Alterations in the gut bacterial microbiome in fungal Keratitis patients

Abstract

Dysbiosis in the gut microbiome has been implicated in several diseases including auto-immune diseases, inflammatory diseases, cancers and mental disorders. Keratitis is an inflammatory disease of the eye significantly contributing to corneal blindness in the developing world. It would be worthwhile to investigate the possibility of dysbiosis in the gut microbiome being associated with Keratitis. Here, we have analyzed fungal and bacterial populations in stool samples through high-throughput sequencing of the ITS2 region for fungi and V3-V4 region of 16S rRNA gene for bacteria in healthy controls (HC, n = 31) and patients with fungal keratitis (FK, n = 32). Candida albicans (2 OTUs), Aspergillus (1 OTU) and 3 other denovo-OTUs were enriched in FK samples and an unclassified denovo-OTU was enriched in HC samples. However, the overall abundances of these ‘discriminatory’ OTUs were very low (< 0.001%) and not indicative of significant dysbiosis in the fungal community inhabiting the gut of FK patients. In contrast, the gut bacterial richness and diversity in FK patients was significantly decreased when compared to HC. 52 OTUs were significantly enriched in HC samples whereas only 5 OTUs in FK. The OTUs prominently enriched in HC were identified as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Lachnospira, Mitsuokella multacida, Bacteroides plebeius, Megasphaera and Lachnospiraceae. In FK samples, 5 OTUs affiliated to Bacteroides fragilis, Dorea, Treponema, Fusobacteriaceae, and Acidimicrobiales were significantly higher in abundance. The functional implications are that Faecalibacterium prausnitzii, an anti-inflammatory bacterium and Megasphaera, Mitsuokella multacida and Lachnospira are butyrate producers, which were enriched in HC patients, whereas Treponema and Bacteroides fragilis, which are pathogenic were abundant in FK patients, playing a potential pro-inflammatory role. Heatmap, PCoA plots and functional profiles further confirm the distinct patterns of gut bacterial composition in FK and HC samples. Our study demonstrates dysbiosis in the gut bacterial microbiomes of FK patients compared to HC. Further, based on inferred functions, it appears that dysbiosis in the gut of FK subjects is strongly associated with the disease phenotype with decrease in abundance of beneficial bacteria and increase in abundance of pro-inflammatory and pathogenic bacteria.

Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye

“…Similar decrease in diversity and abundance was observed in patients with other diseases such as in obese individuals and in patients with asthma, cirrhosis, and autism. 43 At the phylum level, Ascomycota and Basidiomycota were the most dominant in the gut microbiomes of HC and UVT patients, and this observation is in congruence with Bhute et al 15 and our own studies 19,30 on the gut fungal communities from an Indian population. Ascomycota and Basidiomycota were also dominant in healthy subjects and IBD patients.…”

“…For instance, using the same set of HC, we compared the bacterial and fungal microbiomes of individuals with bacterial and/or fungal keratitis or UVT with the microbiomes of HC matched for age, gender, ethnicity, and region of origin. 4,19,30 Such an approach is advantageous since by carefully designing the experiments the same set of control individuals could be recruited for the three different ocular diseases. In this paper, the demographic and the fungal microbiome data of 24 HC was derived from the 31 individuals analyzed by us earlier 30 and was also common to 21 HC, 19 which were published earlier.…”

“…4,19,30 Such an approach is advantageous since by carefully designing the experiments the same set of control individuals could be recruited for the three different ocular diseases. In this paper, the demographic and the fungal microbiome data of 24 HC was derived from the 31 individuals analyzed by us earlier 30 and was also common to 21 HC, 19 which were published earlier. The demographic data of 13 of the 14 UVT patients is also common to the UVT patients in Kalyana Chakravarthy et al 4…”

“…34 We also could not identify a core fungal microbiome in the HC individuals. 19,30 The reasons for the lack of a core gut fungal microbiome could be attributed to the observation that Ascomycota and Basidiomycota, which are the dominant phyla, were mostly inversely correlated, thus creating two groups of HC in which presence of either Ascomycota or Basidiomycota were mutually exclusive. 35 In confirmation, we observed that the 24 HC gut fungal microbiomes formed two clusters (15 and 9 microbiomes) due to the fact that one cluster was dominated by Basidiomycota and the other by Ascomycota (Fig.…”

The Human Ocular Surface Fungal Microbiome

“…30 The removal of low-quality reads (mean Phred score, <25) and chimeric sequences, OTU picking using Quantitative Insights into Microbial Ecology (QIIME) software, and assignment of taxonomic lineages were performed as described previously. 31,32 Sparse OTUs containing <0.001% of the total number of high-quality reads sequenced were removed.…”