{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T19:33:32Z","timestamp":1791660812898,"version":"4.3.4"},"posted":{"date-parts":[[2026,7,17]]},"group-title":"Microbiology","reference-count":118,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R01AI158527"],"award-info":[{"award-number":["R01AI158527"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Trachoma, a chronic ocular disease caused by\n                  <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                  (\n                  <jats:italic>Ct<\/jats:italic>\n                  ), is the leading infectious cause of blindness worldwide. Despite WHO\u2019s SAFE (\n                  <jats:underline>S<\/jats:underline>\n                  urgery,\n                  <jats:underline>A<\/jats:underline>\n                  ntibiotics,\n                  <jats:underline>F<\/jats:underline>\n                  acial cleanliness,\n                  <jats:underline>E<\/jats:underline>\n                  nvironmental improvement) strategy, \u223c100M are at risk of blindness. Using metagenomic shotgun sequencing, we characterized the ocular microbiome of 680 villagers in Amhara Ethiopia, identifying 10 Community State Types (CSTs) associated with different population characteristics. Children with the highest prevalence of inflammatory trachoma and\n                  <jats:italic>Ct<\/jats:italic>\n                  were in CST10, dominated by\n                  <jats:italic>Haemophilus influenzae<\/jats:italic>\n                  and four other\n                  <jats:italic>Haemophilus<\/jats:italic>\n                  spp. Adults with the highest prevalence of scarring trachoma were in CST3 and CST6, dominated by\n                  <jats:italic>Corynebacterium macginleyi<\/jats:italic>\n                  . CST5, dominated by\n                  <jats:italic>Mesomycoplasma hyorhinis<\/jats:italic>\n                  and\n                  <jats:italic>Staphylococcus aureus,<\/jats:italic>\n                  had the lowest prevalence of\n                  <jats:italic>Ct<\/jats:italic>\n                  and trachoma, and was the only CST without zoonotic\n                  <jats:italic>Chlamydia<\/jats:italic>\n                  spp. Both\n                  <jats:italic>M. hyorhinis,<\/jats:italic>\n                  a zoonotic porcine bacterium, and\n                  <jats:italic>S. aureus<\/jats:italic>\n                  are capable of forming biofilms, which may competitively prevent\/down-regulate chlamydial infections. Other CSTs were dominated by environmental species like\n                  <jats:italic>Vibrio<\/jats:italic>\n                  . This is the first microbiome study to develop CSTs for trachoma. Pathogenic and potentially protective microbes showed distinct associations with demographic, clinical, and chlamydial characteristics, which will guide the design of microbial therapeutics as alternatives to antibiotics and strategies for WHO\u2019s global elimination of blinding trachoma.\n                <\/jats:p>","DOI":"10.64898\/2026.07.16.738988","type":"posted-content","created":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T05:10:22Z","timestamp":1784351422000},"source":"Crossref","is-referenced-by-count":1,"title":["Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control"],"prefix":"10.64898","author":[{"given":"Augusta","family":"Uwamanzu-Nna","sequence":"first","affiliation":[{"name":"Department of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, CA, USA"},{"name":"Department of Bioengineering, Joint Program, University of California San Francisco and University of California Berkeley, San Francisco, CA, USA"},{"name":"Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olusola","family":"Olagoke","sequence":"additional","affiliation":[{"name":"Department of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, CA, USA"},{"name":"Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte Xiaoyi","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiwot Degineh","family":"Mengistie","sequence":"additional","affiliation":[{"name":"Bahir Dar Specialty Eye Center, Bahir Dar, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaleb","family":"Asfaha","sequence":"additional","affiliation":[{"name":"Department of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy D.","family":"Read","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4490-1746","authenticated-orcid":false,"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[{"name":"Department of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, San Francisco, CA, USA"},{"name":"Department of Bioengineering, Joint Program, University of California San Francisco and University of California Berkeley, San Francisco, CA, USA"},{"name":"Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA"},{"name":"Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072010001355000_2026.07.16.738988v1.1","doi-asserted-by":"crossref","unstructured":"Dean D . 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