Defining the normal core microbiome of conjunctival microbial communities

Abstract

Bacterial ocular infections are common. Traditional culture and molecular biological methods have obvious limitations to identify the conjunctival microbiota, while metagenomic studies can avoid the defects of these methods. We used the Illumina high-throughput sequencing technology (MiSeq Illumina Sequencing Platform) to sequence the 16S rDNA V3-V4 hypervariable region of all bacteria in conjunctival swab samples. The operational taxonomic units were obtained from the sequences. The bioinformatic analyses of taxonomy, abundance and alpha diversity were performed. A total of 840 373 high-quality sequencing reads were generated from 31 conjunctival samples. The number of the species operational taxonomic units ranged from 159 to 2042, indicating high microbial diversity. The combined bacterial community was classified into 25 phyla and 526 distinct genera. At the genus level, Corynebacterium (28.22%), Pseudomonas (26.75%), Staphylococcus (5.28%), Acinetobacter (4.74%), Streptococcus (2.85%), Millisia (2.16%), Anaerococcus (1.86%), Finegoldia (1.68%), Simonsiella (1.48%) and Veillonella (1.00%) accounted for over 76% of the microbial community, possibly representing the core genera in normal conjunctival microbiota. The composition and diversity of microbiota in the normal adult human conjunctiva were characterized using high-throughput sequencing. A framework for investigating potential roles played by the diverse microbiota in disease related with the ocular surface was provided.

The Pathophysiology of Dry Eye Disease

“…17, 167 This is in sharp contrast to cultures of the lid margin and periocular skin which often grow bacteria. 168, 169 Studies using 16S genomic sequencing have demonstrated an ocular surface microbiome that may have the lowest biomass of any tissue in the body 16, 170, 171 No difference in the quantity and diversity of the ocular microbiome was noted between SS and control subjects; 16 however, significant alterations of the intestinal microbiome were noted in the same cohort with a significant decrease in commensal genera and an increase in pathogenic genera, such as Escherichia/Shigella and Proteobacteria. Mice that had an antibiotic-induced depletion of the microbiome with a cocktail of five oral antibiotics prior to experimental desiccating stress developed significantly worse dry eye than control mice that did not receive antibiotics, suggesting that the intestinal microbiome can modulate ocular surface inflammation and severity of dry eye disease.…”

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice

“…The PCR amplification was performed as previously described (Hu, Yang, Long, Liu, & Rengel, 2016). The PCR products were confirmed, purified, and quantified as previously described (Huang, Yang, & Li, 2016). The quality and quantity of the amplicon library were assessed on a Bioanalyzer (Agilent, Santa Clara, CA, U.S.A.) and with the Library Quantification Kit for Illumina (Kapa Biosciences, Wilmington, MA, U.S.A.), respectively.…”

Active trachoma cases in the Solomon Islands have varied polymicrobial community structures but do not associate with individual non-chlamydial pathogens of the eye

“…It is unclear whether a ‘core’ microbiota persists at the conjunctiva, but profiles closely related to that of the skin have been reported (18). Corynebacterium , Propionibacterium , Staphylococcus and Streptococcus have been consistently dominant, whereas other genera such as Acinetobacter , Brevundimonas , Pseudomonas , Bradyrhizobium , Sphingomonas , Bacillus , Simonsiella and Elizabethkingia have been identified more sporadically (19–21). Conjunctival polymicrobial community composition is known to vary with age and season (22) and appears to be responsive to external stimuli such as regular contact lens wear (23).…”