The Microbiome of the Eye

How is the eye microbiome different from the gut and skin microbiomes and what is its importance to our health?

The human “microbiome,” which encompasses the trillions of microorganisms and the compounds they produce, exists on or within our skin, gut, nose, mouth, and even our eyes! These organisms normally live with us in harmony and are essential for many functions, including keeping our immune systems strong. Most of us have heard of the gut and skin microbiomes, but how is the eye microbiome different and what is its importance to our health?


I Have Bacteria in My Eye?

Actually, you have several different species of bacteria in your eyes! However, the eye microbiome is quite unique compared to the gut and skin microbiomes. Unlike the gut microbiome, which harbors thousands of different species of organisms, the eye microbiome is remarkably less diverse and comprises a lower amount of total bacteria compared to other locations throughout our body.[1]

Researchers commonly measure the amount or density of bacteria in a given location using the scientific term “colony forming units” or CFUs. On the eye, scientists have reported anywhere from 4 to 100 CFUs/swab. By contrast, a swab of the mouth often yields over 1 million CFUs/swab![1,2] This demonstrates the huge difference in the abundance of bacteria in the eye compared to other places in the body.


The Eye Microbiome Protects Us From Eye Infections

In a study from the National Institute of Health (NIH), scientists showed for the first time that microorganisms on the surface of our eye play a vital role in the 1st line of defense protecting us against infections.[3] The researchers discovered that a certain eye bacteria called Corynebacterium mastitidis actually signals white blood cells to launch an immune response and even releases antimicrobial compounds into the tears to fight against infection-causing microorganisms called candida and pseudomonas.


Eye Diseases and the Microbiome

Only a few studies have looked at the eye microbiome in people with different eye conditions. For instance, people with an autoimmune disease called Sjogren’s syndrome have a much higher amount of bacteria living on the eye than healthy people.[4] Similarly, it has been shown that people with non-autoimmune dry eyes have higher amounts of Corynebacterium and Propionibacterium species on their eyes.[5]

Researchers are still unsure how these bacteria may contribute to eye health or disease, but it serves as a first step in understanding that the eye microbiome changes under different eye conditions. We are only just scraping the surface of understanding the role of the eye microbiome in various eye conditions such as dry eyes and overall health. 


How Do Contact Lenses Alter the Eye Microbiome?

Scientists discovered that people who wear contact lenses have much higher bacteria content on their eye surface than people who do not wear contacts.[6] In fact, further investigations revealed that contact wearers had eye microbiomes that were much more similar to the skin microbiome in its abundance and diversity of different bacterial species.[7]

For instance, normal skin bacteria strains of Corynebacterium and Staphylococcus were present in much greater amounts in the eyes of contact wearers compared to those without contact lenses. This is understandable since we likely spread bacteria from our hands onto our eyes as we put in contact lenses.

Researchers have not yet proven that the increased bacterial load in the eyes of contact wearers is directly related to any health risks. There is a known increased risk for eye infections and inflammatory eye conditions in contact wearers, but it is still too early to understand how the normal eye microbiome plays a role.[8]


Concluding Remarks

The human microbiome is an exciting area of research that promises a better future understanding of how the trillions of bacteria that live on and within us influence health and disease. As research on the eye microbiome expands, further well-designed studies will better characterize the microbiota that lives in our eyes.[1]

* This Website is for general skin beauty, wellness, and health information only. This Website is not to be used as a substitute for medical advice, diagnosis or treatment of any health condition or problem. The information provided on this Website should never be used to disregard, delay, or refuse treatment or advice from a physician or a qualified health provider.


  1. Kugadas A, Gadjeva M. Impact of Microbiome on Ocular Health. Ocul Surf.2016;14(3):342-349; PMID: 27189865 Link to research.
  2. Willcox MD. Characterization of the normal microbiota of the ocular surface. Exp Eye Res.2013;117:99-105; PMID: 23797046 Link to research.
  3. St Leger AJ, Desai JV, Drummond RA, et al. An Ocular Commensal Protects against Corneal Infection by Driving an Interleukin-17 Response from Mucosal gammadelta T Cells. Immunity.2017;47(1):148-158 e145; PMID: 28709803 Link to research.
  4. Albietz JM, Lenton LM. Effect of antibacterial honey on the ocular flora in tear deficiency and meibomian gland disease. Cornea.2006;25(9):1012-1019; PMID: 17133045 Link to research.
  5. Graham JE, Moore JE, Jiru X, et al. Ocular pathogen or commensal: a PCR-based study of surface bacterial flora in normal and dry eyes. Invest Ophthalmol Vis Sci.2007;48(12):5616-5623; PMID: 18055811 Link to research.
  6. Larkin DF, Leeming JP. Quantitative alterations of the commensal eye bacteria in contact lens wear. Eye (Lond).1991;5 ( Pt 1):70-74; PMID: 2060675 Link to research.
  7. Shin H, Price K, Albert L, et al. Changes in the Eye Microbiota Associated with Contact Lens Wearing. MBio.2016;7(2):e00198; PMID: 27006462 Link to research.
  8. Szczotka-Flynn LB, Pearlman E, Ghannoum M. Microbial contamination of contact lenses, lens care solutions, and their accessories: a literature review. Eye Contact Lens.2010;36(2):116-129; PMID: 20168237 Link to research.