**6. Gut micobiota diagnostic for diffuse conditions**

Major diseases with more diffuse symptoms such as irritable bowels disease (IBS) (Salonen et al 2010) and depression (Maes et al 2009) could be targets for development of future

Gut Microbiota in Disease Diagnostics 107

The GA-map platform has given rise to a pipeline of assays for analysis of disease based on the microbiota composition. This platform includes a DNA purification module, a module for probe design, a patent protected approach for the actual gut microbiota screening, in addition to a diagnostic database. The GA-map assay will help to utilize information in the

An outline of the GA-map platform for gut microbiota diagnostics is illustrated in Figure 2. The platform can be used to assess health conditions of individuals based on the composition of the gut microbiota. In addition, it can serve both the the pharmaceutical industry and governmental health authorities in epidemiological population screenings and clinical trials. In addition, the technology can be used for early detection of undesirable conditions in the gut that can be corrected before the illnesses are manifested. The core aspects of the technology was developed and patented at the University of Oslo in 1998 (US patent # 6 617 138 Nucleic Acids Detection Methods). The technology has since then been refined at Nofima Mat (Matforsk). Currently the technology is patented worldwide and

A high throughput analysis platform based on this technology will make it possible to gain greater understanding of the relationship between the composition of the gut microbiota

Probe labeling is based on the minisequencing principle, where a DNA polymerase extends the probe with a single labeled dideoxy nucleotide (Syvannen et al., 1990). In the GA-map assay several probes are labeled simultaneously, with the detection by reverse hybridization to the complementary strands spotted on to a solid phase (Vebo et al., 2011). This process is illustrated in Figure 3. The probes are constructed so that the probes hybridize adjacent to discriminative gene positions. If the target bacterium is present then a labeled dideoxynucleotide is incorporated by the polymerase. This is illustrated in Figure 3A. The solid phase (i.e. microarray or beads) is used to separate the probes by hybridization to their respective complementary sequences attached to the solid phase, which is illustrated in

There are several steps in the GA-map array process that can lead to wrong patterns if the probes are not properly designed. The probes may bind to the wrong target, and be labeled that way. Furthermore, the probes may be labeled by using itself as a target, or another probe as target. Finally, the probes may bind to the wrong spots on the array. Successful application of the GA-map assay requires therefore the application of a probe design software that takes into account many of the potentially unwanted reactions mentioned

The probe design is based on a novel way of bacterial classification based on 16S rRNA gene sequences. Rather than classifying bacteria by traditional phylogenetic tree-based approaches, the bacteria are classified in a coordinate system (Rudi et al., 2006). The benefit of this approach is both that very large numbers of bacteria can be analyzed, and that

phylogroups are easily identified for probe design. This is illustrated in Figure 4.

and health, as well as being used as a diagnostic and prognostic tool in the future.

**9. GA-map tecnology platform in gut microbiota diagnostics** 

Genetic Analysis AS has been set up to commercialize the technology.

gut microbiota for diagnostic purposes.

**9.1 GA-map array** 

**9.2 Probe design** 

Figure 3B (exemplified by an array).

above, leading to false results.

diagnostics. These are diseases representing enormous burden and costs to society. If these diseases can be linked to some kind of gut microbiota disorders, then there may also be potential for intervention and treatment.

Discomfort such as abdominal pain, flatulence and bloating affect our everyday life. It has recently been shown correlation between these discomforts and specific gut bacteria (Jalanka-Tuovinen et al., 2011). Although not life threatening, the quality of life can be severely reduced by these discomforts. Diagnosis of the gut microbiota could potentially help in dietary interventions.

Although the severity of IBS is not pronounced, 10% - 20% of people in the Western world suffer from this (Maxion-Bergemann et al 2001). Therefore, a diagnostics for this condition could have major impact, given the potential for advice that would increase the quality of life through reducing discomforts.
