Microorganism Species Analysis and Component Analysis

Importance of the Topic

Microorganisms have a profound impact on human health, food production, biotechnology and environmental sustainability. They are indispensable in fermented foods, antibiotic and vitamin production, wastewater treatment, soil remediation and biotechnological innovations. At the same time pathogenic and antibiotic-resistant species pose serious threats. Advanced analytical solutions are essential to identify, quantify and characterize microbial species, their metabolites and interactions with the environment.

Objectives and Overview

This summary reviews Shimadzu’s integrated analytical portfolio to support microorganism research and control across diverse fields such as medicine, food, environment and industrial biotechnology. It covers key applications for:

• Morphological observation
• Genome and metagenome analysis
• Rapid detection of pathogens
• Chemical classification via low-molecular profiling
• Direct whole-cell mass spectrometry
• Proteomics and metabolomics
• Chromatographic separation of small molecules
• Trace element and metal analysis

Methodology and Instrumentation

Shimadzu’s solutions range from high-resolution microscopy to mass spectrometry, chromatography, spectrophotometry and elemental analysis. Instruments include:

• SPM-9600 scanning probe microscope for detailed bacterial morphology
• DeNOVA-5000HT BioMEMS DNA sequencer for full-length 16S rDNA decoding
• Ampdirect Plus reagent and Norovirus G1/G2 kit for direct PCR-based detection
• MALDI-TOF MS AXIMA series for intact-cell microbial fingerprinting and metabolite profiling
• LCMS-2020 UFLC–MS for isoprenoid quinones, aflatoxins and nucleic-acid derivatives
• Prominence HPLC/UFLC with fluorescence, ELSD and conductivity detectors for amino acids, saccharides and organic acids
• GCMS-QP2010 Plus with metabolite database for rapid amino, fatty and organic acid screening
• BioSpec-nano spectrophotometer and MultiNA microchip electrophoresis for nucleic acid quantitation and fragment analysis
• UV-1800 UV-VIS and RF-5300PC fluorophotometer for protein and antibody assays
• AA-7000 atomic absorption, EDX-GP and µEDX X-ray fluorescence, ICPE-9000 and ICPM-8500 ICP-MS for elemental and metal analysis

Main Results and Discussion

1. High-resolution imaging with the SPM-9600 revealed bacterial shapes and flagella at nanometer scale with minimal sample preparation.
2. DeNOVA-5000HT sequencing of full 16S rDNA enabled accurate taxonomic resolution in wastewater metagenomics, tracking shifts in bacterial communities through treatment stages.
3. LCMS-2020 analysis of menaquinones provided a chemical index for genus-level classification of actinomycetes via isoprenoid quinone profiling.
4. Ampdirect Plus and Norovirus kits achieved direct PCR amplification from fecal or environmental samples without DNA/RNA purification, enabling rapid pathogen screening.
5. AXIMA MALDI-TOF MS facilitated intact-cell microbial identification and high-throughput metabolite fingerprinting of yeast strains, including citric and glutamic acids as discriminators.
6. Proteome analysis combined 2D electrophoresis, in-gel digestion and PMF/MS/MS on AXIMA, identifying key E. coli proteins with high throughput.
7. GCMS-QP2010 Plus with Shimane University’s metabolite database supported batch profiling of over 300 amino, fatty and organic acid derivatives in microbial extracts.
8. Prominence HPLC and UFLC platforms delivered ultra-fast separation and sensitive detection of saccharides, amino acids, organic acids and cephem antibiotics, reducing run times by up to 90%.
9. LCMS-2020 SIM and MS-MS achieved ppb-level aflatoxin quantitation and high-throughput nucleic acid and purine compound analysis in food samples.
10. Spectrophotometric and elemental techniques offered 1–2 µL nucleic acid quantitation, fluorescence antibody assays, and multi-element analysis in powders, liquids and solids at ppb–ppt levels.

Benefits and Practical Applications

Shimadzu’s integrated approach delivers:

• Enhanced sensitivity, specificity and throughput
• Minimal sample preparation and direct analysis of complex matrices
• Comprehensive workflows from morphology and genomics to proteomics, metabolomics and elemental profiling
• Reliable quantitation complying with regulatory standards (e.g. aflatoxins, pathogens, elemental contaminants)
• Scalable solutions for routine QC, research and industrial process monitoring

Future Trends and Possibilities

Advances will focus on real-time, in situ monitoring, single-cell analytics, microfluidic integration and AI-driven data interpretation. Enhanced bioinformatics, cloud connectivity and miniaturized platforms will enable wider adoption in field testing, rapid outbreak response and personalized microbiome and environmental assessment.

Conclusion

Shimadzu’s total solutions for microorganism analysis enable comprehensive and efficient investigation from cellular morphology through multi-omics to elemental composition. This integrated toolkit supports diverse applications in healthcare, food safety, environmental management and industrial biotechnology, driving innovation in microbial science and quality control.