The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface

Abstract

Purpose The ocular surface microbiome has been described as paucibacterial. Until now, studies investigating the bacterial community associated with the ocular surface through high-throughput sequencing have focused on the conjunctiva. Conjunctival samples are thought to reflect and be representative of the microbiome residing on the ocular surface, including the cornea. Here, we hypothesized that the bacterial community associated with the corneal surface was different from those of the inferonasal and superotemporal conjunctival fornices, and from the tear film. Methods Both eyes from 15 healthy piglets were sampled using swabs (inferonasal fornix, superotemporal fornix, and corneal surface, n = 30 each) and Schirmer tear test strips (STT, n = 30). Negative sampling controls (swabs and STT, n = 2 each) and extraction controls (n = 4) were included. Total DNA was extracted and high-throughput sequencing targeting the 16S rRNA gene was performed. Bioinformatic analyses included multiple contamination-controlling steps. Results Corneal surface samples had a significantly lower number of taxa detected (P<0.01) and were compositionally different from all other sample types (Bray-Curtis dissimilarity, P<0.04). It also harbored higher levels of Proteobacteria (P<0.05), specifically Brevundimonas spp. (4.1-fold) and Paracoccus spp. (3.4-fold) than other sample types. Negative control STT strip samples yielded the highest amount of 16S rRNA gene copies across all sample types (P<0.05). Conclusions Our data suggests that the corneal surface provides a distinct environmental niche within the ocular surface, leading to a bacterial community compositionally different from all other sample types.

Porcine Cornea Storage Ex Vivo Model as an Alternative to Human Donor Tissues for Investigations of Endothelial Layer Preservation

“…While human donor corneas are procured in environments controlled for microbial contamination, porcine corneas used in the present study were recovered in slaughterhouse without environmental controls. Moreover, the porcine colonizing microorganisms may differ from human pathogens, 12 , 30 , 31 and these factors strongly impact the initial tissue bioburden. The adopted orbital shaking as well as the time of contact (10 minutes) between PVP-I and the porcine eye bulb, which is longer than what is usually performed in human eye bulbs, 32 aimed at maximizing the exposure of microbial agents to the decontaminating effect of PVP-I without impacting the tissue quality.…”

Evaluation of a commercial NGS service for detection of bacterial and fungal pathogens in infectious ulcerative keratitis

“…In veterinary ophthalmology, NGS has been increasingly used to elucidate the ocular surface genome in various species 33–44 . In a 2020 study, NGS was used to compare conjunctival culture with normal conjunctiva, periocular haired skin, and nasal microbiota in clinically healthy dogs 45 .…”

“…10 In veterinary ophthalmology, NGS has been increasingly used to elucidate the ocular surface genome in various species. [33][34][35][36][37][38][39][40][41][42][43][44] In a 2020 study, NGS was used to compare conjunctival culture with normal conjunctiva, periocular haired skin, and nasal microbiota in clinically healthy dogs. 45 Results of this work may allow ophthalmologists to diagnose causative organisms more rapidly in IUK cases and implement nonempiric treatment plans sooner.…”