EFSA guidelines solve identification issues in whole genome sequencing
Whole genome sequencing (WGS) is an established method for the taxonomic identification of microorganisms (bacteria, yeasts and filamentous fungi) and their derived substances, and for outlining their potential functions.
However, EFSA has been made aware that WGS is a challenging tool with a lack of best practices on how to appropriately use the data in risk assessment of microorganisms used in the food chain. The authority was therefore requested to prepare a document, following public consultation in 2020, to provide guidance to companies who wish to perform this analysis.
The consultation received 37 contributions, including International Probiotics Association, IPA Europe, EuropaBio - the European Association for Bioindustries, IBMA - International Biocontrol Manufacturers Association as well as other public bodies and private companies.
The resulting document provides guidelines for microorganism extraction, data quality control, library construction, sequencing strategy, De novo assembly and annotation, identification of microorganisms, data reporting, and more.
George Paraskevakos, IPA executive director, says these guidelines use a modern approach to safety evaluations and "should solve identification issues once and for all".
He told NutraIngredients: "Initiatives like these only stand to benefit all stakeholders, including consumers, regulators and the serious industry players in the field.
"The only apprehension can be the requirement to provide the actual sequence data, which in the case for most current probiotic strains have had their genomes already sequenced and published but may be different when it comes to next gen probiotics or in cases where microbes are utilised as production organisms."
Antonio Del Casale, CEO & Co-founder at the Italian biotech firm Microbion, told NutraIngredients this document underlines the crucial role of WGS quality in the safety assessment of microorganisms.
"Nowadays genome sequencing can be very cheap but low quality input data can result in meaningless or misleading results. Bioinformatic analysis is a very important step. The choice of the reference DNA sequences and reference genomes as well as the stringency of the query parameters can affect the final results with false positive or false negative results. Bioinformatics can be tricky especially if someone aims to hide unwanted genes, such as viruses or antibiotic-resistance genes, and low quality sequencing may not detect them.
"Our quality standard is to reach the completely assembled genome sequence (or very close to it) even if this is not an explicit EFSA requirement. The complete assembled genome can provide information also of its structure, not only the presence or absence of single genes. This can then be employed for a robust comparison with other strains, can be a means for genome stability assessment, and can spot events of horizontal gene transfer.
"In my opinion the next challenge is to set higher standards in the product quality control, requesting manufactures to develop strain specific quantitative diagnostics."