Disorders of Gut-Brain Interaction (DGBIs) may afflict 1 in 6 Australians, with functional dyspepsia (FD) and the irritable bowel syndrome (IBS) being a major personal and economic burden. Both these disorders lack a defined pathophysiology, so their diagnosis and management remain symptom-based, with treatments often providing only temporary relief from recurrent symptoms. In addition to gut-brain dysfunction and immune activation, the mucosa-associated microbiota of the duodenum (d-MAM) has recently been implicated, with specific bacterial taxa and/or density now shown to be linked with gut motility and/or patient symptoms. Here, we have used an ex-vivo combination of microbe culture with metagenomics to produce the first insights into d-MAM from subjects with different DGBIs: FD characterised as epigastric pain (EPS) or post-prandial distress (PDS); and FD with or without IBS-overlap.
Duodenal biopsies were collected from 19 subjects with DGBIs diagnosed using Rome IV classification. Biopsies were stored anaerobically using a specialised device protecting tissue from saliva/luminal contaminants; and were later transferred into sterile, anaerobic, habitat-simulating medium. Subsamples were used to inoculate fresh medium (in technical triplicate) and after 24h growth, subsamples from these cultures were pooled for DNA extraction, 16S rRNA gene amplicon profiling. The resulting amplicon libraries were quality checked and processed using QIIME2 and mixOmics. The sparse partial least squares-discriminant analyses showed a clear separation of the d-MAM communities between the FD patients with or without IBS. Furthermore, the d-MAM profiles for subjects with EPS with or without PDS overlap were also separable by this supervised analysis. The d-MAM profiles of those subjects with IBS also showed some separation between those subjects reporting diarrhoea and those with mixed symptoms.
This pilot study confirmed the d-MAM profiles of DGBI subjects can be differentiated with respect to different FD subtypes, as well as FD subjects with or without IBS. These findings validate that DGBI pathophysiology is both associated with and may be defined by the structure-function relationships inherent to the d-MAM, both of which offer new targets and opportunities to better diagnose and treat the underlying causes of these conditions.