Genomic Characterization

Whole genome sequencing analysis can provide valuable information on the taxonomic identification of the strains and their potential functional traits, including virulence factors, resistance to antimicrobials, and production of toxic metabolites.

At TAXON, we have developed a proprietary tool that establishes the microbial functional profile based on genomic functions. Our genomic characterization analyses help to support risk assessment for microorganisms seeking approval from regulatory agencies such as the European Union Food Safety Authority (EU/EFSA) and the United States Food and Drug Administration (US-FDA).

Furthermore, as the genome of producer microbes constitutes the inventive part of a productive process, complete genome sequencing is required during patent applications. Finally, by linking genotype with phenotype, companies can select the most suitable microbial candidates to develop their products, relying on our microbial functional profiles.

The service offered by TAXON involves the complete characterization of microbial strains, which is essential for the development and optimization of microorganisms used in food ingredients or as production strains. This service includes complete genome-based strain characterization required for EFSA approval and claims, screening for antibiotic resistance and virulence genes, plasmid detection and identification, and gene of interest screening. TAXON has significant expertise and years of experience in this field.

Deliverables of Genomic Characterization service:

  • Circular representation of the genome (in svg format).
  • The list of relevant features found (in csv, tsv and/or xlxs formats).
  • The region of a sequence of interest (in Genbank format)
  • Absence/presence table of the gene of interest (in csv, tsv and/or xlxs formats).
  • A complete report describing methods and results (in PDF format)

See Our Services in Practice

Enterococcus mundtii is a rare human pathogen. In this case, we conclude that although E. mundtii CRL1656 is phylogenetically closer to E. faecium, frequently responsible for nosocomial infections, this strain does not encode the most relevant virulence factors found in the enterococcal clinical isolates. This strain was isolated from stripping milk cows and, given its bacteriocinogenic capacity, it has been proposed as a probiotic microorganism to prevent mastitis in these mammals. The circular genome representation showed positions of protein-coding genes, foreign DNA, tRNA genes, and putative transposases and integrases. In addition, the encoded function in the 4 putative genomic islands found was described.

Reference: Repizo, G.D., Espariz, M., Blancato, V.S. et al. Genomic comparative analysis of the environmental Enterococcus mundtii against enterococcal representative species. BMC Genomics 15, 489 (2014).

Genome assembly and annotation

Get reliable and comprehensive genomic assembly and annotation tailored to your research needs.

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Microbial Identification

Utilize whole genome sequence analysis for precise taxonomic identification of microorganisms, meeting regulatory requirements for food and production applications.

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New Traits Discovery

Genomic or metagenomic data are searched for genes encoding proteins with exceptional characteristics that can be used for specific industrial, agronomical, or pharmaceutical purposes.

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Comparative Genomics

The whole genomic sequences of various organisms are analyzed and compared through comparative genomics. This helps in determining the uniqueness of the trait of interest.

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