Veterinary ocular microbiome: Lessons learned beyond the culture

Vet Ophthalmol. 2019 Sep;22(5):716-725. doi: 10.1111/vop.12676. Epub 2019 May 9.


Ocular pathogens cause many painful and vision-threatening diseases such as infectious keratitis, uveitis, and endophthalmitis. While virulent pathogens and pathobionts play important roles in disease pathogenesis, the scientific community has long assumed disruption of the ocular surface occurs prior to microbial colonization and subsequent infection. While nonpathogenic bacteria are often detected in corneal and conjunctival cultures from healthy eyes, cultures also frequently fail to yield growth of common ocular pathogens or nonpathogenic bacteria. This prompts the following question: Is the ocular surface populated by a stable microbial population that cannot be detected using standard culture techniques? The study of the microbiome has recently become a widespread focus in physician and veterinary medicine. Research suggests a pivotal symbiotic relationship with these microbes to maintain healthy host tissues, and when altered is associated with various disease states ("dysbiosis"). The microbiota that lives within and on mammalian bodies have long been known to influence health and susceptibility to infection. However, limitations of traditional culture methods have resulted in an incomplete understanding of what many now call the "forgotten organ," that is, the microbiome. With the introduction of high-throughput sequencing, physician ophthalmology has recognized an ocular surface with much more diverse microbial communities than suspected based on traditional culture. This article reviews the salient features of the ocular surface microbiome and highlights important future applications following the advent of molecular techniques for microbial identification, including characterizing ocular surface microbiomes in our veterinary species and their potential role in management of infectious and inflammatory ocular diseases.

Keywords: 16S rRNA sequencing; culture-independent methods; high-throughput sequencing; microbiome; ocular pathogens.

Publication types

  • Review

MeSH terms

  • Animals
  • Bacteria / classification
  • Bacteria / isolation & purification
  • Eye / microbiology*
  • Humans
  • Microbiota*
  • Molecular Typing