Microbial identification

The identification of microorganisms with precision is essential across a range of fields such as medicine, biotechnology, and ecology. Whole genome sequencing technologies are a powerful tool for achieving accurate identification, providing more precise results than traditional 16S rRNA gene sequencing. As a result, regulatory agencies in Europe and the US now require genomic characterization of microorganisms for approval in food and production applications.

TAXON establishes taxonomic identity by ensuring coherence among phylogenetic and genomic characteristics, which is crucial for accurate classification and reliable commercial or industrial applications.

TAXON uses a pipeline for microbe identification that integrates genomic and phylogenomic analyses. First, we calculate Average Nucleotide Identity values and perform complementary analyses such as is- DDH if necessary. Then, core genes using BLAST in all bacterial genomes, followed by individual alignment, concatenation, trimming, selecting the best substitution model, and inferring evolutionary history.

Deliverables of Microbial identification service:

  • Circular representation of the genome (in svg format).
  • Table with ANI values of the strain of interest and type/reference strains (in csv, tsv and/or xlxs formats)
  • Core-based phylogenic tree of the strain of interest and type/reference strains (in Newick and svg formats)
  • A complete report describing methods and microbial identification analysis conclusion (in PDF format)

See Our Services in Practice

In this case study, we combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on > 2100 strains to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel. The figure shows the phylogenomic tree of Clade 1 of B. cereus group strains. The tree was constructed with individually aligned core genes.

Reference: Torres Manno, M.A., Repizo, G.D., Magni, C. et al. The assessment of leading traits in the taxonomy of the Bacillus cereus group. Antonie van Leeuwenhoek 113, 2223–2242 (2020). https://doi.org/10.1007/s10482-020-01494-3

Genome assembly and annotation

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

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Genomic Characterization

Identify genes responsible for desirable traits and ensure the absence of undesirable characteristics, enabling the development of safer and more efficient microorganisms.

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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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