Team:Groningen/Engagement
Public Engagement
Here is described all the people we talked to!
European Meetup iGEM Delft - 6 July
Ferdinand Van Der Graaf - 30 August
Maakfestival - INPUT DATE
NBC - 16 May
Benelux Meetup - INPUT DATE
KIVI Lecture - INPUT DATE
Rathenau Institute - INPUT DATE
Richel Bilderbeek - INPUT DATE
LAB Egmond aan Zee - 28 August
GBB Symposium - INPUT DATE
J. Hille - INPUT DATE
Wouter Ghering - INPUT DATE
Rob Duba - INPUT DATE
Jeantine Lunshof - INPUT DATE
Siger - INPUT DATE
Swart - INPUT DATE
Simon van der Els, NIZO - INPUT DATE
Jeantine Lunshof- INPUT DATE
Cathelijne van Beekvelt, ILT - INPUT DATE
Jaco Westra, RIVM - INPUT DATE
Arla Skype Call - INPUT DATE
How are you currently combating phages? How frequent and in which way are you currently testing for phages? What are the parameters you are monitoring? Are phages infection a big problem for your company? How long does it take you to get result, starting from probe taking to getting the results in the company? We are very interested in the current situation in different dairy production plants so that we can adjust our final product which would suit the current wishes of the industry.
In what way will our product be most useful to the end user? What are desired characteristics (in terms of design and implementation) that you would value the most? Through other talks, we learned that you cannot work with GMOs directly on the factory floor. This makes it that samples have to be taken to another testing place, either within or outside the production facility/plant. This way, our ideal goal is to deliver a system that, with simple maintenance, can continuously survey samples from the main production line for contamination with phages. However, another option is to design a portable device which uses our reporter strain in a contained matter, so you would not need a GMO regulated area. This makes its implementation potentially viable in other settings besides the dairy industry.
What are the parameters for phage infection in a factory (pH, OD600nm, MOI etc.) How does this translate to detection sensitivity? With this information, we could get a better view of the desired environment for our detection system.
On the 22th of August we talked to Arla in Denmark via Skype. We got some tips on how to communicate about the project. For instance using the word ‘virus’ on the homepage of our WIKI could immediately scare people and that is definitely something you do not want. So it is best to use the word phage or bacteriophage and explain what is meant by this. Two researchers from Arla, who also joined the conversation, were really interested in our project and had some questions prepared. We explained everything and also asked questions, because we are really interested in the point of view of the company to our project.
Thijs Kouwen, DSM - 27 June
Thijs Kouwen works as a scientist at DSM cultures and works at starter culture development and is in particular concerned with phage resistance of these cultures. First of all he told us that there is a need for fast phage detection in the dairy industry and that phages form a significant problem. The current detection is performed by both major dairy factories themselves as companies that produce starter cultures such as DSM. Some rough estimates: ¼ of the costumers of DSM has their own testing facility (only the largest) 1/3 of the costumers sends their samples to DSM for testing and other do not test for phages. Of the samples send to DSM ~30% contains phages and in 5-10% of the cases the amount of phages reaches a critical level. Although in most cases measurements can be taken in time, sometimes a complete batch is lost due to an infection. If this happens this results in significant costs for the company, since the milk is almost as expensive as the final product. DSM performs to types of testing a ‘acidification test’ which takes 4-8 hours and during this period the acidification of the medium is measured and the curve gives information about the health of the culture. Another test is an overlaytest and this takes an overnight incubation step and is therefore quite time consuming.
Companies themselves also make use of ‘simple’ microbiological testing techniques and the largest companies use more advance techniques such as qPCR. The main problem for dairy companies is that they usually do not have the microbiological expertise to carry out the testing themselves. Also the testing is seen as a service that starter culture producing companies such as DSM should offer. At low levels of phages the infection will result in slowing down of the fermentation process, this slowing down can also be seen if the pH is followed during the fermentation. If the pH drops to slowly a first measurement is adding more of the starter culture. This is a sign of a phage infection with a low concentration of phages. If the concentration becomes higher there are two possibilities; either clean the whole system thoroughly with acid and basic chemicals/ chlorine. (Sib sytem?). Cleaning is performed by the factories themselves. And it’s done by hand since phages can reside in small corners of the tank. Another possibility is adding another starter culture that is insensitive to the infection that is at hand. The samples DSM gets are often samples after the fermentation is performed and the results of the measurements are therefore often too late for the batch that is measured. Sometimes companies perform multiple fermentations in a day and at the end of the day the samples are send to DSM. After analysis of the samples the best of the two options mentioned above can be carried out before the next fermentations are performed.
The source of the phage can either be from the starter culture or from the milk. The latter seems the most common. Detection can performed (raw milk) or after the fermentation (Wei). In some cases such as with Mozerella it can also be tested during the fermentation process. The measurements that can be taken also depend on the type of fermentation. Dutch cheeses such as Goude use a complex undefined blend ( hundreds of bacterial strains) starter culture. So these companies cannot easily switch to another starter cultures and they will need to clean their tanks after infection. Also these starter cultures contain many types of phages that make sure that not one strain gets the overhand over other strains. However if the production is switched to another product the phages can reside in the tanks and then they can form a problem.
American and Australian cheeses use defined cultures of 3-5 strains, in which is strains has specific tasks. In these fermentations phage problems are much more important. In this case it would be quite easy to change the culture since there are multiple strains that are sensitive to different phages but are interchangeable for the fermentation. For the defined blends phages are the biggest problem and if they could be detected in a fast and quantitative manner companies could react on infections that are rising by adding some resistant strain against the infectious phage. To serve this purpose a detector should have the following characteristics: differentiate/ detect up to 700 species of phages, have a detection limit of 10^2 phages per mL and a detection time of ½ to 1 hourA detection limit of 10^4/10^5 phages per ml would make our project a usefull detector as well, since at these levels infections become problematic. At higher concentrations the infections are too out-of control to be treated. As long as our product contains live GMO it would probably not be used by the most companies. Since they do not have the expertise nor the will to work with GMO’s. Also if a GMO would end up in the final product it would result in immense reputational damage. Therefore our detection system should not be complicated to use and without risks of escaping GMO. At the quality labs of DSM they could use it, but for our project it would be best if it can be used at the site of the factory since that would be the quickest.
The major companies that now use techniques such as qPCR might be possible to get an MLI lab in the factory or on the factory terrain. Further in our final product we need to use several strains of both L. lactis as S. thermophiles (these are the two major bacterial species that get infected), since the sensitivity to phages differs between each strain. Another thing that is done against phage infection is making starter cultures more phage resistant. At DSM this is done by increasing the phage resistance of the different bacterial strains. And by optimizing the combination of several strains to decrease the overlap of sensitivity. Another thing that is done by companies is rotation of starter cultures.
Zoë Robaey - INPUT DATE
Unilever Skype Call - INPUT DATE
Goedhardt, Maaike de Heij - INPUT DATE
Cogem Symposium - INPUT DATE
Christian Hansen, Thomas Jansen - INPUT DATE
Skype call with Thomas Jansen from Christian Hansen company. The company mostly deals with starter cultures. The company tests substances for the presence of bacteria phages. They sometimes use multiplex PCR to identify the species of the phages. However this is not very effective in some cases so they use strain specific tests. One problem is that some cultures are made up of more that one strain and this could lead to a problem in detection since they don’t hand out the single strains to the customers. The service is free of the customer is using their starter cultures. Their testing takes 2-3 days if everything works properly.
Felix explained our project to him, including the fact that we will use a pigment protein and not GFP in a business model If our product produces an answer within a few hours and can be used directly in the factory floor, then our product will have a market. However, our product has GMO’s so cannot be used on the factory floor. A lot of the labs in their companies are not GMO labs. Also, the device will be more useful if it can detect a specific strain. Also, with their current system, they cannot detect all strains of phages, only that which they already know. He mentioned that for our system, we’d need a lot of plasmids.
They detect around 60-100phages. The PCR can detect around 80%, but not the rest. In total, there are over a thousand phages that can affect lactococus. He mentioned that the cases in which the entire product batch is thrown away after a phage attack is very low. Sometimes they use a rotation system to reduce phage attack, it simply takes a big longer. In the cases of delay, this is irritating and you cannot have as much batches ready. This is the less costly potential effect of phages. If they have to throw out the entire batch of milk, then that costs a lot more money. At the beginning of the fermentation, there are a lot less phages. Dairy industries in Denmark are also reluctant to work with GMO’s. They will probably not use our product especially as his company already offers free detection as a complementary product. Also having our own GMO labs could work, but for this we have to detect all the strains. Also, as already mentioned, they offer it free, so our company would probably not survive in Denmark.
The culture is their main business, and a side one would be the enzymes. Offering detection as a free product is a way to keep up with their competition. He does not know how much this is, but they have about 10 people working full time on this in their company. Our company would also need human input, so we probably would not be able to offer much difference in this area. The important questions are to know whether or not there is a phage present, and what group it is,and therefore what culture to use. They can then deliver immune strains. Knowing the specific strain is not necessary. Our device would be useful if it could go faster, sometimes, theirs takes up to 10 hours and they have to do it overnight. If the dairy could do it directly, then that would also be interesting since they can save the time and the money being used to hire workers. Also a higher sensitivity will be interesting. Adjusting the plasmid for different strains seems complicated, and this is a downside of our product. Also if our system can detect new phages and 100% of all existing phages then it would be worth wile as theirs only detects about 80%. The dairy industry will not establish a different lab for our product. We have to compete with a system which works quite nicely and to which they have invested a lot of money. We can send our abstract to him and he could give us feedback on it.
