Species Analysis and Component Analysis

Importance of the Topic

Microorganism analysis underpins critical advances in healthcare, food safety, environmental protection, and biotechnology. Determining which microbes are present, their genetic identity, and their biochemical activity enables rapid detection of pathogens, quality control in manufacturing, exploration of novel bioactive compounds, and monitoring of ecological processes.

Aims and Study Overview

This brochure presents a comprehensive workflow for microorganism research, illustrating methods from basic morphological observation through genome sequencing, chemical profiling, targeted gene detection, and metabolite analysis. It highlights Shimadzu’s solutions designed to accelerate identification, quantification, and functional evaluation of bacteria, fungi, and viruses.

Methodology and Instrumentation

• Microscopy: Optical and scanning probe microscopy (SPM-9600) for high-resolution morphological inspection without extensive sample preparation.
• Genome Analysis: High-throughput BioMEMS DNA sequencing (DeNOVA-5000HT), coupled with sample quantitation by BioSpec-nano and MultiNA microchip electrophoresis.
• Chemical Classification: LC/MS profiling of lipid and quinone biomarkers using the LCMS-2020 combined with Prominence HPLC or Prominence UFLC separations and GCMS-QP2010 Plus for volatile metabolites.
• Targeted Gene Detection: Direct PCR amplification using Ampdirect Plus reagent to bypass DNA purification, with analysis on MCE-202 MultiNA and real-time PCR platforms.
• Viral Screening: RT-PCR detection of norovirus genogroups G1/G2 using a dedicated reagent kit directly on fecal specimens.

Main Results and Discussion

• SPM imaging resolved sub-micron bacterial structures, revealing flagella and cell surface detail not visible by optical microscopy.
• Full-length 16S rDNA sequencing on DeNOVA-5000HT enabled accurate community profiling in wastewater before and after aeration treatment, showing dynamic shifts in microbial populations.
• LCMS-2020 analysis of menaquinone homologues provided distinctive chemical fingerprints for actinomycete species, informing taxonomic classification.
• Ampdirect Plus allowed sensitive detection of Escherichia coli O157 toxins and environmental fungi directly from complex matrices with minimal processing.
• The norovirus RT-PCR kit demonstrated reliable amplification of two genogroups from stool samples without RNA purification steps.

Benefits and Practical Applications

• Reduced sample preparation time and contamination risk through direct amplification reagents.
• High-throughput sequencing and automated electrophoresis accelerate microbial community studies and quality control checks.
• Chemical profiling supplements genetic methods, offering complementary taxonomic and functional insights.
• Rapid pathogen screening supports food safety regulations and clinical hygiene monitoring.

Future Trends and Potential Applications

Advances in integrated microfluidics, metagenomic sequencing, and real-time mass spectrometric monitoring will further streamline microbial workflows. Emerging applications include on-site environmental surveillance, personalized microbiome profiling, and automated bioprocess control.

Conclusion

Shimadzu’s suite of instruments and reagents provides an end-to-end platform for microorganism research, from visualization and genetic identification to targeted detection and metabolite analysis. These solutions enhance accuracy, throughput, and simplicity across diverse fields, supporting ongoing innovation in microbiology.

Použitá instrumentace

• SPM-9600 Scanning Probe Microscope
• DeNOVA-5000HT BioMEMS DNA Sequencer
• BioSpec-nano Spectrophotometer
• MCE-202 MultiNA Microchip Electrophoresis System
• Prominence HPLC and UFLC Systems
• LCMS-2020 UFLC-MS
• GCMS-QP2010 Plus
• Ampdirect Plus PCR Reagent
• Norovirus G1/G2 RT-PCR Detection Kit