Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye

Jayasudha, Rajagopalaboopathi; Chakravarthy, Sama Kalyana; Prashanthi, Gumpili Sai; Sharma, Savitri; Garg, Prashant; Murthy, Somasheila I; Shivaji, Sisinthy

doi:10.1007/s12038-018-9798-6

Cited by 53 publications

(58 citation statements)

References 93 publications

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“…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.…”

Section: Resultsmentioning

confidence: 99%

“…Recently we showed association of gut fungal microbiome with bacterial keratitis. 19 Hence, it is worthwhile to investigate fungal microbiome in UVT patients. The present study aims to characterize the gut fungal microbiomes of healthy controls (HC) and UVT patients from a south Indian cohort to identify whether gut fungal populations are altered in UVT patients and whether dysbiosis in gut fungal communities is associated with UVT that may help to develop new treatment regimen for treating UVT.…”

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confidence: 99%

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

Jayasudha

Chakravarthy

Prashanthi

et al. 2019

Invest. Ophthalmol. Vis. Sci.

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In this study, the gut fungal microbiome of uveitis (UVT) patients was generated and compared with healthy controls (HC) to identify dysbiosis in UVT patients and ascertain the role of gut fungal microbiome in disease pathology. METHODS. In the present study, gut fungal microbiomes were analyzed in the fecal samples of HC (n ¼ 24) and UVT patients (n ¼ 14) using high-throughput Illumina sequencing of ITS2 region of the fungal ribosomal RNA. QIIME and R software were used for data analysis. RESULTS. The gut fungal richness and diversity were significantly decreased in UVT patients compared to HC. Our analyses showed enrichment of several pathogenic fungi including Malassezia restricta, Candida albicans, Candida glabrata, and Aspergillus gracilis in UVT patients. Heatmap and discriminatory OTUs further confirmed the disparities between UVT and HC microbiomes. CONCLUSIONS. This is the first study demonstrating dysbiosis in the gut fungal communities of UVT patients indicating the importance of fungal microbiome in the disease pathology. These initial findings might warrant further investigation into the fungal microbiome, especially interactions between fungal and bacterial that then might give further insight into how probiotics or fecal transplants might benefit.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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

Jayasudha

Chakravarthy

Prashanthi

et al. 2019

Invest. Ophthalmol. Vis. Sci.

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“…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.…”

Section: Taxonomic Classification Of Sequenced Readsmentioning

confidence: 99%

The Human Ocular Surface Fungal Microbiome

Shivaji

Jayasudha

Prashanthi

et al. 2019

Invest. Ophthalmol. Vis. Sci.

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PURPOSE. To enumerate the ocular surface fungal microbiome of healthy human eyes by using next-generation sequencing (NGS). METHODS.Tarsal and fornix conjunctiva from the lower and upper lids of both eyes of healthy individuals were swabbed in duplicate separately. A total of 34 samples were collected from both the eyes of 17 individuals, which were used for the generation of ocular surface fungal microbiomes by NGS. Twenty-four swabs were used for the detection of culturable fungi by the conventional cultivable method. Microbiome generation involved DNA extraction, internal transcribed spacer 2 (ITS2) amplification, library preparation, amplicon sequencing, taxonomic assignment of sequences, diversity analyses, and identification of genera. RESULTS.The cultivable method detected fungi in 3 out of 24 (12.5 %) ocular surface swabs, whereas NGS identified fungi in 25 of the 34 (73.5 %) swabs. In the cultivable method Aspergillus was the only genus detected, whereas NGS detected 65 distinct genera with 12 to 24 genera per microbiome. Genera Aspergillus, Setosphaeria, Malassezia, and Haematonectria were present in the 25 eyes in which fungi were detected. Alpha diversity in the two eyes was similar and sex had no effect, but Chao1 and Simpson indices were altered by age.CONCLUSIONS. This study explored the ocular surface fungal microbiome of healthy individuals using NGS and identified a greater degree of diversity of fungi than with the conventional cultivable method. It was observed that several fungal genera were associated with the healthy conjunctiva.

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“…P. americana exhibited more prevalent species than either P. japonica or P. fuliginosa . Dysgonomonas species present in P. americana , can cause gastroenteritis in immunocompromised individuals (12). S. marcescens has been found to be associated with hospital-acquired infections (HAI), and is an opportunistic pathogen that is often involved in urinary tract and wound infections (13).…”

Section: Discussionmentioning

confidence: 99%

Comparative microbiomes of three species of laboratory-rearedPeriplanetacockroaches

Lee

Kim

et al. 2019

Preprint

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Cockroaches are the most primitive insects, and are often used as the basic insect model in many studies. Three species of Periplaneta cockroaches were raised in the laboratory for many generations under the same conditions. We conducted 16S rRNA-targeted high-throughput sequencing to evaluate the overall bacterial composition in the microbiomes of three species of cockroaches. The number of operational taxonomic units (OTUs) was not significantly different between the three cockroach species. With respect to the Shannon and Pielou indexes, the microbiome of Periplaneta americana presented higher values than that of either P. japonica or P. fulginosa. In terms of species composition, endosymbionts accounted for over half of all the bacterial species in P. japonica and P. fulginosa. The beta diversity analysis showed that P. japonica and P. fulginosa exhibit a similar microbiome composition, which is different from that of P. americana. However, we also identified that P. japonica and P. fulginosa are hosts to distinct bacterial species. Thus, although the composition of the microbiome may vary based on multiple conditions, it is possible to identify distinct compositions of the microbiome among the different Periplaneta cockroach species even when individuals are reared under the same conditions.ImportanceCockroaches inhabit various habitats—which are known to be related to their microbiome—and exhibit different features depending on the species. It is expected that their microbiomes would vary according to species depending on these features. Cockroach microbiomes are known to vary based on the diet or environmental shifts. In this study, we compare the diversity of bacteria in the three cockroach species under conditions of reduced diet and environment shifts. This study can establish the basic microbiomes of three Periplaneta species and can be the basic data for cockroach research.

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Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye

Cited by 53 publications

References 93 publications

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

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

The Human Ocular Surface Fungal Microbiome

Comparative microbiomes of three species of laboratory-rearedPeriplanetacockroaches

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