Dysbiosis in the Gut Bacterial Microbiome of Patients with Uveitis, an Inflammatory Disease of the Eye

Abstract

Uveitis (UVT), an inflammatory disease of the eye significantly contributes to vision impairment and blindness. Uveitis is associated with systemic infectious and autoimmune diseases, but in most cases, the aetiology remains unidentified. Dysbiosis in the gut microbiome has been implicated in autoimmune diseases, inflammatory diseases, cancers and mental disorders. In a mice model of autoimmune UVT, it was observed that manipulating the gut microbiome reduces the inflammation and disease severity. Further, alterations in the bacterial gut microbiome and their metabolites were reported in UVT patients from a Chinese cohort. Hence, it is worth comparing the bacterial gut microbiome of UVT patients with that of healthy controls (HC) to ascertain whether dysbiosis of the gut microbiome has implications in UVT. Our analyses showed reduced diversity of several anti-inflammatory organisms including Faecalibacterium, Bacteroides, Lachnospira, Ruminococcus and members of Lachnospiraceae and Ruminococcaceae families, and enrichment of Prevotella (proinflammatory) and Streptococcus (pathogenic) OTUs in UVT microbiomes compared to HC. In addition, decrease in probiotic and antibacterial organisms was observed in UVT compared to HC microbiomes. Heatmap and PCoA plots also indicated significant variations in the microbiomes of UVT versus HC. This is the first study demonstrating dysbiosis in the gut bacterial communities of UVT patients in an Indian cohort and suggests a role of the gut microbiome in the pathophysiology of UVT.

Keywords: Dysbiosis; Gut microbiome; Illumina Miseq; Uveitis; V3–V4 region of 16S rRNA gene.

Conflict of interest statement

The authors declare that they have no conflict of interest.Informed consent was taken from all the study subjects prior to sample collection. The study protocols were approved by the Institutional Review Board of L. V. Prasad Eye Institute, Hyderabad (Ethics Ref. No. LEC 06-14-060) and all methods were performed in accordance with relevant guidelines and regulations.

Figures

Fig. 1

a Rarefaction curves of the 26 gut bacterial microbiomes from healthy controls (HC) and Uveitis (UVT) patients. b Box-plots illustrating alpha diversity indices (Shannon diversity, Simpson index, Observed number of OTUs and Chao1) in gut microbiomes of healthy controls (HC) and Uveitis (UVT) patients. Median values (horizontal line) and interquartile ranges have been indicated in the plots. c Abundance of different bacterial phyla in the gut microbiomes of healthy controls (HC) and Uveitis (UVT) patients. “Other phyla” includes phyla with < 1% mean abundance. “Other” includes singletons, unassigned reads and sparse OTUs (< 0.001% of total abundance). d Abundance of different bacterial families in gut microbiomes of healthy controls (HC) and Uveitis (UVT) patients. “Other families” includes families with < 1% mean abundance. “Other” includes singletons, unassigned reads and sparse OTUs (< 0.001% of total abundance)

Fig. 2

a Bacterial OTUs exhibiting significant (BH corrected P < 0.05) differential abundance in the gut microbiomes of Uveitis patients (UVT) compared to healthy controls (HC). OTUs having a median abundance of > 0.01% in at least one group of samples (HC or UVT) have been depicted. Out of 204 OTUs, 180 were enriched in HC and 24 were enriched in UVT patients. Data is represented as log2 fold change. Each circle denotes an OTU; OTUs to the right of zero line and shown in pink are enriched in UVT compared to HC and OTUs to the left of zero line and shown in blue are depleted in UVT compared to HC. OTUs are organized according to the lowest taxonomic classification along the y-axis. b Bacterial OTUs exhibiting significant (BH corrected P < 0.05) differential abundance in the gut microbiomes of healthy controls (HC, green) and Uveitis patients (UVT, red). Only the top 5 abundant OTUs enriched in HC or UVT samples have been depicted. The median abundances and the interquartile ranges have been indicated in the plots. c Principal Coordinate Analysis (PCoA) based on JSD (Jensen–Shannon divergence) distances between bacterial OTU abundance in the microbiomes of healthy controls (HC, blue) and Uveitis patients (UVT, red). Samples plotted along first two principal coordinates PC1 and PC2 showed distinct clustering of healthy controls (HC) and Uveitis (UVT) microbiomes

Fig. 3

a Bacterial genera exhibiting significant (BH corrected P < 0.05) differential abundance in gut microbiomes of healthy controls (HC) compared to Uveitis (UVT) patients. Genera having a median abundance of > 0.1% in at least one group of samples (HC or UVT) have been depicted. Median abundances (horizontal line) and interquartile ranges have been indicated in the plots. b Two dimensional heatmap depicting rank normalized abundances (scaled between 0 and 1) of the 17 bacterial genera (median abundance > 0.1% in at least one group [HC or UVT] which were differentially abundant in the gut microbiomes of healthy controls (HC) compared to the Uveitis (UVT) patients. The discriminating genera as well as the samples (HC and UVT) were arranged along the two dimensions (axes) based on hierarchical clustering. c Principal Coordinate Analysis (PCoA) based on OTU abundances in the bacterial microbiomes of healthy controls (HC, blue), idiopathic Uveitis patients (UVT_ID, black) and autoimmune Uveitis patients (UVT_AD, red). JSD was used as a distance metric. Except 2 samples, all healthy controls (HC) samples clustered together, and all Uveitis patients (UVT_ID and UVT_AD) irrespective of their aetiology clustered together when plotted along the first two principal coordinates PC1 and PC2

Fig. 4

a Bacterial interaction network in the gut microbiome of healthy controls (HC) showing significant co-occurrence and co-exclusion relationships at genus level. Each node represents a genus and the node sizes in the network correspond to their degree of interaction. The positive and negative correlations/associations have been indicated with green and red edges respectively. b Bacterial interaction network in the gut microbiome of Uveitis (UVT) patients showing significant co-occurrence and co-exclusion relationships at genus level. Each node represents a genus and the node sizes in the network correspond to their degree of interaction. The positive and negative correlations/associations have been indicated with green and red edges respectively

Fig. 4

a Bacterial interaction network in the gut microbiome of healthy controls (HC) showing significant co-occurrence and co-exclusion relationships at genus level. Each node represents a genus and the node sizes in the network correspond to their degree of interaction. The positive and negative correlations/associations have been indicated with green and red edges respectively. b Bacterial interaction network in the gut microbiome of Uveitis (UVT) patients showing significant co-occurrence and co-exclusion relationships at genus level. Each node represents a genus and the node sizes in the network correspond to their degree of interaction. The positive and negative correlations/associations have been indicated with green and red edges respectively