P685 Gut microbiota in patients with Inflammatory Bowel Disease during remission

Pisani, A.(1);Rausch, P.(2);Ellul, S.(3);Bang, C.(2);Tabone, T.(1);Marantidis Cordina, C.(4);Zahra, G.(5);Ellul, P.(1);Franke, A.(2);

(1)Mater Dei Hospital, Department of Gastroenterology, Msida, Malta;(2)Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology, Kiel, Germany;(3)Mater Dei Hospital, Division of Paediatric Surgery- Department of Surgery, Msida, Malta;(4)Mater Dei Hospital, Department of Microbiology, Msida, Malta;(5)Mater Dei Hospital, Molecular Diagnostics- Department of Pathology, Msida, Malta


Dysbiosis in patients with active IBD has been described in many studies and populations. There is, however, minimal data on whether dysbiosis persists during remission and the extent to which it does. The aim of this study was to assess the gut microbiota in Maltese IBD patients who are in remission as compared to a healthy control population.


Stool samples of patients with IBD in remission and healthy controls were analyzed by 16S rRNA sequencing. High quality Amplicon sequence variants (ASV) were derived and classified via DADA2.


Ninety-eight patients with IBD (UC: 67.3%; CD: 32.7%) and 97 controls were recruited. Patients with IBD had a decrease in alpha diversity compared to healthy controls (Figure 1) with significant differences in beta diversity (Bray-Curtis dissimilarity, Jaccard distance and Generalized UniFrac distance: all p=0.0001). At the phylum level, abundances differed significantly with respect to health condition (Figure 2). Twenty-five ASVs that were differentially abundant between the different cohorts were identified (Table 1); 13 being over abundant in healthy individuals, while 6 being least abundant among controls. In both CD and UC, 3 different ASVs were found to be more abundant.

Figure 1: Alpha diversity via the Chao1 species richness in the different cohorts ** = P ≤ 0.01

Figure 2: Phylum abundances with respect to IBD status, keeping the same colour scheme as Figure 1

** = P ≤ 0.01, ***= P ≤ 0.001, # = P = 0.05931

Direction: CD>Control/UC Organism p-value
  Dorea uncl. 0.000000
  Subdoligranulum uncl. 0.000007
  Escherichia/Shigella uncl. 0.000007
Direction: Control>CD/UC Organismp-value
  Alistipes uncl. 0.000007
  Coprococcus uncl. 0.000101
  Oxalobacter uncl. 0.000000
Akkermansia muciniphila 0.000000
Bacteroides uncl. 0.001900
  Lachnospiraceae uncl. 0.000000
Oscillibacter uncl. 0.000011
  Clostridiales uncl. 0.000000
  Anaerostipes uncl. 0.000000
  Clostridiales uncl. 0.003265
  Faecalibacterium uncl. 0.000911
  Haemophilus parainfluenzae 0.000149
  Sutterella uncl. 0.000000
Direction: CD/UC>Control Organismp-value
  Dialister invisus 0.000043
  Flavonifractor plautii 0.000000
Oscillibacter uncl. 0.000000
  Bacteroides uncl. 0.000000
  Acidaminococcus uncl. 0.000000
  Ruminococcaceae uncl. 0.000000
Direction: UC>Control/CD Organismp-value
  Parabacteroides uncl. 0.000002
Faecalibacterium uncl. 0.000000
  Parasutterella uncl. 0.002668

Table 1: Differential abundance analysis relevant to health condition


Despite remission, the faecal gut microbiota in IBD is dysbiotic. Future studies could be directed at assessing whether species identified as being more abundant in controls can be used as probiotics to either reduce or be able to stop the standard medications.