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The eye has a normal community of bacteria, or 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 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."

Finally, a discussion of the eye's microbiota (microbial community). From The Scientist:

Visualizing the Ocular Microbiome

Ophthalmologists have treated pathogenic eye infections for many decades, and the advent of contact lenses has made such infections more common. But little is known about the bacteria that live on the surface of a healthy human eye, and how this microbial make-up differs when a pathogenic strain takes over. Many bacteria known to live on the eye are difficult to culture, making them virtually invisible to researchers. Adapting sequencing technologies to study the ocular microbiome has opened up new avenues for understanding what’s really happening under the eyelids.

About five years ago, Valery Shestopalov of the Bascom Palmer Eye Institute at the University of Miami was speaking with his microbiology colleagues about what bacteria are found on normal, healthy eyes. Conventional wisdom at that time held that healthy eyes don’t harbor much microbial life, tears and blinking tend to clear away foreign objects, including bacteria. But Shestopalov’s early tests revealed something different. “The tests ran positive. All exposed mucosal epithelium are populated densely,” he said. 

The team found that about a dozen bacteria genera dominated the eye’s conjunctiva, a third of which could not be classified. On the corneal surface, they found a slightly different community. Again, about a dozen genera dominated. And everywhere they’ve looked, the researchers have found more than just bacteria. “We haven't published on this yet, but I have been surprised by how often we find phage or viruses on the normal ocular surface,” Van Gelder told The Scientist in an e-mail.

“People can have a huge variation in microflora and still have healthy eyes, making our job difficult, but really amazing,” Shestopalov said.

The researchers also found that during keratitis infections—infections of the cornea—only about half as many bacterial varieties were present, most prominently Pseudomonas strains. The changes typically occurred well before a diagnosis of an eye infection, suggesting the ocular microbiome could inform future diagnostics, Shestopalov noted. 

One factor that may be expected to impact the composition of the ocular flora is the use of contact lenses. Contact lens wear is one of the biggest factors leading to corneal infection... Researchers believe contact lenses make it easier for pathogens to colonize the surface of the eye by giving the bacteria something to adhere to. Sequencing biofilms from used contact lenses, Shestopalov’s team found evidence of microbial communities that were different from the ocular microbiomes of people who don’t use contacts. On the lenses themselves, the researchers have found much less diversity—many of the bacterial genera that dominate the conjunctiva and cornea were depleted. In their place, Staphylococcus dominated.

Whether the bacteria identified living on the surface of the eye are permanent residents or transient colonizers remains to be seen. The work of deconstructing the ocular microbiome is just getting started, but preliminary results have suggested it is distinct from the rest of the bacterial community that inhabits our bodies. “It stands apart,” Shestopalov said. “There’s statistical evidence of its difference from any other human microbiome.”

Important to know about this nasty bacterial strain for those who use contact lenses. From Science Daily:

Bacteria survive longer in contact lens cleaning solution than previously thought, study shows

Each year in the UK, bacterial infections cause around 6,000 cases of a severe eye condition known as microbial keratitis -- an inflammation and ulceration of the cornea that can lead to loss of vision. The use of contact lenses has been identified as a particular risk factor for microbial keratitis. New research, presented today at the Society for General Microbiology Annual Conference in Liverpool, shows that a bacterial strain associated with more severe infections shows enhanced resistance to a common contact lens disinfectant solution.

Researchers from The University of Liverpool and The Royal Liverpool University NHS Trust tested different strains of the keratitis-causing bacterium Pseudomonas aeruginosa for their ability to survive in a commonly used contact lens cleaning solution. The team compared nine clinical strains of P. aeruginosa, taken from hospital patients in the UK, with P. aeruginosa strain 9027, the standard strain used by lens solution manufacturers.

The results showed that the majority of clinical strains tested were killed within 10 minutes of being immersed in the contact lens solution, comparable with the standard reference strain. However, one clinical isolate, P. aeruginosa strain 39016 -- associated with a more severe case of keratitis with a prolonged healing time -- was able to survive for over four hours, much longer than the reference strain.

Professor Craig Winstanley, who led the research, says: "Microbial keratitis can be devastating for a patient -- it is important that the risk of developing this condition is reduced in contact lens wearers by improving contact lens disinfectant solutions."