Comparison of Mucosal and Faecal Microbiomes in Patients With Cirrhosis

The colonic sigmoid mucosal microbiome is reportedly different from the faecal microbiome in patients with cirrhosis. This exploratory study is aimed at comparing the luminal and mucosal microbiome in patients with cirrhosis, with a specific focus on the proximal intestine.

Mucosal and faecal samples were obtained from 12 patients with cirrhosis. The microbiome was quantified with V4 16S rRNA gene sequencing. Relative abundance, alpha and beta diversity were calculated, compared between the mucosal and faecal samples and correlated with stage of cirrhosis.

Faecal samples displayed lower microbial diversity than mucosal samples (Shannon diversity, p = 0.025) and the microbiome profiles differed significantly: Operational taxonomic units primarily of the phyla Firmicutes and Actinobacteria were more abundant in faecal samples, whereas biopsy samples contained units spanning all six phyla. Microbial composition of faecal samples were more similar to faecal samples from other patients rather than to the individual's corresponding biopsy sample (principal coordinate analysis, p = 0.004). At the family level, Lachnospiraceae, Erysipelotrichaceae and Enterobacteriaceae were significantly more abundant in faecal samples, whereas biopsy samples contained more Streptococcaceae (p = 0.011) and Prevotellaceae (p = 0.031). Faecal samples from patients in Child-Pugh Stage C contained less Bacteroidetes but significantly more Streptococcaceae than Stage B samples (p = 0.04); however, biopsy samples did not differ significantly.

This exploratory study in a small sample of patients with cirrhosis observed significant differences in the microbial signature of faecal versus biopsy samples from the proximal intestine. Future studies are needed to further investigate the relationship between different gastrointestinal microbial sites and cirrhosis.