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Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
M. Aaron MacNeil & Taylor Gorham

Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL, USA
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Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
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Australian Institute of Marine Science, Arafura Timor Research Facility, Darwin, Northern Territory, Australia
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School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, USA
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International Pole and Line Foundation, Malé, Maldives
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Centro de Investigaciones de Ecosistemas Costeros (CIEC), Cayo Coco, Morón, Ciego de Ávila, Cuba
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Habitat and Living Marine Resources Program, Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
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Réseau requins des Antilles Francaises, Kap Natirel, Vieux-Fort, Guadeloupe
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Mahonia Na Dari Research and Conservation Centre, Kimbe, Papua New Guinea
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Anthony T. F. Bernard

Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
Anthony T. F. Bernard

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Bren School of Environmental Sciences and Management, University of California Santa Barbara, Santa Barbara, CA, USA
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Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
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University of the West Indies, Discovery Bay Marine Laboratory, Discovery Bay, Jamaica
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Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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Albion College, Albion, MI, USA
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Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
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Environmental Research Institute Charlotteville, Charlotteville, Trinidad and Tobago
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School of Biosciences, Cardiff University, Cardiff, UK
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ARC Centre of Excellence in Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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Waitt Institute, La Jolla, CA, USA
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Center for Shark Research, Mote Marine Laboratory, Sarasota, FL, USA
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Operation Wallacea, Spilsby, Lincolnshire, UK
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Benedict Kiilu

Ministry of Fisheries and Marine Resources, Development, Kiritimati, Kiribati
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Tanzania Fisheries Research Institute, Dar Es Salaam, Tanzania
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University of the West Indies, Kingston, Jamaica
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School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
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Wasage Divers, Wakatobi and Buton, Indonesia
Muslimin Kaimuddin

Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, Western Australia, Australia
Stephen J. Newman & Michael J. Travers

Island Conservation Society Seychelles, Victoria, Mahé, Seychelles
Josep Nogués

CORDIO East Africa, Mombasa, Kenya
Clay Obota & Melita Samoilys

The Centre for Ocean Research and Education, Gregory Town, Eleuthera, Bahamas
Owen O’Shea

Department of Environment and Geography, University of York, York, UK
Kennedy Osuka

Center for Fisheries Research, Ministry for Marine Affairs and Fisheries, Jakarta Utara, Indonesia
Andhika Prasetyo

Universitas Dayanu Ikhsanuddin Bau-Bau, Bau-Bau, Indonesia
L. M. Sjamsul Quamar

Pristine Seas, National Geographic Society, Washington, DC, USA
Enric Sala

Department of Zoology, University of Oxford, Oxford, UK
Melita Samoilys

HJR Reefscaping, Boquerón, Puerto Rico
Michelle Schärer-Umpierre

SalvageBlue, Kingstown, Saint Vincent and the Grenadines
Nikola Simpson

School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
Adam N. H. Smith

Indo Ocean Project, PT Nomads Diving Bali, Nusa Penida, Indonesia
Lauren Sparks

Manchester Metropolitan University, Manchester, UK
Akshay Tanna & Alexandra M. Watts

Reef Check Dominican Republic, Santo Domingo, Dominican Republic
Rubén Torres

Institut de Recherche pour le Développement, UMR ENTROPIE (IRD-UR-UNC-CNRS-IFREMER), Nouméa, New Caledonia
Laurent Vigliola

Secretariat of the Pacific Regional, Environment Programme, Apia, Samoa
Juney Ward

Department of Life Science, Tunghai University, Taichung, Taiwan
Colin Wen

School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
Aaron J. Wirsing

Corales del Rosario and San Bernardo National Natural Park, GIBEAM Research Group, Universidad del Sinú, Cartagena, Colombia
Esteban Zarza-Gonzâlez

D. Chapman and M. Heithaus conceived the study with assistance from M. Heupel, C.A.S., M.M., E.H. and M.A.M. D. Chapman, M. Heithaus, M. Heupel, C.A.S., M.M. and E.H. directed fieldwork run by J.G., J.K., M.E.B., L.M.C.-R., C.W.S., K.I.F., J.V.-A., G.C. and C.S.S. Database management was by T. Gorham. M.A.M. and D. Chapman drafted the manuscript, with help from M. Heithaus, M. Heupel, C.A.S., J.E.M.C., M.M., E.H., J.G., J.K., M.E.B., L.M.C.-R., C.W.S., C.S.S., M.J.R., V.U. and T. Gorham. All other authors contributed equally, made substantial contributions to data collection, provided input and approved the text in the manuscript. More

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Cohort
Based on the power and pairwise sample-size estimator for permutational multivariate analysis of variance (PERMANOVA) application Micropower14, a low abundance 16S rRNA dataset similar to previous ocular microbiome studies12 would require a minimal sample size of 30 to generate a discriminatory power of 0.8 with a significance level of 0.05. Therefore, we aimed for at least 35 subjects per study arm. Table 1 shows the demographics and clinical characteristics of the enrolled participants. Based on a post-enrolment exam and two clinical surveys, after informed consent, participants were classified as dry eye or controls (Supplemental S1). The resulting 36 control and 36 dry eye subjects were then stratified by clinical severity of eye disease (Fig. 1 and Supplemental Table 1). The study arms were randomized to daily saline eye wash upon awakening or non-intervention. A baseline closed eye tear sample was collected at randomization and the final sample after one month, yielding 144 samples. We did not observe significant differences between the stratifications normal versus mild and moderate versus severe with respect to microbial ecology (Fig. 2), however clear separation was present between the mild and moderate samples, indicating this more granular stratification introduced a false dichotomy in the data. Therefore, we combined subjects stratified as none or mild into one cohort, now termed normal, and we combined subjects stratified as moderate or severe into another cohort, now termed dry eye (Fig. 3). We used this simplified stratification system for all subsequent analyses (Methods).
Table 1 Participant demographics and clinical characteristics.
Full size table

Figure 1

Subjects were allocated, stratified and randomized to treatment or control. Schematic of collection of closed eye tears in sterile saline, followed by 16S rRNA metabarcoding of the bacterial microbiome. Diagram of subject allocation and randomization. Figure generated with BioRender.

Full size image

Figure 2

Patients with dry eye disease have a different closed eye microbiome. (a) Individuals with dry eye disease have different alpha diversity of the closed eye microbiome as quantified by the richness (ANOVA, f = 4.8, P = 7.5 × 10−5), evenness (ANOVA, f = 13, P = 2.1 × 10−12) and Shannon diversity (ANOVA, f = 12, P = 5.9 × 10−12) indices. (b) The beta diversity of the closed eye microbiome in individuals with dry eye disease is distinct by principal coordinate analysis (PCoA) of Bray–Curtis dissimilarity (R2 = 0.21 P = 0.00033), redundancy analysis (RDA, variance = 95.25, f = 3.71, P = 0.001) and canonical correspondence analysis (CCA, chi2 = 0.16 f = 3.64 P = 0.001). (c) Relative abundance of bacterial orders. Log2(CSS), log2 transformation of cumulative-sum scaling. Two-way ANOVA, *P = 0.01, **P = 0.001, ***P = 0.0001. (d) Spearman network analysis at the operational taxonomic unit level. Positive correlations with a P value More

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