DNA Isolation for Difficult Strains: No Problem!

DNA Isolation for Difficult Strains: No Problem!

Whole genome sequencing (WGS), the gold standard for microbial characterization, needs DNA isolation. Biosafe has solid experience with DNA isolation and optimization, no matter how challenging the strain.

Whole genome sequencing (WGS) has become the gold standard for microbial characterization. Since the outbreak of the SARS-CoV-2 virus, there are already 16,380 nucleotide records for this virus at the NCBI database. Similarly, strains causing bacterial outbreaks are rapidly sequenced to identify the correct antibiotics for clinical treatment.

At Biosafe, our laboratory isolates DNA for WGS sequencing from dozens of customer samples every year. These comprise representatives from filamentous fungi, yeasts and bacteria, including both genetically modified and non-modified strains. However, it is not always easy. The samples we handle are typically used in industrial applications for fermentation, and the strains are very versatile. Some of them even represent new species that have not been characterized previously.

The normal DNA isolation protocol configured for normal E. coli works sometimes, but often this is not the case. We prefer long-read sequencing, such as PacBio, to get a good representation of the genome. However, the DNA quality requirements for a PacBio library are significantly higher than those for Illumina sequencing. We often face problems related to DNA degradation, which means that we have to change the isolation method, culture conditions or culture time. Thus far, we have always succeeded in obtaining high-quality, high-molecular weight DNA suitable for PacBio sequencing, but sometimes this has required multiple rounds of optimization.

The major factor affecting the efficacy of DNA isolation is the microbial cell wall, which is a peptidoglycan layer. The glycan strands form chains that are further cross-linked, and this structure confers cell rigidity. The number of glycan chains and their cross-linking affects the strength of the cell wall. Breaking this down is tough in fungi and yeasts, but sometimes it seems challenging in bacteria too. A specific strain from a species that is normally easy in terms of DNA isolation can be unexpectedly difficult. We have speculated that this could be due to genetic modifications or other strain development factors that affect the cell wall.

Another challenge can be the slow growth or very poor growth of the bacteria on normal culture media. To ensure adequate growth, we usually ask our customers to specify the culture conditions. With this information, we can grow enough material for successful DNA isolation.

Any additional optimization steps increase our turnaround time for sequencing and the subsequent bioinformatics analysis. Over time, we have optimized our processes for all the steps involved, to make delivery as streamlined and smooth as possible. However, biology and nature cannot be entirely controlled, and challenging strains are part of our normal, with problem solving driving us forward. Like our Laboratory Manager, Dr. Arja Tervahauta puts it: “Oh no, a difficult strain again. Well, we will find a way, no problem!”.


Regulated microbes and their products: News and challenges in EU risk assessment – Register for the seminar

Regulated microbes and their products: News and challenges in EU risk assessment
Online interactive seminar series – Register here

Microorganisms are used in the food chain as well as production organisms or viable microorganisms. This 4-part series of online, interactive seminars provides an overview of the relevant regulatory bodies within the EU, with an emphasis on the use and regulation of microorganisms in the food chain. The new EFSA regulation concerning transparency and sustainability in the food chain and its consequences will be addressed in depth. Further, questions and problems that are regularly encountered by the applicants will be considered at the practical level.

In case of technical problems, please contact

Program and schedule

Timeslots for questions and discussion are available during and after each talk. Questions can be asked throughout the interactive seminar. If you would prefer to ask a question anonymously, please send your question(s) to as early as possible.

September 16, 2020: 9.00-10.30 CET (10.00-11.30 EST)
8.45 Welcome and webinar instructions. Please join the seminar to make sure the connection works
9.00 Risk assessment of microorganisms intentionally used in the food chain with a focus on feed additives
Dr. Montserrat Anguita (EFSA)
9.45 Qualified Presumption of Safety: Can my microbe get a QPS status and what should I do to get it? What is the advantage of having the status?
Lieve Herman (ILVO, Belgium, Chair of the EFSA QPS working group)

October 14, 2020: 9.00-10.30 CET

8.45 Welcome and webinar instructions
9.00 Case of microbes/microbial products in feed additives
Prof. Atte von Wright (Biosafe)
9.45 Quality criteria for analytical studies
Dr. Jouni Heikkinen (Biosafe)
November 12, 2020: 9.00-10.30 CET
8.45 Welcome and webinar instructions
9.00 Genes of concern (primarily concerning AMR)
Prof. Sirpa Kärenlampi (Biosafe)
9.45 Absence of cells, presence of DNA; sampling and other things to consider
Dr. Pauliina Halimaa (Biosafe)

December 10, 2020: 9.00-10.30 CET

8.45 Welcome and webinar instructions
9.00 Transparency regulation, what are the consequences for the industry?
Ruud Bremmers, (Managing Director, Regal B.V.)
9.45 Whole genome sequencing and bioinformatics analysis; new guidance from EFSA; how to understand/use the data; what can WGS achieve/not achieve
Dr. Jenny Makkonen and Dr. Daniel Blande (Biosafe)

Please send any queries or advance session questions to All sessions will be recorded and made available for download to registered participants.

Price: 200 €* / company unit / four seminars (max 3 attendees/company unit)
Individual seminar 50 €*

*Does not include VAT (if applicable). The participation fee is non-refundable.

Please remember to register for the second seminar by 12.00 CET on October 13, 2020.

Register here

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More information
Pauliina Halimaa
+35840 640 3225