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Cmbio
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  5. Microbial Strain Assessment Services

Microbial Strain Assessment Services

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At Cmbio, we deliver fast and affordable microbial strain characterization services to support your research at every stage. Our services and state-of-the-art technologies uncover critical insights into microbial strains in order to explore their diversity, functionality, and applications. 

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We offer rapid and cost-effective microbial strain characterization services, supporting your research, from isolate identification to full genomic DNA insights. Our team has extensive genomics experience and continuously develops cutting-edge bioinformatics and sequencing methods (read about it in Nature Methods), ensuring valuable insights for our customers.

Our microbial strain characterization services include:

  • Whole Genome Sequencing (WGS)
    Whole-genome sequencing (WGS), de novo assembly, gene annotation, and bacterial isolate genome sequencing provide detailed taxonomic identification and insights into functional potential. Whole genome sequencing data is crucial for understanding gene expression and methylation patterns, strain typing, virulence factors, and antibiotic susceptibility. 

  • Long-Read DNA sequencing/Oxford Nanopore Technologies (ONT)
    Long-read DNA sequencing (Oxford Nanopore Technologies) is the superior method for closed reference-grade prokaryote genomes. 

  • Short-Read DNA Sequencing 
    We also offer short-read DNA sequencing for special use cases, although it is not recommended by default. For some microbial species, especially higher eukaryotes, it is advisable to supplement long-read data with some low-coverage short-read data for the final polishing of genome assembly.

Following 6 simple steps, our process turns your raw sample data into detailed strain characterization reports:

  1. Sample preparation & shipment
  2. DNA extraction
  3. DNA sequencing
  4. Genome de novo assembly
  5. Bioinformatics analysis
  6. Reporting
  • Optional pre- and post-project meetings with a specialist
    We offer optional pre and post-project meetings with a specialist member of our team to support the sampling process and answer any questions.
  • DNA extraction and library preparation
    Once we receive samples, we extract, purify and optionally size-select DNA.
  • Sequencing
    We sequence each sample using state-of-the-art third generation long-read DNA sequencing technology
  • Pre- and post-sequencing quality control
    We subject each sample to rigorous quality control.
  • De novo assembly
    We subject each sample to de novo
  • Taxonomic profiling & Gene annotation
    We annotate genes, extract rNA genes, classify genomes, and perform customer-specific analyses.
  • Access to raw data, result files, and a detailed project report
    You receive a detailed report, raw data, relevant files and analysis figures.
Antimicrobial Resistance (AMR) Profiling

Our AMR pipeline identifies resistance genes and mechanisms that are crucial to understand for clinical applications and regulatory processes. We support clinical microbiology and epidemiology studies by linking strains to specific outbreaks or contamination events.

Source Tracking & Contamination Resolution

Whole-genome sequencing is also useful for bacterial source tracking, especially in food safety, clinical settings, and manufacturing. By comparing isolates from contamination sites, we help identify contamination sources and ensure regulatory compliance.

Regulatory & IP Support

We provide genomic reporting and dossier support for regulatory submissions, including those to FDA, EFSA, and other authorities. Whether for clinical trials or probiotics development, our services ensure that your genomic data meets regulatory requirements.

Methylation patterns

When performing long-read sequencing, we provide detailed analysis of methylation patterns, which are essential for understanding microbial epigenetics. Methylation patterns can influence gene expression and regulation, adding another layer of insight into microbial behavior, pathogenicity, and adaptation. This epigenetic information is crucial for understanding strain-specific functions and interactions.

Phylogenetic Analysis

Whole-genome sequencing allows us to compare isolates at the single-nucleotide polymorphism (SNP) level and generate phylogenetic trees to determine strain relatedness. For novel or poorly classified organisms, we predict taxonomy based on average nucleotide identity (ANI) with related genomes.