Design

In order to establish the protocols for the recovery of the nematodes from the faeces, a process of trial and error has proven necessary. This has lead to the process being divided in 3 main steps:

Nematodes isolation & purification

Nematodes sterilization
Nematodes separation The first two steps allow the retrieval of sterile small strongyles samples, ready for the following parts of our project, while the last step was necessary for the obtainment of large strongyles. After the obtainment of sterile samples, some were used for co-culturing, and some for phage display. The co-culturing has been performed with varying amounts of sterilized nematode samples and E. coli MG1655. Nematode isolation & purification From the fecal samples provided by Vidilab we needed to extract the worms in order to perform experiments on them later. For each extraction, approximately 20 g of faeces are used. Figure 1: measurement of faeces for incubation The first step is the incubation of the faeces in a plastic cup in a 29 degree oven for one week. During this time the eggs hatch and the nematodes reach the third larval stage. This is the infectious stage of the strongyles and the end of its development in the faeces/grass. Figure 2: cups incubated at 29°C After the one week incubation period, the cup was filled almost to the brim with physiological saline solution and left upside down on a petri dish overnight. This allowed the worms to swim out of the feces and into the water -- which is easy to recover in different falcon tubes. Nematode purification Even though most of fecal debri was left in the cup some smaller impurities were still present in some of the falcons. This debris would drastically reduce the efficiency of the sterilization process, since contaminant organisms would be able to survive inside the debris. In order to remove it, we set up a simple filter system using pasteur pipettes to which we added a small amount of cotton, loosely inserted. The worm and debris solution is inserted in the pasteur pipette and is left above the cotton filter for a time between 30 minutes and 1 hour. In this time the nematodes get to swim through the filter, while larger impurities are stopped. The solution recovered was pure enough to proceed to the sterilization step. Nematode sterilization The purified worm solutions have undergone sterilization. This was done for the following phage display and co-culturing. In the co-culturing, If the sterilization step is not done or is insufficient, it could lead to upregulation of other genes than those that are under investigation, which in turn would lead to the accumulation of false positives. Therefore this step is fundamental. The sterilization was done by applying a solution of bleach to the nematodes. The concentration of bleach was kept at a sufficient level so that the nematodes survived and the bacteria died. After the sterilization washes was made with sterile physiological solution (saline). This led to the removal of the bleach and created a sterile environment in which the nematodes could survive. In order to make sure that the sterilization had succeeded a control was made by putting an aliquot of the sterilized worm solution into a small flask of LB. This was then put into incubation overnight. If nothing had started growing in the flask sufficient sterilization had been achieved. An example of this can be seen below in figure X where the sample that was put into the rightmost flask was shown to be sterile while the others was not. Figure 4: shows the result from a sterilization test. The aliquote that was put Into the rightmost flask proved to be sterile. Nematode separation To investigate the possibility of adapting the workflow of the development of the diagnosis tool for small strongyles to large strongyles, samples containing uniquely large strongyles is needed. Since small strongyles can be present in horses without large strongyles, but the opposite doesn’t occur, a system to separate the two types of strongyles was needed. The only pre-existing system employed by researchers that intend to collect nematodes of a certain class is the use of a pick under a microscope. This however is very time consuming and doesn’t allow obtaining a high concentration of nematodes and therefore a different procedure was needed. With this goal a microfluidic chip has been created. The chip presented a single channel that splits in 2. The solution containing both types of nematodes, and any kind of contaminant, can be pumped inside the single channel. 2 valves, connected to the 2 split channels, can be used to redirect the flow from the main channel to one of the 2. Positioning this chip under a microscope, and analysing a strongyle when reaching the bifurcation allows the determination of the nature of the nematode. The flow is then directed towards the collection tubes. This system, even though it doesn’t allow an immediate separation of all the large strongyles from the sample, leads to a quicker separation compared to hand picking. A low flow pump, such as a pressure or a syringe pump, is required. These details are described in the protocol we developed. Co-culturing So, having achieved sterilisation of the small strongyles, the question is what do we do with them? The next step was the co-culturing. In this process we grew bacteria in media containing the newly sterilised nematodes. The bacteria are cultured with the nematodes for around 4 h, enough time to allow the bacteria to develop a genetic response to the presence of the strongyles in the media, in order to detect the response on the transcriptomic level. We chose to work with MG1665 as our E. coli strain as it closely resembles the K-12 wild-type, which is the strain closest to the E. coli that is naturally found in the gut of horses, having a higher probability of possessing a response system for the presence of nematodes. As growth media we chose M9, a minimal media, in order to minimise the noise from the expression of common metabolism related proteins. The co-culture was started from an OD of around 0.05, and was allowed to grow until an OD of 0.8. Once the bacteria were done growing, the strongyles had to be removed, which was achieved by vacuum filtration through a Whatman n°1 filter, which allows the passage of bacteria but not of the nematodes. The filtration done, the bacteria were ready to be handed over to the transcriptomics group for further study.