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The eye has a normal community of microbes or eye microbiome, just like other body sites (i.e., the gut, the sinuses, the mouth). This community of bacteria is thought to offer resistance from invaders (such as pathogenic bacteria).

The researchers of a recent study found differences in the eye microbiome of contact lens wearers as compared to non-lens wearers. The results indicate that wearing contact lenses "alters the microbial structure of the ocular conjunctiva, making it more similar to that of the skin microbiota" (the community of microbes living on the skin).

Further research is needed to determine whether these differences in the eye microbiome in contact lens wearers is the reason why contact lens wearers develop more eye conditions and infections (such as giant papillary conjunctivitis and keratitis). Over 30 million Americans wear contact lenses so these are important issues.

From Science Daily: Contact lenses alter eye bacteria, making it more skin-like

Contact lenses may alter the natural microbial community of the eyes, according to a study published this week in mBio®, an online open-access journal of the American Society for Microbiology. In a study of 58 adults seeking outpatient eye care, researchers at New York University School of Medicine found that contact lenses make the eye microbiome more skin-like, with higher proportions of the skin bacteria Pseudomonas, Acinetobacter, Methylobacterium, and Lactobacillus and lower proportions of Haemophilus, Streptococcus, Staphylococcus, and Corynebacterium.

It's unclear how these changes occur, said senior study author Maria Dominguez-Bello, PhD, an associate professor of medicine at the university, "if these bacteria are transferred from the fingers to the lens and to the eye surface, or if the lenses exert selective pressures on the eye bacterial community in favor of skin bacteria." Wearing contact lenses has been identified as a risk factor for the development of eye infections such as giant papillary conjunctivitis and keratitis, "so these questions are important," she said.

Researchers used a laboratory technique called 16s rRNA sequencing to compare the bacterial communities of the conjunctiva (the eye surface) and the skin under the eye from 58 adults. They also analyzed samples from 20 of the study participants (9 lens wearers and 11 non-lens wearers) at three time points over the course of six weeks....researchers found a higher diversity of bacteria on the ocular surface than on the skin under the eye or on the contact lenses, which was a surprising result, Dominguez-Bello said.

The ocular surface microbiota of those who wore contact lenses was more skin-like compared to those who did not wear lenses. It was enriched in the bacteria Pseudomonas, Acinetobacter, Methylobacterium, and Lactobacillus. In non-lens wearers, these bacteria were detected at a higher relative abundance in skin samples compared to the eye (except for Lactobacillus), suggesting that these bacteria could be classified as skin bacteria. The bacteria Haemophilus, Streptococcus, Staphylococcus, and Corynebacterium were depleted in the ocular microbiota of lens wearers compared to non-lens wearers.

New research shows that wearing contact lenses could significantly change the bacteria of the eye’s surface, making it more susceptible to infection. NYU Langone Medical Center researchers analyzed swabs from both contact-wearers and non-wearers to determine the number and type of bacterial species that lived on the surface of their eyes—the eye’s microbiome as well as the skin below the eye.

They found that the eye microbiome of contact lens wearers is more similar in composition to the microbiome of their skin than the eye microbiome of non-lens wearers.

Note that infections often come when people don’t take proper care of their lenses—sleeping in them overnight, or not cleaning them well or often enough so most eye doctors have shifted to recommending daily lenses. 

From Medical News Today: Alterations to the eye microbiome of contact lens wearers may increase infections

Contact lens wearers - ever wondered why you are more likely to experience eye infections than your contacts-less friends? Researchers from NYU Langone Medical Center in New York City think they may have found the answer, in a study that used high-precision genetic tests to map the human microbiome....the NYU Langone researchers report that micro-organisms residing in the eyes of people who wear contact lenses daily more closely resemble micro-organisms residing in eyelid skin than the bacteria usually found in the eyes of people who do not wear contacts.

The researchers took hundreds of swabs of different parts of the eye, including the skin directly beneath the eye. Genetic analysis of swabs and used contact lenses allowed the team to identify which bacteria were present. Comparing nine contact lens wearers with 11 non-contacts users, the team found three times the usual proportion of the bacteria Methylobacterium, Lactobacillus, Acinetobacter and Pseudomonas on the eye surfaces (conjunctiva) of contact lens wearers than on the eye surfaces of the control group.

Examining the bacterial diversity using a plotted graph, the team observed that the eye microbiome of contact lens wearers is more similar in composition to the microbiome of their skin than the eye microbiome of non-lens wearers

Interestingly, the researchers say, Staphylococcus bacteria was found in greater amounts in the eyes of non-lens wearers. Staphylococcus is linked with eye infections, but is usually more prominent on the skin. However, the researchers are unable to explain why non-lens wearers have greater amounts of this bacteria, despite this group traditionally having fewer eye infections than people who wear contacts.

Study author Dr. Jack Dodick, professor and chair of ophthalmology at NYU Langone, says:"There has been an increase in the prevalence of corneal ulcers following the introduction of soft contact lenses in the 1970s. A common pathogen implicated has been Pseudomonas. This study suggests that because the offending organisms seem to emanate from the skin, greater attention should be directed to eyelid and hand hygiene to decrease the incidence of this serious occurrence."