Microorganism Species Analysis and Component Analysis

Significance of the Topic

Microorganisms play pivotal roles across food production, environmental remediation, pharmaceutical development, clinical diagnostics and biotechnology. Their applications range from fermentation processes (e.g., sake, beer, yoghurt), antibiotic and vitamin synthesis, to wastewater treatment and soil cleanup. Conversely, pathogens such as E. coli O157, norovirus and antibiotic-resistant bacteria (MRSA) pose serious health risks. Comprehensive analytical methods are therefore essential for identification, quantitation and functional characterization of microbial species and their metabolites.

Aims and Overview

The brochure presents Shimadzu’s integrated solutions for microorganism analysis, spanning microscopy, genomic, proteomic, metabolomic and elemental methods. Key objectives include:

• High-resolution morphological observation
• Accurate species identification and community profiling by full-length 16S rDNA sequencing
• Rapid detection of specific pathogens and viruses
• Chemical classification via microbial component analysis (lipids, quinones, metabolites)
• Proteome and metabolome profiling using MS techniques
• Fast, high-sensitivity quantitation of amino acids, organic acids, saccharides and toxins
• Elemental analysis of trace and major metal constituents

Methodology and Instrumentation

Shimadzu offers a broad instrument portfolio:

• Scanning Probe Microscope SPM-9600 for submicron morphology of bacteria and flagella
• DeNOVA-5000HT BioMEMS DNA Sequencer plus BioSpec-nano and MultiNA for high-throughput full-length 16S rDNA metagenomics
• LCMS-2020 and GCMS-QP2010 Plus for lipid (menaquinone) profiling and metabolite databases (amino acids, fatty acids, organic acids)
• Prominence HPLC and UFLC systems with fluorescence, ELSD and conductivity detectors for rapid analysis of amino acids, saccharides and organic acids
• Ampdirect® Plus reagent and Norovirus G1/G2 Detection Kit for direct PCR/RT-PCR detection of pathogens without elaborate nucleic acid purification
• AXIMA MALDI-TOF MS (Performance, Confidence, Assurance) for intact-cell microbial profiling, peptide, lipid and metabolite screening, and proteomic PMF and MS/MS sequencing (with PPSQ sequencer)
• UV-VIS spectrophotometers (UV-1800/2550) and RF-5300PC spectrofluorometer for nucleic acid and protein quantitation
• Energy-dispersive XRF (EDX-GP, µEDX series) and inductively coupled plasma (ICPE-9000, ICPM-8500) and AA-7000 atomic absorption for elemental analysis

Main Results and Discussion

• SPM-9600 revealed detailed bacterial surface features and flagella at 10,000× magnification with minimal sample prep.
• DeNOVA-5000HT achieved >4 Mb/day decoding of full-length 16S rDNA, enabling clear differentiation of closely related species and monitoring of microbial shifts in aerated wastewater treatment.
• LCMS-2020 profiling of actinomycete menaquinones provided genus-level chemotaxonomic markers, while GC/MS plus metabolite libraries enabled fast identification of >300 metabolites with high retention index accuracy.
• Ampdirect® Plus and Norovirus kits delivered pathogen gene detection in complex matrices (feces, foods) in under three hours, eliminating DNA/RNA extraction steps and reducing cross-contamination risks.
• AXIMA MALDI-TOF MS intact-cell analysis differentiated species by unique spectral fingerprints and profiled yeast metabolites and bioactive peptides/lipids directly from colonies in minutes; proteome PMF workflows identified E. coli proteins from 2D gels.
• Prominence HPLC/UFLC applications achieved sub-10 min separations of amino acids, organic acids, saccharides and cephem antibiotics with high resolution and reproducibility.
• LCMS-2020 SIM methods quantified aflatoxins at 0.5 ppb with S/N > 60 conforming to official regulations; nucleic acid base/nucleotide analysis by LCMS delivered sensitive profiling in fermented beverages.
• BioSpec-nano simplified nucleic acid quantitation using 1–2 µL drops; UV and fluorescence systems extended biomolecule assays with high S/N and automated sampling. EDX and ICP methods provided non-destructive and multi-element quantitation down to ppt levels.

Benefits and Practical Applications

The integrated Shimadzu ecosystem streamlines workflows, reduces sample prep, boosts throughput and enhances sensitivity across life-science, food safety, environmental monitoring, clinical diagnostics, QA/QC and industrial biotechnology. Users achieve rapid pathogen screening, comprehensive microbiome characterization, chemotaxonomic classification, metabolomic and proteomic analyses, and precise elemental assays within a unified platform.

Future Trends and Possibilities

Innovations will focus on higher-throughput genomics and metagenomics, real-time online monitoring in bioprocesses, AI-driven spectral interpretation, miniaturized portable MS instruments, integrated multi-omics platforms, and greener reagents/protocols for sustainable laboratory practices.

Conclusion

Shimadzu’s total solutions for microorganism analysis leverage advanced microscopy, sequencing, chromatography, mass spectrometry and spectroscopy to address the entire analytical workflow. Their high sensitivity, speed and automation capabilities empower researchers and industry practitioners to tackle complex microbial challenges and drive innovation in health, food, environment and biotechnology.

References

• Shimadzu Corporation. Microorganism Solutions Brochure, 3295-12904-15A-NS.
• JQA-0376 Certification, Shimadzu Corporation, Tokyo, Japan.