title: Diversity of bacteria at healthy human conjunctiva.
abstract: OBJECTIVE
  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.
authors.affiliation: Department of Biological Sciences, University of North Texas, Denton, Texas, USA.
authors.forename: Qunfeng
authors.initials: Q
authors.lastname: Dong
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Brulc
authors.forename: Alfonso
authors.initials: A
authors.lastname: Iovieno
authors.forename: Brandon
authors.initials: B
authors.lastname: Bates
authors.forename: Aaron
authors.initials: A
authors.lastname: Garoutte
authors.forename: Darlene
authors.initials: D
authors.lastname: Miller
authors.forename: Kashi V
authors.initials: KV
authors.lastname: Revanna
authors.forename: Xiang
authors.initials: X
authors.lastname: Gao
authors.forename: Dionysios A
authors.initials: DA
authors.lastname: Antonopoulos
authors.forename: Vladlen Z
authors.initials: VZ
authors.lastname: Slepak
authors.forename: Valery I
authors.initials: VI
authors.lastname: Shestopalov
mesh_terms: D000328:Adult; D001419:Bacteria / Q000235:genetics*; D003228:Conjunctiva / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D015723:Gene Library; D020459:Genes, rRNA / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D054892:Metagenome / Q000502:physiology*; D008875:Middle Aged; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S