DNA Extraction

High-quality DNA extraction is the first vital step to a successful microbial genomics project. We apply various protocols tailored to specific sample types, f.x. colonies, soils, sediments, swabs, filters, and plant/animal tissues. Only proven commercially available kits are used.

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Table of Contents

Key Specs
  • DNA From Pure Cultures For NGS, 99 Kr. (€ 15)

  • Microbiome DNA For NGS, 199 Kr. (€ 29)

  • HMW DNA From Pure Cultures For Long-Read Sequencing, 299 Kr. (€ 45)

  • Microbiome HMW DNA For Long-Read Sequencing, 399 Kr. (€ 59)

  • Use Proven DNA Isolation Kits Designed For Microbial Cultures And Environmental Microbiomes.

  • Turnaround Time: Typically Days To A Week.

Sample Requirements

For DNA samples submitted, Customer is required to ensure the Quality Control (QC) data at the time of sample submission meets the minimum requirements concerning the total amount, concentration, and quality of the DNA submitted. For microbial culture or direct environmental samples submitted, Customer is obligated to ensure that the sample submitted is non-pathogenic to humans and does not contain any substance that may pose a health risk to the personnel working with the samples in our laboratory.

DNA sample
  • Total quantity ≥ 1.0 µg (short-insert library) or ≥ 5 µg (PCR-free library);

  • Concentration ≥ 20 ng/µL;

  • Purity: A260/280=1.8-2.0.



(1)  The final concentration of each sample will be measured using QUBIT or an equivalent fluorometer after the samples are received. If the samples do not pass QC, We will notify the Customer, and Customer shall either notify us to cancel the failed samples or re-send the samples concerned within ten workdays. Customer can request that the “QC-failed samples” be sequenced, in which case we will prepare the library and sequence the “QC-failed samples” without bearing any responsibility for the data quality. Customer should notify whether plasmid, chondriosome, chloroplast, and other non-bacterial-origin DNA exist in the samples submitted. Customer should notice that, If the DNA originates from a mixture of multiple microbial species, the quality of final assembly and genome annotation will be compromised significantly, and we will not attempt to separate all assemblies into individual species by any means.

(2)  An aliquot of DNA sample may be stored temporarily in case of a failed library preparation. All DNA samples will be discarded within 3 months after the project is completed.

Microbial pure culture sample

Agar plates: 

colonies should be easily visible and cover > 20% of the surface area on a standard-size petri dish (⌀ 90mm); the agar should not dry out and maintain a good texture for easy collection of cells with a standard sterile loop used in microbiology laboratories.


Bacterial pellets should be placed in a 1.5 mL or 2 mL centrifuge tube. The size of the pellet shall not be less than that generated by centrifuging 2 mL of E. coli cultures grown in LB overnight at 37 °C, typically covering a round area of ⌀3-5 mm.


Customer should pay close attention to contamination on agar plates or in bacterial pellets. Customer must ensure each sample submitted is a single pure culture without being mixed with other species. In any case, we will continue the workflow and sequence the genomic DNA extracted from the samples submitted. We will not accept the complaint on the culture’s purity issue filed by Customer based on the genome sequence data generated in this project.

Environmental sample

The direct submission of soil, lake water, filters, swabs, plant or animal materials, any items or objects colonized by microbes, and other types of environmental samples that contain microbial inhabitants for genomic investigation at our laboratory is subject to individual agreement by email or in other written form between Customer and us concerning the sample type, quantity, and quality before the commence of this agreement.


The project will only commence when we receive the last batch of qualified samples. When a project is successfully completed, we will provide the following items as the standard deliverables:

  • DNA QC report;

  • DNA solution in TE, EB or pure deionised water.

Sample deliverables
  • DNA QC report
Pricing & Turnaround Time

For short-read applications, standard DNA isolation methods are of sufficient quality with prices set as 99 kr./sample for pure cultures and 199 kr./sample for environmental microbiome samples. For long-read applications, high-molecular-weight (HMW) DNA is desired. Thus we either use specifically designed DNA isolation kits for HMW DNA or carry out additional short DNA fragments removal steps to enrich long DNA fragments from standard DNA extracts.  The prices for HMW DNA isolation are 299 kr./sample for pure cultures and 399 kr./sample for microbiome samples. Only proven commercially available DNA isolation kits will be used in all cases.

The project turnaround time is typically one week, depending on the sample size, counted from when the last batch of samples arrives at our laboratory. Please be aware that we are an international team; thus, holidays include Denmark, UK, and China. For the contract reason, we set a relatively safe time frame of max. two weeks to complete a DNA isolation project. In most cases, a project can be finished earlier. 

Payment Term

All payments set forth on the invoice are due within 30 days from the date of the invoice. We may impose a service charge on past due amounts between one and one-half percent (1.5%) and three percent (3%) per month, not to exceed the maximum amount permitted by law. Upon the Customer’s request, we will provide a statement within ten days.

The service agreement should be governed by and construed in accordance with the law in Denmark.

Service Contract

Draft Agreement

Q: What kind of sample do you take?

We accept most types of samples as long as they do not pose any health risk to our staff working in the laboratory. In other words, we do not work with samples that potentially contain human pathogens, f.x. fresh saliva swabs from COVID-19 patients. But if such samples are pre-treated with chemical preservation solutions that kill viable entities before being sent to us, we will accept them.

Q: Do you have a minimum quantity requirement for samples?

This can vary significantly among different projects. Thus, we avoid proposing a general requirement for all types of samples regarding the sample quantity. We will have a detailed discussion during a project meeting or a general inquiry. As a rule of thumb, 1/4 to half of a 1.5 mL centrifuge tube of soils or sediments is sufficient.  But much more quantity will be required for samples with low microbial cell abundance.

Q: Do you accept DNA or soil samples preserved in a freezer for years?

Yes, we do. DNA is amazingly stable when stored in TE buffer under a freezing temperature. Frequent thaw-freeze may break DNA double strands to some level but generally has a minor effect on sequencing output and data quality. We also accept frozen soil samples and provide professional services to extract high-quality DNA from these samples. Please be aware that sequencing results from a fresh soil sample can differ a lot from the same sample put in a freezer for years since microbial communities change slowly, even under freezing temperatures.

Q: What if you fail in some samples or produce very little DNA?

We usually regard 1 ng/µL DNA  as the minimum acceptable concentration for DNA isolation. We will handle these cases individually. If it is because of human errors that happen during our processing of the samples, we will charge no fees for these samples. We will repeat the whole process on the same sample in such cases. If it still does not work out well, we will conclude that the submitted samples are unsuitable for DNA isolation using standard protocols, and we will charge a small reagent fee of 30 kr./sample. We will do our best to avoid such a situation by carefully examining the samples and consulting with clients for more details about samples before commencing a project.

Q: Do you provide any discount for a large project involving hundreds of samples?
Yes, but please don’t hold high expectations. Between 5-10% off is a possible offer we can provide for a large project. Generally, we adopt a transparent pricing policy without discrimination for any customer, whether a big pharma or a startup. So you are clear upfront before contacting us. We always strive to keep the cost for our customers low so that everyone can benefit from technological advances in microbial genomics. Please contact us for a quote on a specific project.

See more at mBioWorks FAQ.

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