Background
Obesity and overweight affect two in three Australians. Obesity is associated with oral and gut microbiome changes, but some signatures are inconsistent. This can arise from geographic differences and healthy control selection.
Aims
This interim analysis uses the Healthy Optimal Australian Microbiome (HOAM) as the control to characterise the Australian obese gut and oral microbiomes.
Methods
Oral swabs and stool samples were collected from inactive obese (n=10) and age- and sex-matched healthy active controls (n=29). Shotgun metagenomic sequencing was performed on the DNA extracted from these. Taxonomic profile and functional pathways were determined with Kraken2 and bracken2 with reference to GTDB R95 and HUMAnN3.8 databases respectively. R package, MaAslin2 generated differential abundancies while controlling for age and sex.
Results
The obese stool bacterial composition differed from controls (PERMANOVA; R2 = 0.076, p<0.01) with a marginal reduction in Shannon index for alpha diversity (Kruskal-Wallis, p=0.053).
Fewer genera were enriched in obese stool samples than controls (obesity = 3, control = 25, p<0.001). Notably, Prevotella (MaAslin2, coeff: -2.0, p<0.001) and Bacteroides (coeff: -2.2, p<0.001) were reduced. Obesity is also associated with fewer enriched species (obesity = 4, control = 15, p<0.001). Alistipes senegalensis (coeff: -1.7, p<0.01) and Faecalibacterium prausnitzii (coeff:-2.3, p<0.01) were reduced while Bacteroides fragilis (coeff: 2.6, p<0.01) was enriched.
Four functional pathways were enriched in obesity (obesity = 4, control = 0, p<0.001) including a super-pathway for N-acetylglucosamine degradation (coeff: 0.12, p<0.001) which was associated with Faecalibacterium.
Oral bacterial composition differed between groups (PERMANOVA; R2 = 0.067, p<0.05). The phylum, Acidobacteriota was increased in obesity (coeff: 0.24, p<0.001).
Conclusion
This study shows bacterial composition dysbiosis of oral and stool microbiomes in obese Australians. While some of the depleted taxa are associated with glucose metabolism and appetite regulation, further metabolite analysis can better determine how the microbiome impacts obesity.