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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. 

Our Expertise in Microbial Strain Characterization

At Cmbio, we offer rapid and cost-effective microbial strain characterization services, supporting your research from isolate identification to full genomic insights.

Whole-genome sequencing (WGS), de novo assembly, gene annotation, and bacterial isolate genome sequencing provide detailed taxonomic identification and insights into functional potential and are crucial for understanding gene expression and methylation patterns, strain typing, virulence factors, and antibiotic susceptibility. WGS provides more data than other methods like 16S rRNA sequencing or phenotypic tests.

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

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Our standard package

Whenever you sequence your strains with us, we always provide the following:

  • Optional pre- and post-project meetings with a specialist

  • DNA extraction and library preparation

  • Sequencing

  • Pre- and post-sequencing quality control

  • De novo assembly

  • Taxonomic profiling

  • Gene annotation

  • Access to raw data, result files, and a detailed project report

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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.

What is Bacterial Isolate Whole Genome Sequencing?

Bacterial isolate whole genome sequencing (WGS) allows you to quickly characterize and identify a bacterial isolate. Whole Genome Sequencing is used to accurately determine the identity of bacterial genomes, their genotypic characteristics, virulence factors, antibiotic susceptibility, and other essential epidemiologic information.

WGS provides more data than other methods like 16S rRNA sequencing or phenotypic tests and can be used to identify novel bacterial species. Sequencing complete genomes is an invaluable tool for public health surveillance, live biotherapeutics, food safety testing, and outbreak investigations.

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.

Our CLIA-certified laboratories and in-house bioinformatics platform offer you the highest quality data interpretation and analysis of your bacterial genome sequence. We also provide value-added services such as custom sample preparation, data sharing with our customers, and clinical report generation.