Case studies on EFSA and FDA strain safety assessment projects

While the European (EU / EFSA) and American (US-FDA) regulatory bodies have established guidelines for the approval of novel microbial strains in food and feed applications, these guidelines are regularly updated and in some cases are difficult to interpret, making it challenging for the industry players to determine whether their current and new products meet the requirements of the regulatory bodies.

By Dr. Radhika Bongoni, Dr. Adalberto Costessi and Dr. Derek Butler. 

With more than 25 years of expertise in microbial genomics, BaseClear has been assisting clients by designing and implementing projects tailored to address these requirements. BaseClear’s expertise and services also extend to delivering EFSA and/or FDA compliant reports that include interpretation of the genomic data with regard to the safety of the strain of interest. The report we deliver is an integral part of the complete dossier.

Here we give some examples of EFSA and FDA-related regulatory affairs questions that BaseClear has solved for its clients.

Case study 1 – Is our probiotic strain safe?

The product marketed was a mix of probiotic strains intended to have a positive effect on gut health. However, the strains used were not yet on EFSA’s QPS list, though they have been used historically without any concerns. Questions addressed during this project included the verification of the strains taxonomy which was performed using a customized biomarker based approach. Additionally, we analysed and interpreted the genome sequence data with regard to the presence of partial antibiotic resistance genes in the genome in combination with the mobile genetic elements (including plasmids). This approach was taken to assess the potential of the AMR genes to become active and thus made conclusive remarks on the safety of the strain for consumption and the environment.

Case study 2 – Does our end product / beverage contain microbial DNA?

A European client produces a fermented beverage using a purified enzyme of microbial origin. BaseClear was asked to determine the level of DNA from the production strain in the end product. Typically these projects are performed using molecular diagnostic techniques, specifically a combination of qPCR and next generation sequencing. For this project, BaseClear developed a semi-quantitative PCR-based assay for the full length gene to determine the presence or absence of antibiotic-resistance gene and plasmid in the final product.

Case study 3 – Could you help us establish the safety of our probiotic strain?

Our USA based client identified a yeast strain that has the potential to provide a specific health benefit. They decided to submit a “GRAS notice” to the FDA to support the safety of the yeast strain. BaseClear performed the genomic analysis for the dossier including identification of specific genes which were linked to functions that are positively involved in human health, such as genes that take part in a specific nutrient metabolism. Furthermore, a customized bioinformatic approach was employed to screen for genes associated to probiotic properties of the strain. A complete genome without gaps was also delivered to conclusively establish the safety of the strain.

Case study 4 – Which of our isolates is the best potential candidate strain for regulatory approval?

An innovative Latin American client regularly collects a variety of environmental samples from deep seabed samples to dirty water, to screen for microbial strains with specific genes coding for novel enzymes for various industrial and food (probiotic) applications. Novel approaches for identifying and discovering genes that encode new bio-molecules and enzymatic activity are always of interest in an industrial biotechnology field. These applications demand robust microbial genome sequencing services and advanced analysis pipelines. At BaseClear, we have established a rigorous screening pipeline that includes biomass-specific gDNA isolation, culturomics, WGS, and customised bioinformatics pipeline for metabolic pathway-level analyses to identify potential candidate strains for regulatory approval.

Case study 5 – Are the genetic modifications of our production strain correct and stable?

A number of bioactives such as vitamins are produced using genetically-modified (GM) microbial strains. The origin, characteristics and stability of the genetic modifications are of critical importance in the context of a safety assessment for regulatory purposes. The genomes of the GM organisms must be characterized using state-of-the-art techniques and compared to the parental strains. Furthermore, the sequences of the genetic modifications identified in the whole genome sequence data must correspond to the sequences expected based on the genetic modification approach. Our client assigned us the crucial task of determining if their GM production strains complied with these requirements and if the genetic modifications in the strains were stable after a number of generations under production conditions.

Case study 6 – How safe are our fungal and yeast production strains across generations?

A Spanish biotechnology firm focused on sustainability, produces bio-based products for skin care, industrial biotechnology applications, and food ingredients (such as enzymes) – typically using fungi and yeast as production strains. BaseClear provided extensive genome analysis of the production strains (both GMOs and non GMOs) including determination of the small nucleotide changes in strains across generations, as well as large insertions and deletions. In addition to this, analyses required by EFSA, including yeast and fungal strain identity confirmation, genome annotation (e.g., Augustus model development & parameter training), copy number analysisand virulence factor detection were provided for our client’s EFSA dossier filing.


There is a huge number of microbial applications in food and health industries. Applications range from dietary supplements such as probiotics and bioactives; biotechnological applications such as fermentation and enzyme optimisation; and pharma applications such as vaccine development and production. Therefore microbes have tremendous economic impact!

To regulate the safe use of microbial strains across industries, governing bodies have passed stringent regulations. Some microbes (and their applications) demand a rather straight-forward approach to establish their safety. While in most cases, many challenges are involved in assessing and proving the safety of candidate microbial strains.

At BaseClear, we partner with our clients at various levels, for example to understand and link the historic use of a strain by performing and interpreting genomic analysis. We facilitate and simplify our clients dossier filing for regulatory approval!

Want to know more? BaseClear regularly organises experts meetings to discuss challenges and opportunities in strain safety assessment. For the complete overview visit

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