Borroni D, et al. BMJ Open Ophth 2019;4:e000248. doi:10.1136/bmjophth-2018-000248 1 Review Metagenomics in ophthalmology: current findings and future prospectives Davide Borroni,  1,2,3,4 Vito Romano, 1,3 Stephen B Kaye, 1,3 Tobi Somerville, 1,3 Luca Napoli, 5 Adriano Fasolo, 4 Paola Gallon, 4 Diego Ponzin, 4 Alfonso Esposito, 6 Stefano Ferrari 4 To cite: Borroni D, Romano V, Kaye SB, et al. Metagenomics in ophthalmology: current findings and future prospectives. BMJ Open Ophthalmology 2019;4:e000248. doi:10.1136/ bmjophth-2018-000248 Received 10 November 2018 Revised 4 February 2019 Accepted 19 February 2019 1 St Paul's Eye Unit, Department of Corneal and External Eye Diseases, Royal Liverpool University Hospital, Liverpool, United Kingdom 2 Department of Doctoral Studies, Riga Stradins University, Riga, Latvia 3 Department of Eye and Vision Science, University of Liverpool, Liverpool, United Kingdom 4 Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy 5 Dipartimento di Specialità Medico-Chirurgiche, Scienze Radiologiche e Sanita Pubblica, Universita degli Studi di Brescia, Brescia, Italy 6 Centre for Integrative Biology (CIBIO), Trento University, Trento, Italy Correspondence to Dr Davide Borroni; info.borroni@ gmail.com © Author(s) (or their employer(s)) 2018. Re-use permitted under CC BY. Published by BMJ. ABSTRACT Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a ‘hypothesis-free’ approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases. CURRENT KNOWLEDGE ABOUT THE EYE MICROBIOME The ocular surface (OS) microbiome is an understudied topic, compared with other host-associated environments. While the Human Microbiome Project initially studied five main body areas—the skin, the gastrointes- tinal tract, the urogenital tract, the oral and the nasal mucosa 1 —an emerging area of research is focusing on the eye and the micro- biota of the OS. 2 Recent studies demonstrated that OS hosts a number of commensal microorganisms. 3 Earlier culture-based surveys suggested that the OS are colonised by microbial communities dominated by Gram-positive Firmicutes, in particular, species belonging to the Staphylococcus, Streptococcus, Corynebac- terium and Propionibacterium. 4 A screening including approximately 1000 16S rRNA reads revealed that the diversity of healthy conjunctiva was higher than previously thought. 5 Other recent studies based on traditional microbiological techniques have examined the microbiota of the OS, 6–11 although a more comprehensive analysis of microbial diversity of OS has been hindered by the limitations of conventional cultiva- tion techniques. 12–14 More recent screening of OS-associated microbiome, using molec- ular metagenomic techniques, extended further the knowledge about OS microbial diversity. 2 5 15 16 Shestopalov and colleagues estimated using real-time PCR that in 1 ng of extracted DNA, the number of bacterial genomes (ie, bacterial richness) was on average 79.8 and 729 in the conjunctiva and cornea, respectively. Significant amounts (22 over 55) were detected in the eye for the first time. 17 Dong et al detected 59 distinct bacterial genera using a 16S rDNA gene pyrosequencing approach on the OS of four healthy individuals 15 (figure 1). Despite the low number of individuals examined, this is one of the first studies focusing on the bacte- rial diversity of the OS microbiome. Healthy OS microbiome is dominated by Proteobac- teria, Actinobacteria and Firmicutes. The most common taxa at the genus level were Pseu- domonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta and Methylobacte- rium (figure 1). This is in general agreement with the previous studies, although many false positives may derive from contamina- tion. 4 Microbial invasion into the OS compro- mises corneal clarity and causes inflammation in blinding conditions like keratitis, endoph- thalmitis and trachoma. Herpes simplex type 1, hepatitis B and C viruses can be detected using PCR in the tears of asymptomatic volun- teers, 18 thus suggesting that simply focusing solely on the bacterial constituents of the OS may result in an incomplete understanding of the OS microbiome. In recent time, Zhou et al 19 showed how the changes in the conjunc- tival microbiome occur in trachomatous disease compared with normal controls. Wen et al 20 showed how the microbiome of healthy OS is shaped by age and sex and how the ocular microbiome of house finches changed during experimentally induced mycoplasmal conjunctivitis. 21 Study of microbiome in OS disease has significant potential to improve the diagnosis, treatment and management of potential blinding diseases. on April 24, 2020 by guest. Protected by copyright. http://bmjophth.bmj.com/ BMJ Open Ophth: first published as 10.1136/bmjophth-2018-000248 on 4 June 2019. Downloaded from on April 24, 2020 by guest. Protected by copyright. http://bmjophth.bmj.com/ BMJ Open Ophth: first published as 10.1136/bmjophth-2018-000248 on 4 June 2019. Downloaded from on April 24, 2020 by guest. Protected by copyright. http://bmjophth.bmj.com/ BMJ Open Ophth: first published as 10.1136/bmjophth-2018-000248 on 4 June 2019. Downloaded from