GI360 (Comprehensive Molecular Stool Profile)

Multiplex PCR and quantitative PCR detect organism-specific nucleic acid sequences directly from stool, without requiring culture. This allows detection of defined enteric bacterial, parasitic, and viral pathogens, including organisms that are difficult or slow to culture, and quantitative estimation of selected commensal targets.

Molecular detection is sensitive and validated for identifying defined enteric pathogens and is a genuine strength of this profile relative to culture-only testing. A key limitation is that PCR detects nucleic acid whether or not the organism is viable, so a positive result must be correlated with the clinical picture, particularly shortly after treatment, and detection does not always equate to active infection.

This component quantifies selected keystone and commensal organisms by qPCR and combines them into a composite index benchmarked against a reference population intended to represent a healthy gut community. It assesses a defined panel of organisms rather than the full microbiome, and is not equivalent to shotgun metagenomic sequencing.

Quantitative measurement of selected taxa is more reliable than culture for those specific targets. However, the composite Dysbiosis Index is a proprietary score whose clinical validity for diagnosing 'dysbiosis' or directing treatment is not established, and it should be read as a deviation flag relative to a reference group rather than a diagnosis. It must not be used in isolation to justify probiotic or antimicrobial regimens.

Pancreatic elastase-1 is a pancreas-specific protease that resists intestinal degradation, so its faecal concentration reflects exocrine pancreatic output. Microscopic products of digestion reflect the completeness of luminal digestion and absorption.

Faecal pancreatic elastase-1 is a validated, established non-invasive marker of exocrine pancreatic insufficiency. The microscopic products-of-digestion markers are qualitative and operator-dependent, and are interpreted supportively rather than diagnostically.

Calprotectin is a neutrophil-derived protein released into the lumen during mucosal inflammation and rises with neutrophilic gut inflammation. Secretory IgA is the dominant mucosal antibody, and eosinophil protein X reflects eosinophil activation.

Faecal calprotectin is validated for distinguishing inflammatory bowel disease from functional bowel disorders and for guiding the decision to proceed to endoscopy. Secretory IgA and eosinophil protein X are less standardised, and their use to characterise 'gut immune status' is interpretively contested and should not drive diagnosis in isolation.

Short-chain fatty acids are products of bacterial fermentation of dietary fibre that provide energy to colonocytes and support mucosal integrity. Beta-glucuronidase is a bacterial enzyme that can deconjugate glucuronidated compounds, and faecal pH reflects fermentation balance.

These markers describe microbial metabolic activity, but their clinical validity for guiding individual diagnosis or treatment is not established and their interpretation is contested. They are used exploratorily and should not be relied upon in isolation to direct management.

Culture with MALDI-TOF identification recovers and identifies organisms that grow under laboratory conditions and provides antimicrobial and antifungal susceptibilities. Microscopy detects ova and parasites, which are shed intermittently, so combining it with immunoassays for Giardia, Cryptosporidium, and Entamoeba histolytica increases yield.

Culture with susceptibilities and MALDI-TOF identification can guide targeted therapy when a specific bacterial or fungal organism is recovered, and multi-specimen parasitology with immunoassays is a recognised approach for parasite detection. Culture nevertheless recovers only a culturable subset of the microbiome, so it complements rather than replaces the molecular components for community assessment.