Diversity of bacteria at healthy human conjunctiva

Qunfeng Dong, Jennifer M. Brulc, Alfonso Iovieno, Brandon Bates, Aaron Garoutte, Darlene Miller, Kashi V. Revanna, Xiang Gao, Dionysios A. Antonopoulos, Vladlen Z Slepak, Valery I Shestopalov

Research output: Contribution to journalArticle

113 Citations (Scopus)

Abstract

PURPOSE. Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis of microbial diversity at the OS has been impossible because of the limitations of conventional cultivation techniques. This pilot study aimed to explore true diversity of human OS microbiota using DNA sequencing-based detection and identification of bacteria. METHODS. Composition of the bacterial community was characterized using deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The DNA sequences were classified and the diversity parameters measured using bioinformatics software ESPRIT and MOTHUR and tools available through the Ribosomal Database Project-II (RDP-II). RESULTS. Deep sequencing of conjunctival rDNA from four subjects yielded a total of 115,003 quality DNA reads, corresponding to 221 species-level phylotypes per subject. The combined bacterial community classified into 5 phyla and 59 distinct genera. However, 31% of all DNA reads belonged to unclassified or novel bacteria. The intersubject variability of individual OS microbiomes was very significant. Regardless, 12 genera-Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium-were ubiquitous among the analyzed cohort and represented the putative "core" of conjunctival microbiota. The other 47 genera accounted for <4% of the classified portion of this microbiome. Unexpectedly, healthy conjunctiva contained many genera that are commonly identified as ocular surface pathogens. CONCLUSIONS. The first DNA sequencing-based survey of bacterial population at the conjunctiva have revealed an unexpectedly diverse microbial community. All analyzed samples contained ubiquitous (core) genera that included commensal, environmental, and opportunistic pathogenic bacteria.

Original languageEnglish
Pages (from-to)5408-5413
Number of pages6
JournalInvestigative Ophthalmology and Visual Science
Volume52
Issue number8
DOIs
StatePublished - Jul 1 2011

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Conjunctiva
Microbiota
Bacteria
High-Throughput Nucleotide Sequencing
DNA Sequence Analysis
Streptophyta
DNA
Methylobacterium
Sphingomonas
Propionibacterium
Bradyrhizobium
Corynebacterium
Acinetobacter
Ribosomal DNA
Pseudomonas
Streptococcus
Computational Biology
Staphylococcus
Gene Library
rRNA Genes

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience
  • Medicine(all)

Cite this

Diversity of bacteria at healthy human conjunctiva. / Dong, Qunfeng; Brulc, Jennifer M.; Iovieno, Alfonso; Bates, Brandon; Garoutte, Aaron; Miller, Darlene; Revanna, Kashi V.; Gao, Xiang; Antonopoulos, Dionysios A.; Slepak, Vladlen Z; Shestopalov, Valery I.

In: Investigative Ophthalmology and Visual Science, Vol. 52, No. 8, 01.07.2011, p. 5408-5413.

Research output: Contribution to journalArticle

Dong, Q, Brulc, JM, Iovieno, A, Bates, B, Garoutte, A, Miller, D, Revanna, KV, Gao, X, Antonopoulos, DA, Slepak, VZ & Shestopalov, VI 2011, 'Diversity of bacteria at healthy human conjunctiva', Investigative Ophthalmology and Visual Science, vol. 52, no. 8, pp. 5408-5413. https://doi.org/10.1167/iovs.10-6939
Dong, Qunfeng ; Brulc, Jennifer M. ; Iovieno, Alfonso ; Bates, Brandon ; Garoutte, Aaron ; Miller, Darlene ; Revanna, Kashi V. ; Gao, Xiang ; Antonopoulos, Dionysios A. ; Slepak, Vladlen Z ; Shestopalov, Valery I. / Diversity of bacteria at healthy human conjunctiva. In: Investigative Ophthalmology and Visual Science. 2011 ; Vol. 52, No. 8. pp. 5408-5413.
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T1 - Diversity of bacteria at healthy human conjunctiva

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AU - Brulc, Jennifer M.

AU - Iovieno, Alfonso

AU - Bates, Brandon

AU - Garoutte, Aaron

AU - Miller, Darlene

AU - Revanna, Kashi V.

AU - Gao, Xiang

AU - Antonopoulos, Dionysios A.

AU - Slepak, Vladlen Z

AU - Shestopalov, Valery I

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N2 - PURPOSE. Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis of microbial diversity at the OS has been impossible because of the limitations of conventional cultivation techniques. This pilot study aimed to explore true diversity of human OS microbiota using DNA sequencing-based detection and identification of bacteria. METHODS. Composition of the bacterial community was characterized using deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The DNA sequences were classified and the diversity parameters measured using bioinformatics software ESPRIT and MOTHUR and tools available through the Ribosomal Database Project-II (RDP-II). RESULTS. Deep sequencing of conjunctival rDNA from four subjects yielded a total of 115,003 quality DNA reads, corresponding to 221 species-level phylotypes per subject. The combined bacterial community classified into 5 phyla and 59 distinct genera. However, 31% of all DNA reads belonged to unclassified or novel bacteria. The intersubject variability of individual OS microbiomes was very significant. Regardless, 12 genera-Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium-were ubiquitous among the analyzed cohort and represented the putative "core" of conjunctival microbiota. The other 47 genera accounted for <4% of the classified portion of this microbiome. Unexpectedly, healthy conjunctiva contained many genera that are commonly identified as ocular surface pathogens. CONCLUSIONS. The first DNA sequencing-based survey of bacterial population at the conjunctiva have revealed an unexpectedly diverse microbial community. All analyzed samples contained ubiquitous (core) genera that included commensal, environmental, and opportunistic pathogenic bacteria.

AB - PURPOSE. Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis of microbial diversity at the OS has been impossible because of the limitations of conventional cultivation techniques. This pilot study aimed to explore true diversity of human OS microbiota using DNA sequencing-based detection and identification of bacteria. METHODS. Composition of the bacterial community was characterized using deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The DNA sequences were classified and the diversity parameters measured using bioinformatics software ESPRIT and MOTHUR and tools available through the Ribosomal Database Project-II (RDP-II). RESULTS. Deep sequencing of conjunctival rDNA from four subjects yielded a total of 115,003 quality DNA reads, corresponding to 221 species-level phylotypes per subject. The combined bacterial community classified into 5 phyla and 59 distinct genera. However, 31% of all DNA reads belonged to unclassified or novel bacteria. The intersubject variability of individual OS microbiomes was very significant. Regardless, 12 genera-Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium-were ubiquitous among the analyzed cohort and represented the putative "core" of conjunctival microbiota. The other 47 genera accounted for <4% of the classified portion of this microbiome. Unexpectedly, healthy conjunctiva contained many genera that are commonly identified as ocular surface pathogens. CONCLUSIONS. The first DNA sequencing-based survey of bacterial population at the conjunctiva have revealed an unexpectedly diverse microbial community. All analyzed samples contained ubiquitous (core) genera that included commensal, environmental, and opportunistic pathogenic bacteria.

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