Introduction
Disorders of gut brain interaction (DGBI) including functional dyspepsia (FD) and irritable bowel syndrome (IBS) have overlapping pathophysiological mechanisms.1 The complexity of DGBI creates challenges in identifying possible objective biomarkers to differentiate DGBI from health. The isolation of Streptococcus salivarius (AGIRA0003), an oral microbiome commensal in the duodenal tissues of patients with FD suggests that the oral microbiome can translocate to the duodenum and may predict duodenal microbiome alterations in DGBI.2 The oral microbiome is a simple and non-invasive tool that could be used to explore DGBI biomarkers.
Aims & Methods
We aimed to compare the buccal microbiome profile in DGBI with healthy controls and identify species associated with FD and IBS subtypes. The buccal samples of patients recruited into the Digestive Health Biobank and meeting the ROME IV diagnostic criteria for FD or IBS were retrieved. Shot-gun metagenomic sequencing results were annotated using MetaPhlAn4 and results analyzed using R-studio for alpha diversity (Shannon), beta diversity (Aitchison distance matrix), and linear discriminant analysis effect size (LEfSe) was used to determine differentially abundance taxa with a log10 linear discriminant (LDA score) indicating the effect size across groups. Taxa with p<0.05 were considered statistically significant.
Results
There were 92 buccal samples, comprising of 63 with DGBI and 29 age and sex matched healthy controls (Table 1). There was no significant difference in microbiome alpha diversity between the patients with DGBI and controls (P=0.19), DGBI phenotypes (FD, IBS, FD/IBS overlap) p=0.20, FD phenotypes (EPS, PDS, EPS/PDS overlap) p=0.39 or IBS phenotypes (IBS-D and IBS-M) p=0.47 (Table 1). Beta diversity analysis showed no significant difference in the microbial composition between DGBI and control (R2=0.01, p=0.24), DGBI phenotypes (R2=0.03, p=0.38), FD phenotypes (R2=0.06, p=0.13) or IBS phenotypes (R2 =0.05, p=0.75). The LEfSe analysis showed an increased relative abundance of phylum Candidatus Saccharibacteria in FD cohorts compared to IBS or FD/IBS overlap (LDA score=2.88, p=0.04). Sub-group analysis showed a significantly enriched Candidatus Saccharibacteria in EPS (LDA score=3.69, p=0.03) and genus Megasphaera in EPS/PDS overlap (LDA score=3.20, p=0.01) vs PDS. IBS-D had an increased abundance of genus Prevotella compared to IBS-M (LDA score=4.86, p=0.04).
Table 1: The socio-demographic characteristics of the study population.
| Characteristics | DGBI | Control | p-value |
| Sex |
|
| Female | 55(87.3%) | 25(86.2%) | 0.82 |
| Male | 7(11.1% | 4(13.8%) |
|
| Prefer not to stay | 1(1.6%) | 0(0.0%) |
|
|
Age(years) Mean± SD
Age range(years) | 47.2±15.10
22-73 | 52.2±15.10
19-77 | 0.12
|
| BMI (kg/m2) Mean± SD | 26.5±5.08 | 28.5±5.44 | 0.17 |
| Alcohol ingestion | 37(64.9%) | 20(35.1%) | 0.49 |
| Smoking history | 22(73.3%) | 8(26.7%) | 0.61 |
BMI-Body mass index, SD-standard deviation
Conclusion
There was no significant difference in the diversity of the buccal microbiome between DGBI patients and healthy controls. However, differentiating species were detected in DGBI subtypes, suggesting that the buccal microbiome may be a useful tool in differentiating DGBI subtypes.
References
- Drossman DA, Hasler WL. Rome IV-Functional GI Disorders: Disorders of Gut-Brain Interaction. Gastroenterology 2016;150:1257-61.
- Hoedt EC, Shanahan ER, Keely S, et al. Draft Genome Sequence of Streptococcus salivarius AGIRA0003, Isolated from Functional Gastrointestinal Disorder Duodenal Tissue. Microbiol Resour Announc 2021;10:e0075821.
Disclosure
SK: Patent: “Diagnostic marker for functional gastrointestinal disorders” (Australian Patent Application WO2022256861A1) via the University of Newcastle and UniQuest (University of Queensland). Grants from National Health and Medical Research Council (Ideas Grant and Centre for Research Excellence), grants from Viscera Labs (Research contract), grants from Microba Life Science (Research contract), grants from Anatara Lifescience (Research contract), personal fees from Gossamer Bio, personal fees from Anatara Lifescience, personal fees from Immuron, personal fees from Microba Life Science.
Prof. N. Talley: Norgine (2021)(IBS interest group), personal fees from Allakos (gastroduodenal eosinophilic disease) (2021), twoXAR Viscera Labs, (USA 2021) (IBS-diarrhoea), IsoThrive (2021) (esophageal microbiome), BluMaiden (microbiome advisory board) (2021), Rose Pharma (IBS) (2021), Intrinsic Medicine (2022) (human milk oligosaccharide), Comvita Mānuka Honey (2021) (digestive health), Astra Zeneca (2022) Biocodex, France (functional dyspepsia tool 2024-2025) Brown University (fiber and laxation systematic review 2024-2025), outside the submitted work. In addition, Dr. Talley has a patent Nepean Dyspepsia Index (NDI) 1998, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692, ”Methods and compositions for treating age-related neurodegenerative disease associated with dysbiosis” US Application No. 63/537,725.
Financial support: Dr. Talley is supported by funding from the National Health and Medical Research Council (NHMRC) to the Centre for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant
