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Microbial Strain Characterization

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. 

Microbial Strain Characterization

At Cmbio, we specialize in delivering fast and affordable microbial strain characterization services to support your research at every stage. From accurately identifying isolates to providing detailed genomic analysis, our services are designed to meet the needs of researchers across various disciplines. With a focus on precision and efficiency, we use advanced technologies to uncover critical insights into microbial strains, helping you explore their diversity, functionality, and applications. 

Services for Microbial Strain Assessment

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.
 

Our Process

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
Processing Steps Graphic 1 on 1
 

Our standard package provides:

  • 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.
A laboratory expert using a pipette to measure drops of activator for sampling

Benefit from Cmbio’s Laboratory Expertise

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.

The Role of Bacterial Isolate Whole Genome Sequencing

Cmbio rapidly sequences whole bacterial isolates to identify bacterial species, genotypic traits, virulence factors, and antibiotic resistance.

Cmbio’s WGS services are designed to help you achieve the most accurate results in the shortest time frame, sequencing entire bacterial isolates in one run. Our high-throughput sequencing platform and optimized bioinformatics pipeline allow us to accurately identify the presence of any bacterial species from a single sample.

Operating from CLIA-certified labs and in-house bioinformatics platform, we deliver the highest quality data interpretation and analysis of your bacterial genome sequence. We also offer custom sample preparation, data sharing, and clinical report generation. 

By leveraging next-generation sequencing, we provide a comprehensive solution for public health surveillance, outbreak investigations, and food safety testing.

Who Uses Our Analysis and Characterization Reports

Our comprehensive microbial strain characterization services are designed for a broad range of clients engaged in microbial research of the human genome, environmental genome, developmental biology and more. Key users include:

  • Food Safety & Microbial Testing Researchers: Compared different bioinformatic tools to assess microbial strain characterization for improved food safety testing and pathogen detection. ¹
  • Environmental Microbiologists & Ecologists: Investigated cyanobacterial harmful algal blooms (cyanoHABs) using 16S rRNA sequencing and metagenomics to characterize microbial communities and phage-host interactions in Lake Okeechobee. ²
  • Clinical Microbiologists & Infectious Disease Specialists: Applied metagenomic next-generation sequencing on nasopharyngeal swabs from COVID-19 patients to characterize microbial strains. ³
  • Bioinformaticians & Metagenomics Researchers: Evaluated tool performance for microbial strain characterization—assessing precision, accuracy, and recall—to guide optimal tool selection for clinical diagnostics and environmental monitoring. ₄

References

  1. National Center for Biotechnology Information. PubMed article, PMID: 31897401. https://pubmed.ncbi.nlm.nih.gov/31897401/
  2. National Center for Biotechnology Information. PubMed article, PMID: 38856205. https://pubmed.ncbi.nlm.nih.gov/38856205/
  3. National Center for Biotechnology Information. PubMed article, PMID: 33219095. https://pubmed.ncbi.nlm.nih.gov/33219095/
  4. National Center for Biotechnology Information. PubMed article, PMID: 28934964. https://pubmed.ncbi.nlm.nih.gov/28934964/