DNA sequencing of microorganisms and microbiota

Purpose

DNA is the foundation of most microbial biology, making sequencing a powerful tool with many applications. It can be used to trace microbial contamination in production facilities, analyze microbiota composition in clinical samples, identify infection biomarkers and vaccine candidates, or detect resistance genes in isolated bacteria. Beyond harmful microbes, we also work with beneficial microorganisms in products, processes, microbiota, or the environment (e.g., food production microbes or bacteria that degrade persistent compounds). For example, we can monitor microbiota changes during fermentation or product storage.

A key advantage of sequencing is the ability to analyze the entire microbiome—not just cultivable organisms.

How RISE can support your sequencing project?

We conduct sequencing projects involving viruses, bacteria, yeasts, and molds, as well as antimicrobial resistance and other traits. Our expertise spans sampling and DNA extraction from complex samples, with deep understanding of customer needs. Our knowledge is built through in-house research and close collaboration with industry in applied and contract research.

We can also complement genomics or metagenomics with other omics approaches (e.g., transcriptomics, proteomics) to gain deeper insights. Multi-omics enables solving complex problems previously out of reach, especially when integrated using advanced data analysis and AI.

We offer full or partial project support, including:

• Study design and planning: methodology, sampling strategy, sequencing technique selection, and analysis planning.
• Sampling from complex environments, products, and biological materials.
• Sample preparation and DNA extraction in Bio Safety Level 2 (BSL2) labs.
• Sequencing using short-read (e.g., Illumina) and long-read (e.g., Oxford Nanopore) technologies:
  • Whole genome sequencing of bacterial isolates for identification, outbreak tracing, resistance gene detection, virulence markers, novel functions, etc.
  • Amplicon sequencing (e.g., 16S rRNA, ITS) for microbiota composition analysis.
  • Shotgun metagenomics for characterizing unknown microorganisms and microbiota.
• Bioinformatics analysis (e.g., strain comparison, SNP analysis, MLST, cgMLST, genome assembly from metagenomes) for product development, quality control, benchmarking, outbreak tracing, microbiome profiling, biomarker discovery, etc.
• AI-driven integration of genomics/metagenomics with other omics data for interpretation and decision support.
• Customized training

Methodology

We use modern high-throughput sequencing technologies, including Next-Generation Sequencing (NGS, e.g., Illumina) and third-generation sequencing (e.g., Oxford Nanopore). Depending on project needs, we apply and adapt microbiological methods from sampling and DNA extraction to sequencing and data interpretation.

We can also integrate other omics methods such as transcriptomics, proteomics, metabolomics, glycomics, and lipidomics.

Project overview DNA sequencing

1. Sample collection
   Representative samples are collected from products, processes, clinical materials, or environments. Microorganisms are isolated or microbial DNA is extracted, purified, and quality-checked.
2. Library preparation and sequencing
   Extracted DNA is prepared for sequencing and processed in sequencing instruments that read the DNA sequence.
3. Bioinformatics
   Powerful computing tools filter and analyze the large volumes of sequencing data. Genomes are reconstructed and compared to reference databases (e.g., ENA, GenBank) to identify organisms and genes of interest (e.g., resistance, virulence).
4. Analysis and interpretation
   Our research team interprets the findings, studying genetic variants and their implications using databases, literature, and custom scripts tailored to the project.
5. Results
   A report is produced summarizing the sequencing findings and analyses. If needed, we also provide oral presentations to support decision-making.

Deliverables

The results are summarized in a report and presented orally to the client.