Abstract
Background
The role of microbiome with the alteration between commensal and pathogenic bacteria, has been linked to IBD. Meanwhile Escherichia coli Nissle 1917, Lactobacillus rhamnosus GG (LGG) and faecal transplantation are used in IBD. The aim of this study was to prospectively determine faecal microbiota composition of newly diagnosed treatment naïve IBD patients.
Methods
Patients diagnosed with IBD between January 2018-September 2019 were recruited. Clinical data was collected and patients asked to submit stool samples for microbiome analysis. Stool samples from a control population were recruited and analysed via the bacterial 16s rRNA gene sequencing on illumine MiSeq.
Results
100 IBD patients (CD: n=46, UC: n=53 & IBDU: n=1) and 97 controls with specific inclusion and exclusion criteria collected.
IBD patients were noted to display reduced average species richness and community evenness compared to healthy controls (Alpha- Diversity) (Figure 1).
Beta-diversity between microbial communities of healthy individuals and IBD patients was significantly different, but no observed separation between the two types of IBD was noted (Figure 2).
11 ASVs were abundant in CD patients including: ASV-70 – Lactobacillus gasseri, Klebsiella uncl., Candidatus-saccharibacteria, ASV-157 - Acteroides clarus and ASV 249- Parasutterella uncl. In UC cohort, 10 ASVs were abundant including: ASV 6-Escherichia/Shigella uncl., ASB-41-Sutterella wadsworthensis, ASV 44- Bacteroides faecis and Actinobacteria. An association between UC and ASV 313 (Faecalibacteria) was present. In the microbiome of healthy controls, 20 ASVs were abundant, including: ASV-14 G-Alistipes uncl., ASV 20-(Akkermansia muciniphila),(bacterium belonging to the phylum Verrucomicrobia), ASV 321 (Clostridia uncl.), ASV 96 (Rumminococcaceae uncl.), Alistepes uncl. (ASV 61), Subdoligranulum uncl. (ASV 453) and the unclassifiable bacteria. A higher amount of Verrucomicrobia was present in the healthy group as opposed to the IBD.
Conclusion
ASV 249- Parasutterella unlc., was indicative of CD associated microbiome through the indicator species analysis. Typical microbiome changes in IBD patients include increased abundance of the pro-inflammatory species with a reduction in anti-inflammatory bacterial species, with a noticeable reduction in alpha and beta diversity. In the local cohort, a particular change in the local α- and β diversity was noted to be present between healthy controls and IBD cohort. This could be a potential way in which targeted therapeutic approaches using specific dosage and durations of probiotic or faecal transplant can be used to alter faecal microbiome using specific bacteria present in healthy controls and with elimination of potentially harmful bacteria in IBD patients.
Figure 1: Alpha diversity between different Groups using Chao1 species richness and Simpson 1-D
Figure 2: Beta diversity between different groups using Bray-Curtis dissimilarity, Jaccard distance.
Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota
