Sequencing and bioinformatics services

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Download the brochure: Genome analysis of microorganisms

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Download the brochure: Genome analysis of microorganisms

Get the latest news and insights from the world of food safety and subscribe also to our newsletter.

Safety assessment of microorganisms


 

Why?

Why?

Today, genome analysis guides the safety assessment. EFSA requires the analysis of whole genome sequence for bacteria and yeasts.

When microorganisms are used in the food chain or as biopharmaceuticals, their safety has to be assessed before the authorization of the organisms or derived products in the EU. Today, genome analysis guides the safety assessment. EFSA requires the analysis of whole genome sequence for bacteria and yeasts. It is only recommended for filamentous fungi because the genome data are less complete.

How?

Bioinformatics services at Biosafe Ltd provide genome-based safety assessments of microorganisms. Usually we start with DNA isolation and carry out genome assembly and annotation after sequencing. A pipeline has been developed in-house to obtain the needed information from the genome in a cost-effective manner. As bioinformatics is a fast-developing field, no exact methods are recommended by EFSA or by other authorities. Biosafe Ltd is closely monitoring possible changes in the requirements and adjusts the pipeline without delay.

Unequivocal taxonomic identification at the species level is a key requirement. It is also essential for granting the QPS (qualified presumption of safety) status for a microorganism. Sometimes the taxonomic analysis leads to the description of a new species.


Genes of concern are searched for from the genome. These include putative antimicrobial resistance genes as well as those related to toxicity and pathogenicity.

 

EFSA recommends certain identity, similarity and coverage thresholds for those genes that should be reported and assessed. Usually we assess the genome safety in parallel with phenotypic tests, such as antimicrobial susceptibility. This helps in the interpretation of the data, e.g. If the antimicrobial resistance can be linked to the presence of a known resistance gene.

For genetically modified microorganisms, we describe the genetic modifications in detail. Secondary metabolite biosynthesis clusters are searched for and assessed case-by-case.

Biosafe has assessed hundreds of genomes and has gained valuable knowledge about the characteristics of common industrial microorganisms, and what can be expected and not expected during the hazard identification step. The study reports include expert data interpretation in the light of current scientific knowledge and are as such ready to be delivered to the authorities.

Sequencing

Biosafe Ltd offers comprehensive sequencing services in collaboration with our sequencing partners. We sequence microbial genomes, plasmids or individual genes based on specific needs. All sequencing projects are unique and designed together with the customers, including selection of the sequencing platform.

Allergenicity & celiac disease - bioinformatics


 

Why?

One key aspect in the safety assessment of enzymes and other proteins is the potential allergenicity. The assessment is a stepwise process, in which bioinformatic analysis is usually the first screening step.

How?

The DNA sequence from which the protein sequence can be inferred, or the actual protein sequence, will be used for the analysis. Several databases are available, which are built based on different principles. Some of them are very stringent in the inclusions, whereas others include proteins based on protein similarity without any real evidence for allergenicity. Some of the databases include proteins, which can be used for the assessment of the potential contribution to celiac disease.

A routine, internationally accepted approach is to run a sliding window search of 80 amino acids through the protein and look for any window having 35% or higher identity. It is also possible to predict all proteins from the whole genome sequence of a microorganism and make an allergen database search.

Biosafe Ltd uses several databases, compares the results and carefully assesses the outcome.

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