While the European (EFSA) and American (FDA) regulatory bodies have established guidelines for the approval of novel microbial strains in food and feed applications, these guidelines are often changed 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.

With more than 25 years of expertise in microbial genomics, BaseClear has been assisting customers 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.

Below are some examples of  EFSA/FDA-related genome analysis questions we have solved for our clients:

1. Is our probiotic strain safe and eligible for QPS listing?

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 by  using a customized biomarker based approach to, and to perform Whole Genome Sequencing (WGS).  Additionally, we analyzed and interpreted the genome sequence data with regard to the presence of partial antibiotic resistance genes on the genome in combination with the mobile genetic elements (including plasmids). This approach was taken to assess the potential of the ABR genes turning active and thus made conclusive remarks on the safety of the strain for consumption and to environment.

2. Does our end product/beverage contain microbial DNA?

A European based customer 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.

3. Could you help us establish the safety and efficacy of our probiotic strain?

Our USA based client identified a yeast strain that has the potential to provide a specific health benefit. However, they were required to file a dossier for FDA/GRAS approval to establish 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.

4. Which of our isolates is the best potential candidate strain for regulatory approval?

An innovative Latin American customer regularly collects a variety of environment 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.

5. Are there any GMO elements present in our production strain?

A number of bioactives such as vitamins are now produced using microbial production strains. However, the origin and characteristics of these strains are of critical importance in determining if these bioactives can be marketed as organic. For this, genomes of these should be characterised using state-of-the-art techniques. Production of Coenzyme Q₁0 is a good example of this issue as it needs to be produced in large quantities for the food and animal feed markets. Our client assigned us the crucial task of determining whether the fungal strain – producing CoQ₁0 – has GMO elements. Customized bioinformatic analysis for homologous and heterologous genes including copy number analysis were performed as a part of this project, which went along with other WGS analyses asked by EFSA for QPS list approval.

6. How safe are our fungal and yeast production strains across generations?

An 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 in 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 analysis, ABR and virulence factor detection, as well as toxin gene analyses were provided for our client’s EFSA dossier filing.


There are 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 both directly or indirectly!

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 prove safety. While in most cases, many challenges are involved in assessing and proving the safety of candidate microbial strain.

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!

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