Genetic Analysis, a one-year-old molecular diagnostics company, this week launched its high-throughput GA-map microarray test, which is designed to screen the gut microbiota of infants.
The company also said it plans to debut next year a second GA-map array, this one for adult microbiota, as it looks to help researchers study diseases believed to be associated with gut flora.
According to CEO Morten Isaksen, a number of diseases are thought to be linked to an imbalance in the gut microbiome, including inflammatory bowel disease, necrotizing enterocolitis, allergies, and autism. GA's new array platform enables users to form a more global perspective in studying microbial profiles, as opposed to testing patients for the presence of particular bacteria one at a time, he said.
Based on technology developed at the Norwegian Food Research Institute, Oslo-based GA's GA-map assay consists of probes and primer sets for between 30 and 200 different bacterial species, detected on the firm's microarray platform, that are present in the infant and adult gastrointestinal tract.
According to the firm, total bacterial DNA is extracted for the GA-map assay from a stool sample. The cells from the sample are then disrupted mechanically by using magnetic beads. From the total bacterial DNA, the 16S rRNA gene is amplified, and GA uses its GA-map Probe Tool to identify probes that can be used for a specific phyla, genera, family, or individual strain.
The GA-map assay then relies on a two-step single nucleotide-extension reaction that fluorescently labels the DNA. If bacteria represented by the probe is present in the stool sample, the probe will bind and be labeled. After hybridization, the array is scanned using conventional equipment, and a microbial profile is generated and is ready for analysis, according to the firm.
Isaksen said in a statement that GA envisages 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 said 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."
Isaksen told BioArray News this week that the company is offering a new approach to looking at bacteria present in the gut. "People are used to looking for specific bacteria," Isaksen said. "We look at the whole profile because one event, like IBD, is not one bacterium," he said. "We see that it's a complex interplay of what happens in the gut," he added.
"By looking at one or two or three bacteria, you will not be able to understand that interplay," Isaksen continued. "By looking at the whole profile, we will see different patterns that influence different disease states."
Isaksen said there are a number of markets for GA's platform. "We see a lot of different users for this technology. The first market is the general research market that ... can benefit from using our technology to generate data more quickly using 200 samples a day," he said. "Other approaches take weeks to process one or two samples."
According to Isaksen, researchers these days are using sequence-based metagenomics to look at microbial communities. While the field of metagenomics, typically powered by second-generation sequencers, is new, he described it as a "discovery technology," while GA's array platform is a "diagnostic technology," as it can test in a high-throughput manner for a large amount of microbes and generate a profile for them.
GA also sees the personal care market as a potential target, as well as the food and drug industries. "We believe that people are interested in determining the relationship between a gut profile and various disease states and what can be done to improve on that," Isaksen said.
While GA is currently focused on selling its GA-map arrays for infant and adult samples, the company would like to develop ways for preclinical researchers to use the chips to study IBD, NEC, allergy, autism, and other diseases, and to ultimately assess patient health, Isaksen said.
He said the market for GA-map is "considerable," and that the company has talked to "various research groups and companies and everyone is interested in the technology once we have time to explain to them how it works."
Other researchers and companies have also developed array-based tools to look at microbiota in the gut. This year, a team of researchers led by Oleg Paliy at Wright State University in Ohio published results of a study in which they used a phylogenetic array to analyze human intestinal microbiota (see BAN 5/5/2009).
This year, researchers led by Peter O'Toole at University College Cork in Ireland published a description of an internally developed human intestinal tract chip for similar studies.
There are several projects underway that may feed demand for such technologies. Among the largest is the US National Institutes of Health's Human Microbiome Project, part of its Roadmap for Medical Research that funds various studies to determine how microbial cells impact human health.
"That project is perfect for us," Isaksen said. "They generate a lot of information from these bacteria. The more information that comes from there, the more useful our technology will become."