Altered gut microbiota in Rett syndrome

Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Massimo Pindo, Daniela Renzi, Lisa Rizzetto, Irene Stefanini, Antonio Calabrò, Carlotta De Filippo, Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Massimo Pindo, Daniela Renzi, Lisa Rizzetto, Irene Stefanini, Antonio Calabrò, Carlotta De Filippo

Abstract

Background: The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT's gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status.

Results: Our findings revealed the occurrence of an intestinal sub-inflammatory status in RTT subjects as measured by the elevated values of faecal calprotectin and erythrocyte sedimentation rate. We showed that, overall, RTT subjects harbour bacterial and fungal microbiota altered in terms of relative abundances from those of healthy controls, with a reduced microbial richness and dominated by microbial taxa belonging to Bifidobacterium, several Clostridia (among which Anaerostipes, Clostridium XIVa, Clostridium XIVb) as well as Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia/Shigella and the fungal genus Candida. We further observed that alterations of the gut microbiota do not depend on the constipation status of RTT subjects and that this dysbiotic microbiota produced altered short chain fatty acids profiles.

Conclusions: We demonstrated for the first time that RTT is associated with a dysbiosis of both the bacterial and fungal component of the gut microbiota, suggesting that impairments of MeCP2 functioning favour the establishment of a microbial community adapted to the costive gastrointestinal niche of RTT subjects. The altered production of short chain fatty acids associated with this microbiota might reinforce the constipation status of RTT subjects and contribute to RTT gastrointestinal physiopathology.

Keywords: Constipation; Gut microbiota; Intestinal dysbiosis; Metataxonomics; Mycobiota; Rett syndrome; SCFAs.

Figures

Fig. 1
Fig. 1
Measures of bacterial diversity. aAlpha-diversity calculated on the number of observed OTUs; ***p < 0.0001; **p < 0.001; ns, not significant; Wilcoxon rank-sum test. b, c PCoA plots of bacterial beta-diversity based on b the Weighted UniFrac distance and c the Bray-Curtis dissimilarity analysed according to individuals’ health status. Constipated Rett syndrome subjects (RTT-C), non-constipated Rett syndrome subjects (RTT-NC) and healthy controls (HC) are coloured in red, orange or green, respectively
Fig. 2
Fig. 2
PhyloRelief analysis (RTT vs HC) of bacterial OTUs using the unweighted UniFrac distance. The heat-map shows the relative abundances of the OTUs that are differentially represented in Rett syndrome (RTT) subjects and healthy controls (HC) (PhyloRelief selected clades with FDR-corrected p < 0.01, Kruskal-Wallis test). OTUs are classified according to their genus on the left side of the figure. The OTUs more represented in RTT subjects than HC are highlighted in bold characters. The ultrametric pruned phylogenetic tree of the OTUs is shown on the right side of the figure. RTT subjects and healthy controls are coloured in red and green, respectively. Abundances are expressed in terms of their z-score
Fig. 3
Fig. 3
Cladogram showing the most discriminative bacterial clades identified by LEfSe. Coloured regions/branches indicate differences in the bacterial population structure between Rett syndrome (RTT) subjects and healthy controls (HC). Regions in red indicate clades that were enriched in RTT subjects compared to those in HC, while regions in green indicate clades that were enriched in HC compared to those in RTT subjects
Fig. 4
Fig. 4
Absolute quantification of Bifidobacterium. qPCR analysis of a the genus Bifidobacterium and b the species Bifidobacterium longum ssp. longum in Rett syndrome (RTT) subjects versus healthy controls (HC); **p < 0.01, *p < 0.05, Wilcoxon rank-sum test
Fig. 5
Fig. 5
SCFAs faecal content. Bar-plot representation of the median values of faecal SCFAs in Rett syndrome (RTT) subjects and healthy controls (HC); *p < 0.05, **p < 0.005, ***p < 0.0005, Wilcoxon rank-sum test
Fig. 6
Fig. 6
Measures of fungal beta-diversity. PCoA plots of fungal beta-diversity based on a the Weighted UniFrac distance and b the Bray-Curtis dissimilarity analysed according to individuals’ health status. Constipated Rett syndrome subjects (RTT-C), non-constipated Rett syndrome subjects (RTT-NC) and healthy controls (HC) are coloured in red, orange or green, respectively

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