Genetic Analysis (GA; Oslo, Norway), a startup molecular diagnostics company, has developed a Gut Associated-microarray platform (GA-map) test designed for high throughput screening of gut microbiota in infants.
At the recent Sackler Colloquium on Microbes and Health in Irvine, California, the company presented data from evaluation screens that show its potential as a tool for probing the mechanisms of disease in conditions associated with the gut flora.
"What we see out there in the literature is a lot of research now emerging that links some diseases to an imbalance in the" microbial profile of the gut, Morten Isaksen, PhD, CEO of Genetic Analysis, told Medical Device Daily.
For some, like inflammatory bowel disease, Necrotizing Enterocolitis, allergies and autism, the specific disease mechanisms involved are poorly understood, the company said. Studying the differences between gut microbiota in the diseased state and in the rest of the population could provide crucial clues to the causes of disease, according to GA.
The newly developed GA-map technology is based on sets of unique probes that are highly specific to their target groups of bacteria, GA noted. The company says it is thereby taking a different approach than the more common in-depth analyses of a few samples. The GA-map microarray allows a very large number – more than 200 samples – to be processed a day. This allows routine and population based analysis not possible with alternative techniques, Isaksen explained.
"We can look at up to hundreds of different types of bacteria or classes of bacteria at the same time," he said. "We can look at things that other people haven't been able to look at."
In the evaluation screen, a team led by Professor Knut Rudi of Genetic Analysis used the GA-map microarray to model the abundance of gut bacteria in stool samples from infants between one day and two years old. Using the GA-map array, they could predict children's ages simply by looking at the profile of their gut flora, the company noted.
"This is kind of ten years or so of research that basically looked at different ways of classifying different bacteria," Isaksen said. "So we're using a different classification system than [other techniques]."
Isaksen said that GA envisions GA-map as a platform technology "that opens up a black box, where you can see an overall map of the gut microbiota, which can then point you in different directions depending on the disease being studied." He added that GA-map can also be used for monitoring ongoing changes in the patterns of a child's microbiota that lead to diseases such as allergies, NEC and autism. This information can then be used to assist in disease intervention, according to the company.
"Our aim is to be able to look at these changes happening early ... detect this before other methods can detect the onset of disease," Isaksen said. "Because we can't say that in every disease that it starts with the gut, but the gut is definitely influenced by the disease."
GA provided MDD with a technical description of how the GA-map technology works, which involves a six-step process.
The source of material is stool samples. For transportation purposes, special tubes will be used, the company said.
Total bacterial DNA is extracted from the fecal sample by mechanic disruption of the cells, and by using magnetic beads. The result is pure total bacterial DNA from the fecal sample, according to the company.
From the total bacterial DNA, the 16S rRNA gene is amplified. For this purpose, a novel universal primer pair covering most of the 16S rRNA gene. According to GA, the unique combination of primers are able to give a good representation of the complete bacterial DNA in a single reaction, giving scientists the amplicon that can be used for further analysis.
In order to find specific probes within the 16S rRNA amplicon generated by the universal PCR primer pairs, a specialized computer program – the GA-map ProbeTool – has been developed, the company explained. This program is using several levels of criteria by which a unique probe can be used to identify a specific phyla, genera, family, or individual strain.
The designed probes from the GA-map ProbeTool program is added to the 16S rRNA amplicon. The probes will bind to the complimentary 16S rRNA sequence if it is present in the solution, the company said. The GA-map ProbeTool program designs the probes so that the next nucleotide to be added is a specific nucleotide carrying a fluorescent label. This means that if the bacteria represented by the probe was present in the stool sample, the probe will bind and be labeled, GA explained.
This labeling of the probes is done in a cyclic manner, giving rise to free labeled probes in solution. The next step in the process is that the labeled probes are placed on arrays on a glass slide. The hybridization is not relying on high specificity, but general complimentary sequences.
By scanning the array, spots on the array will appear, which reflects the amount of bacteria present in the original stool sample, the company said. The image created is analyzed and the spots quantified. The information gathered from the image is then analyzed in order to gather all useful information.
The data generated from the GA-map technology is stored in a database, together with the available information of the patient that the stool sample comes from, GA said. The ability of the database to interpret the data will increase as the database is filled with data, the company noted.
When asked about the regulatory pathway GA will have to take to commercialize the GA-map technology, Isaksen told MDD that the company is still "a ways away" from that. "We are more in the phase now to start to gather data to run through samples and so far we have in the pipeline of our development the opportunity to run somewhere between 5,000 and 10,000 samples through the system from various diseases and various candidates," he said. Once that has been processed, Isaksen said GA will have a much clearer picture of the documentation it will need for regulatory purposes.
"Looking further ahead, the technology could be used to develop intelligent treatments based on personalized medicine," Isaksen said. "How different food or drugs are metabolized can be affected by the gut microbiota. Therefore, the GA-map technology could also become important for the food and pharmaceutical industry."
Amanda Pedersen, 229-471-4212;