GI360™ Microbiome Profile

There isn’t a stool test that permits direct diagnosis of SIBO, and breath testing can be difficult to administer. Although not practical, gavage sampling from the upper bowel followed by culture or PCR has been used in the research setting.

PCR is a well-established method for detection of microbe specific, nucleotide sequences. It is very sensitive and specific. However, it can only detect what one has probes for. Culture can identify any bacteria and yeast that are aerobic or facultative anaerobes and abundant enough to grow out. Microscopy can identify any parasites that can be detected via standardized, high-quality O&P. The combined methodologies are the paragon of complementation.

Both the GI360 and CSAP are excellent tests providing actionable information.  The GI360™, built on the CSAP, with an additional PCR platform. The GI360™ includes indexes of Abundance, Dysbiosis and Diversity, which are calculated from the results of the Microbiome Profile (PCR). The CSAP utilizes growth-based culture and ID by MALDI-TOF, PCR for specific pathogenic microbes, important stool chemistries, and microscopy to detect and assess the status of commensals, dysbiotic and pathogenic bacteria, yeast and parasites. The GI360™ built on the CSAP with addition of an additional PCR platform. Both the GI360™ and the CSAP include PCR analysis for a total of 14 pathogenic bacteria, viruses and parasites.

Not all PCR platforms are equal. There are currently no specific requirements for molecular testing in the clinical laboratory so clinicians should consider published performance characteristics for a given PCR platform.  Very strict assay performance evaluation is required for FDA/EU (CE-marked) clearance. The performance characteristics of the primary PCR platform that DDI uses (CE-marked) has been published in a peer-reviewed journal (doi:10.1111/apt.13236) and confirmed in-house.  The PCR testing at Doctor’s Data has been evaluated against Illumina deep sequencing.

The microbiota abundance and diversity section of the report is a novel test within the GI360™ test. Using a unique approach, the specific probes were selected to cover consensus observations from published literature regarding the most clinically significant bacteria with respect to dysbiosis associated with IBD and the different classifications of IBS. A scientific process was applied to select DNA probes targeting ≥300 bacterial species, based on the ability to confidently discern dysbiosis in that clinical setting. The specific set of probes and the model has been rigorously tested and validated to identify and characterize dysbiosis. Doctor’s Data also utilizes additional DNA probes for pathogenic bacteria, viruses and parasites, separate from the Abundance and Diversity test. The latter probe set includes the probes that are used in an FDA cleared panel for the detection of microbes most commonly associated with diarrheagenic disease.

One certainly can get an idea about imbalance among those predominant phyla by looking at the web diagram on the first page of the report (Abundance and Diversity). Defining a robust, clinically meaningful F:B ratio was not an objective of the incorporated dysbiosis model. However, obtaining information about gut imbalances that may contribute to obesity, insulin resistance, and heart disease is a feature of the GI360.

Hundreds of resistance markers can be detected in a “stool pool” of well patients.  Resistance markers may be present in the microbiome as a result of previous exposure to antibiotics and environmental exposures; elemental mercury is a classic example. Resistance mechanisms may very well be associated with non-pathogenic, commensal organisms.  Simply evaluating the presence of resistance markers in a total stool DNA extract, without direct connection to a specific pathogenic bacteria, has no value in clinical microbiology or patient care.  

Direct susceptibility testing (included in the GI360™) is performed with highly standardized and validated techniques with regards to natural antibacterial and prescriptive agents.  Bona fide susceptibility testing provides actionable results that aid in targeted clinical intervention. 

Yes, GI360 includes direct susceptibility testing for cultured pathogenic and dysbiotic bacteria, and all cultured yeast. Susceptibilities to antibiotics and natural/botanical agents are provided for each individual patient’s pure isolates- no “wall charts.”

There isn’t a single perfect method for addressing all clinical questions regarding the gastrointestinal microbiota. Culture and PCR are extremely comprehensive and complimentary methods to investigate clinically important issues regarding the gastrointestinal microbiota. Culture with proteomic identification via MALDI-TOF MS remains clinically significant for determining the presence and robustness of aerobic and facultative anaerobic organisms. PCR addresses the question – Is it there? However, PCR is limited to the number of probes used. The GI360 is able to identify >1,600 genera and species of bacteria and yeast. Additionally, clinically applicable susceptibility testing requires cultured isolates of live bacteria and yeast.

Diversity of species is an important component of health for any ecosystem, and the gastrointestinal microbiome is no exception.  Recent research clearly indicates that greater diversity is associated with a robust and healthy microbiome.  Greater diversity is important for redundancy with respect to important functional guilds, i.e. butyrate production. For the GI360™ the Diversity Score is calculated from the microbiota abundance data (PCR), using the well-established Shannon’s diversity index. Data from DDI indicates that the Dysbiosis Index and Diversity Score are inversely correlated- the higher the Dysbiosis Index, the lower the Diversity Score. As such, a Diversity Score would be expected to improve with successful clinical intervention to restore normobiosis.

Yes, all samples are pooled regardless of how many days are collected and submitted.

We do not have a guideline for this as the little one’s immune system is changing and growing over the first years of their life.  The ordering practitioner needs to be aware of this possible cause for elevations in pediatric patients when ordering and interpreting the results.

We do not have an age limit for stool testing to be performed on children or pediatrics.  If the sample is collected from a diaper, the collector needs to make sure to not collect any stool that has been sitting in urine.

GI360 and CSAP are testing options for pediatric populations. The CSAP may be more appropriate for those under 2 years of age. The Microbiome Abundance and Diversity portion of the GI360 is best utilized for ages 2 and above due to expected variations in the microbiome before the age of 2.

There are clinical nuances when interpreting stool reports in pediatric populations. For example, breast fed infant stool contains higher levels of inflammatory markers, calprotectin and lactoferrin. Pediatric patients are more frequent carriers of C. difficile than adults. Cultures of stool “normal” and “abnormal” organisms and quantities differ in pediatric patients vs. adults and require careful interpretation before treatment. GI pathogens and parasites, however, are significant findings, irrespective of age.

Pediatric reference ranges have not been established for stool testing, including the GI360, CSAP and microbiology test.

Visit the payment information page for an overview of payment options and procedures along with insurance coverage overview.

NOTE: Insurance coverage for testing is based on several factors such as the type of procedure, diagnosis, and insurance policy guidelines. Patients are encouraged to contact their insurance company to check for coverage and to provide the procedure codes (CPT codes) and diagnostic codes (ICD-10 codes). The CPT codes can be found on the billing information page, while ICD-10 codes are provided by the practitioner.

Please refer to your test’s specific Test Preparation and Instructions for more information regarding the potential effects of medications, foods, and supplements on this test. You should also consult your healthcare provider prior to making any changes to your medications.

Stool samples should be shipped only on Mondays, Tuesdays, or Wednesdays. If doing a multiple day collection, it is important to collect samples on three separate days, with a minimum gap of 12 hours between collections using the vials contained in the collection kit. All of the stool specimens should be shipped together within five days of the first collection.

For the GI360 profiles it is recommended that you collect for 3 days. For parasite analysis the CDC recommends 3 days.  However, if you have difficulty collecting for multiple days you can send in just 1, or 2 days specimens. Follow the instructions in the specimen collection instructions that come in your test kit and contact your healthcare provider if you have questions about this.