{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:25:20Z","timestamp":1792794320269,"version":"4.5.0"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,11,27]],"date-time":"2025-11-27T00:00:00Z","timestamp":1764201600000},"content-version":"vor","delay-in-days":330,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100001263","name":"National Philanthropic Trust","doi-asserted-by":"publisher","award":["23\u20137825575"],"award-info":[{"award-number":["23\u20137825575"]}],"id":[{"id":"10.13039\/100001263","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2128073"],"award-info":[{"award-number":["2128073"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"USDA National Institute of Food and Agriculture Hatch Formula","award":["NJ01180"],"award-info":[{"award-number":["NJ01180"]}],"id":[{"id":"https:\/\/ror.org\/05qx3fv49","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigated microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes and correlated their abundance with disease phenotypes, which revealed significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses in our dataset that increase in abundance in SCTLD-affected corals and are present in existing coral data from other Caribbean regions. In addition, we identified the first putative instance of asymptomatic\/resistant SCTLD-affected corals. These are apparently healthy colonies that share the viral profile of diseased individuals. However, these colonies contain a different prokaryotic microbiome than do diseased corals, suggesting microbe-induced resilience (i.e. beneficial microbiome) to SCTLD. Finally, utilizing differential abundance analysis and gene inventories, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.<\/jats:p>","DOI":"10.1093\/ismeco\/ycaf226","type":"journal-article","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T13:09:28Z","timestamp":1764162568000},"source":"Crossref","is-referenced-by-count":7,"title":["Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD)"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3119-7768","authenticated-orcid":false,"given":"Shrinivas","family":"Nandi","sequence":"first","affiliation":[{"name":"Microbial Biology Graduate Program, Rutgers University , 76 Lipman Drive, New Brunswick, NJ, 08901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1554-7175","authenticated-orcid":false,"given":"Timothy G","family":"Stephens","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Microbiology, 59 Dudley Road, Rutgers University , New Brunswick, NJ, 08901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasey","family":"Walsh","sequence":"additional","affiliation":[{"name":"Microbial Biology Graduate Program, Rutgers University , 76 Lipman Drive, New Brunswick, NJ, 08901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9482-8540","authenticated-orcid":false,"given":"Rebecca","family":"Garc\u00eda-Camps","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Puntacana, Marine Innovation Centre, Puntacana Resort & Club, Punta Cana \u00a0 23000"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9764-0706","authenticated-orcid":false,"given":"Maria F","family":"Villalpando","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Dominicana de Estudios Marinos, Marine Research Dominican Republic, Calle Los Manantiales, Bayahibe , La Altagracia, 23000 ,","place":["Dominican Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8236-8575","authenticated-orcid":false,"given":"Rita I","family":"Sellares-Blasco","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Dominicana de Estudios Marinos, Marine Research Dominican Republic, Calle Los Manantiales, Bayahibe , La Altagracia, 23000 ,","place":["Dominican Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1549-5464","authenticated-orcid":false,"given":"Ainhoa L","family":"Zubillaga","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Puntacana, Marine Innovation Centre, Puntacana Resort & Club, Punta Cana \u00a0 23000"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8880-9338","authenticated-orcid":false,"given":"Aldo","family":"Croquer","sequence":"additional","affiliation":[{"name":"The Nature Conservancy, Caribbean Division, Central Caribbean Program , Avenida 27 de Febrero, Plaza Central 1, Santo Domingo, 10148 ,","place":["Dominican Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debashish","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Microbiology, 59 Dudley Road, Rutgers University , New Brunswick, NJ, 08901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,11,27]]},"reference":[{"key":"2025122707061844500_ref1","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/S0006-3207(00)00073-2","article-title":"The significance of coral disease epizootiology for coral reef conservation","volume":"96","author":"Green","year":"2000","journal-title":"Biol Conserv"},{"key":"2025122707061844500_ref2","doi-asserted-by":"publisher","first-page":"113855","DOI":"10.1016\/j.marpolbul.2022.113855","article-title":"The role of coral diseases in the flattening of a Caribbean coral reef over 23 years","volume":"181","author":"Randazzo-Eisemann","year":"2022","journal-title":"Mar Pollut Bull"},{"key":"2025122707061844500_ref3","doi-asserted-by":"publisher","DOI":"10.1038\/srep31374","article-title":"Unprecedented disease-related coral mortality in Southeastern Florida","volume":"6","author":"Precht","year":"2016","journal-title":"Sci Rep"},{"key":"2025122707061844500_ref4","doi-asserted-by":"publisher","first-page":"815698","DOI":"10.3389\/fmars.2021.815698","article-title":"Reef sediments can act as a stony coral tissue loss disease vector","volume":"8","author":"Studivan","year":"2022","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref5","doi-asserted-by":"publisher","first-page":"1321271","DOI":"10.3389\/fmars.2023.1321271","article-title":"Stony coral tissue loss disease: a review of emergence, impacts, etiology, diagnostics, and intervention","volume":"10","author":"Papke","year":"2024","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref6","doi-asserted-by":"publisher","first-page":"790818","DOI":"10.3389\/fmars.2022.790818","article-title":"Differences in the progression rate of SCTLD in Pseudodiploria strigosa are related to colony size and morphology","volume":"9","author":"Camacho-Vite","year":"2022","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref7","doi-asserted-by":"publisher","first-page":"163","DOI":"10.3389\/fmars.2020.00163","article-title":"Spatial epidemiology of the stony-coral-tissue-loss disease in Florida","volume":"7","author":"Muller","year":"2020","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref8","doi-asserted-by":"publisher","first-page":"591881","DOI":"10.3389\/fmars.2020.591881","article-title":"Coupled Epidemio-hydrodynamic Modeling to understand the spread of a deadly coral disease in Florida","volume":"7","author":"Dobbelaere","year":"2020","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref9","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1038\/s43705-022-00126-3","article-title":"Experimental transmission of stony coral tissue loss disease results in differential microbial responses within coral mucus and tissue","volume":"2","author":"Huntley","year":"2022","journal-title":"ISME Communications"},{"key":"2025122707061844500_ref10","doi-asserted-by":"publisher","first-page":"709764","DOI":"10.3389\/fmars.2021.709764","article-title":"Considering commercial vessels as potential vectors of stony coral tissue loss disease","volume":"8","author":"Rosenau","year":"2021","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref11","doi-asserted-by":"publisher","first-page":"1009407","DOI":"10.3389\/fmars.2022.1009407","article-title":"Biofilms as potential reservoirs of stony coral tissue loss disease","volume":"9","author":"Evans","year":"2022","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref12","doi-asserted-by":"publisher","first-page":"715329","DOI":"10.3389\/fmars.2021.715329","article-title":"The emergence and initial impact of stony coral tissue loss disease (SCTLD) in the United States Virgin Islands","volume":"8","author":"Brandt","year":"2021","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref13","doi-asserted-by":"publisher","first-page":"GCFI1","DOI":"10.18785\/gcr.3301.03","article-title":"Stony coral tissue loss disease and other diseases affect adults and recruits of major reef builders at different spatial scales in the Dominican Republic","volume":"33","author":"Cr\u00f3quer","year":"2022","journal-title":"GCR"},{"key":"2025122707061844500_ref14","doi-asserted-by":"publisher","first-page":"e8069","DOI":"10.7717\/peerj.8069","article-title":"A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean","volume":"7","author":"Alvarez-Filip","year":"2019","journal-title":"PeerJ"},{"key":"2025122707061844500_ref15","doi-asserted-by":"publisher","first-page":"507","DOI":"10.5343\/bms.2022.0015","article-title":"Coral reefs of southeastern Dominican Republic hit by two simultaneous epizootic events","volume":"98","author":"Villalpando","year":"2022","journal-title":"bms"},{"key":"2025122707061844500_ref16","volume-title":"Coral Disease & Health Consortium","author":"Stony Coral Tissue Loss Disease (SCTLD)"},{"key":"2025122707061844500_ref17","doi-asserted-by":"publisher","first-page":"273","DOI":"10.3354\/meps266273","article-title":"Disease and immunity in Caribbean and Indo-Pacific zooxanthellate corals","volume":"266","author":"Sutherland","year":"2004","journal-title":"Mar Ecol Prog Ser"},{"key":"2025122707061844500_ref18","doi-asserted-by":"publisher","first-page":"e15836","DOI":"10.7717\/peerj.15836","article-title":"Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)","volume":"11","author":"Evans","year":"2023","journal-title":"PeerJ"},{"key":"2025122707061844500_ref19","doi-asserted-by":"publisher","first-page":"2181","DOI":"10.3390\/microorganisms9112181","article-title":"Characterization of the microbiome of corals with stony coral tissue loss disease along Florida\u2019s coral reef","volume":"9","author":"Clark","year":"2021","journal-title":"Microorganisms"},{"key":"2025122707061844500_ref20","doi-asserted-by":"publisher","first-page":"e0304925","DOI":"10.1371\/journal.pone.0304925","article-title":"Microbiomes of three coral species in the Mexican Caribbean and their shifts associated with the stony coral tissue loss disease","volume":"19","author":"Arriaga-Pi\u00f1\u00f3n","year":"2024","journal-title":"PLoS One"},{"key":"2025122707061844500_ref21","doi-asserted-by":"publisher","first-page":"681","DOI":"10.3389\/fmicb.2020.00681","article-title":"Rhodobacterales and Rhizobiales are associated with stony coral tissue loss disease and its suspected sources of transmission","volume":"11","author":"Rosales","year":"2020","journal-title":"Front Microbiol"},{"key":"2025122707061844500_ref22","doi-asserted-by":"publisher","first-page":"e9289","DOI":"10.7717\/peerj.9289","article-title":"Effectiveness of topical antibiotics in treating corals affected by stony coral tissue loss disease","volume":"8","author":"Neely","year":"2020","journal-title":"PeerJ"},{"key":"2025122707061844500_ref23","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3389\/fmars.2022.859740","article-title":"Antibiotic treatment ameliorates the impact of stony coral tissue loss disease (SCTLD) on coral communities","volume":"9","author":"Forrester","year":"2022","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref24","doi-asserted-by":"publisher","first-page":"1465173","DOI":"10.3389\/fmars.2024.1465173","article-title":"The relative effectiveness of chlorine and antibiotic treatments for stony coral tissue loss disease","volume":"11","author":"Forrester","year":"2024","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref25","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1038\/s42003-023-04590-y","article-title":"Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease","volume":"6","author":"Ushijima","year":"2023","journal-title":"Commun Biol"},{"key":"2025122707061844500_ref26","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1007\/s00338-024-02610-9","article-title":"The effects of probiotics and stony coral tissue loss disease exposure on coral recruits","volume":"44","author":"Demko","year":"2025","journal-title":"Coral Reefs"},{"key":"2025122707061844500_ref27","doi-asserted-by":"publisher","first-page":"2244","DOI":"10.3389\/fmicb.2019.02244","article-title":"Microbial community shifts associated with the ongoing stony coral tissue loss disease outbreak on the Florida reef tract","volume":"10","author":"Meyer","year":"2019","journal-title":"Front Microbiol"},{"key":"2025122707061844500_ref28","doi-asserted-by":"publisher","first-page":"776859","DOI":"10.3389\/fmars.2021.776859","article-title":"Bacterial metabolic potential and micro-eukaryotes enriched in stony coral tissue loss disease lesions","volume":"8","author":"Rosales","year":"2022","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref29","doi-asserted-by":"publisher","first-page":"750658","DOI":"10.3389\/fmars.2021.750658","article-title":"Viral-like particles are associated with endosymbiont pathology in Florida corals affected by stony coral tissue loss disease","volume":"8","author":"Work","year":"2021","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref30","doi-asserted-by":"publisher","first-page":"2915","DOI":"10.1038\/s41467-023-38612-4","article-title":"Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae","volume":"14","author":"Beavers","year":"2023","journal-title":"Nat Commun"},{"key":"2025122707061844500_ref31","doi-asserted-by":"publisher","first-page":"e01199","DOI":"10.1128\/mra.01199-21","article-title":"Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S","volume":"11","author":"Veglia","year":"2022","journal-title":"Virgin Islands Microbiol Resour Announc"},{"key":"2025122707061844500_ref32","doi-asserted-by":"publisher","first-page":"jkae137","DOI":"10.1093\/g3journal\/jkae137","article-title":"Novel metagenomics analysis of stony coral tissue loss disease","volume":"14","author":"Heinz","year":"2024","journal-title":"G3"},{"key":"2025122707061844500_ref33","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1038\/s41396-023-01526-6","article-title":"Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins","volume":"17","author":"Howe-Kerr","year":"2023","journal-title":"The ISME Journal"},{"key":"2025122707061844500_ref34","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/s00338-024-02595-5","article-title":"Pathology of lesions in corals from the US Virgin Islands after emergence of stony coral tissue loss disease","volume":"44","author":"Work","year":"2025","journal-title":"Coral Reefs"},{"key":"2025122707061844500_ref35","doi-asserted-by":"publisher","first-page":"678","DOI":"10.3389\/fmars.2019.00678","article-title":"Pathogenesis of a tissue loss disease affecting multiple species of corals along the Florida reef tract","volume":"6","author":"Aeby","year":"2019","journal-title":"Front Mar Sci"},{"key":"2025122707061844500_ref36","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s12859-020-03585-4","article-title":"ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data","volume":"21","author":"Kieser","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2025122707061844500_ref37","doi-asserted-by":"publisher","first-page":"e63","DOI":"10.1093\/nar\/gkae528","article-title":"Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing","volume":"52","author":"Espinoza","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025122707061844500_ref38","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref39","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref40","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"2025122707061844500_ref41","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref42","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","article-title":"Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy","volume":"3","author":"Sieber","year":"2018","journal-title":"Nat Microbiol"},{"key":"2025122707061844500_ref43","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1099\/mgen.0.000823","article-title":"Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure","volume":"8","author":"Pronk","year":"2022","journal-title":"Microbial Genomics"},{"key":"2025122707061844500_ref44","doi-asserted-by":"publisher","first-page":"e76","DOI":"10.1093\/nar\/gkac294","article-title":"How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner","volume":"50","author":"Vollmers","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025122707061844500_ref45","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref46","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1038\/s41592-024-02248-z","article-title":"Author correction: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"21","author":"Chklovski","year":"2024","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref47","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1038\/s41592-023-02018-3","article-title":"Fast and robust metagenomic sequence comparison through sparse chaining with skani","volume":"20","author":"Shaw","year":"2023","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref48","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref49","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025122707061844500_ref50","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025122707061844500_ref51","doi-asserted-by":"publisher","first-page":"000685","DOI":"10.1099\/mgen.0.000685","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microbial Genomics"},{"key":"2025122707061844500_ref52","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref53","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.12688\/f1000research.12232.1","article-title":"BlobTools: interrogation of genome assemblies","volume":"6","author":"Laetsch","year":"2017","journal-title":"F1000Res"},{"key":"2025122707061844500_ref54","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1186\/s12864-018-4857-9","article-title":"Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes","volume":"19","author":"Shoguchi","year":"2018","journal-title":"BMC Genomics"},{"key":"2025122707061844500_ref55","doi-asserted-by":"publisher","first-page":"39734","DOI":"10.1038\/srep39734","article-title":"Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle","volume":"6","author":"Aranda","year":"2016","journal-title":"Sci Rep"},{"key":"2025122707061844500_ref56","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1016\/j.cub.2013.05.062","article-title":"Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure","volume":"23","author":"Shoguchi","year":"2013","journal-title":"Curr Biol"},{"key":"2025122707061844500_ref57","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/s42003-018-0098-3","article-title":"Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis","volume":"1","author":"Liu","year":"2018","journal-title":"Commun Biol"},{"key":"2025122707061844500_ref58","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s12915-021-00994-6","article-title":"Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium","volume":"19","author":"Gonz\u00e1lez-Pech","year":"2021","journal-title":"BMC Biol"},{"key":"2025122707061844500_ref59","doi-asserted-by":"publisher","first-page":"eadn2218","DOI":"10.1126\/sciadv.adn2218","article-title":"Whole-genome duplication in an algal symbiont bolsters coral heat tolerance","volume":"10","author":"Dougan","year":"2024","journal-title":"Sci Adv"},{"key":"2025122707061844500_ref60","doi-asserted-by":"publisher","first-page":"wrae059","DOI":"10.1093\/ismejo\/wrae059","article-title":"Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates","volume":"18","author":"Shah","year":"2024","journal-title":"The ISME Journal"},{"key":"2025122707061844500_ref61","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/s12915-020-00782-8","article-title":"Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions","volume":"18","author":"Stephens","year":"2020","journal-title":"BMC Biol"},{"key":"2025122707061844500_ref62","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref63","doi-asserted-by":"publisher","first-page":"btaf147","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"CoverM: read alignment statistics for metagenomics","volume":"41","author":"A Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref64","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.3389\/fmicb.2017.02224","article-title":"Microbiome datasets are compositional: and this is not optional","volume":"8","author":"Gloor","year":"2017","journal-title":"Front Microbiol"},{"key":"2025122707061844500_ref65","doi-asserted-by":"publisher","first-page":"e6","DOI":"10.5808\/GI.2019.17.1.e6","article-title":"Statistical analysis of metagenomics data","volume":"17","author":"Calle","year":"2019","journal-title":"Genomics Inform"},{"key":"2025122707061844500_ref66","doi-asserted-by":"publisher","first-page":"2244139","DOI":"10.1080\/19490976.2023.2244139","article-title":"Statistical normalization methods in microbiome data with application to microbiome cancer research","volume":"15","author":"Xia","year":"2023","journal-title":"Gut Microbes"},{"key":"2025122707061844500_ref67","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/s41592-023-02092-7","article-title":"Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures","volume":"21","author":"Lin","year":"2024","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref68","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/2049-2618-2-15","article-title":"Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis","volume":"2","author":"Fernandes","year":"2014","journal-title":"Microbiome"},{"key":"2025122707061844500_ref69","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR\u00a0: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref70","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1038\/s41467-022-28034-z","article-title":"Microbiome differential abundance methods produce different results across 38 datasets","volume":"13","author":"Nearing","year":"2022","journal-title":"Nat Commun"},{"key":"2025122707061844500_ref71","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/s40168-017-0237-y","article-title":"Normalization and microbial differential abundance strategies depend upon data characteristics","volume":"5","author":"Weiss","year":"2017","journal-title":"Microbiome"},{"key":"2025122707061844500_ref72","doi-asserted-by":"publisher","first-page":"btad547","DOI":"10.1093\/bioinformatics\/btad547","article-title":"PyDESeq2: a python package for bulk RNA-seq differential expression analysis","volume":"39","author":"Muzellec","year":"2023","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref73","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2025122707061844500_ref74","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025122707061844500_ref75","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2025122707061844500_ref76","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J Mol Biol"},{"key":"2025122707061844500_ref77","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025122707061844500_ref78","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/s43705-023-00220-0","article-title":"A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies","volume":"3","author":"Rosales","year":"2023","journal-title":"ISME Communications"},{"key":"2025122707061844500_ref79","doi-asserted-by":"publisher","first-page":"fuad005","DOI":"10.1093\/femsre\/fuad005","article-title":"The coral microbiome: towards an understanding of the molecular mechanisms of coral\u2013microbiota interactions","volume":"47","author":"Mohamed","year":"2023","journal-title":"FEMS Microbiol Rev"},{"key":"2025122707061844500_ref80","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1146\/annurev-micro-102215-095440","article-title":"Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems","volume":"70","author":"Bourne","year":"2016","journal-title":"Ann Rev Microbiol"},{"key":"2025122707061844500_ref81","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1038\/s41579-019-0223-4","article-title":"Coral microbiome dynamics, functions and design in a changing world","volume":"17","author":"van Oppen","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2025122707061844500_ref82","doi-asserted-by":"publisher","first-page":"e01594","DOI":"10.1128\/JVI.01594-20","article-title":"Diversity of sea star-associated Densoviruses and transcribed endogenous viral elements of Densovirus origin","volume":"95","author":"Jackson","year":"2020","journal-title":"J Virol"},{"key":"2025122707061844500_ref83","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1007\/BF00349482","article-title":"Evidence that reef-wide patterns of coral bleaching may be the result of the distribution of bleaching-susceptible clones","volume":"121","author":"Edmunds","year":"1994","journal-title":"Mar Biol"},{"key":"2025122707061844500_ref84","doi-asserted-by":"publisher","first-page":"e70037","DOI":"10.1002\/ece3.70037","article-title":"Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype","volume":"14","author":"Chille","year":"2024","journal-title":"Ecology and Evolution"},{"key":"2025122707061844500_ref85","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.jembe.2009.03.011","article-title":"Response of two species of Indo-Pacific corals, Porites cylindrica and Stylophora pistillata, to short-term thermal stress: the host does matter in determining the tolerance of corals to bleaching","volume":"373","author":"Fitt","year":"2009","journal-title":"J Exp Mar Biol Ecol"},{"key":"2025122707061844500_ref86","doi-asserted-by":"publisher","first-page":"e110759","DOI":"10.1371\/journal.pone.0110759","article-title":"Genetic susceptibility, Colony size, and water temperature drive white-pox disease on the coral Acropora palmata","volume":"9","author":"Muller","year":"2014","journal-title":"PLoS One"},{"key":"2025122707061844500_ref87","doi-asserted-by":"publisher","first-page":"e35066","DOI":"10.7554\/eLife.35066","article-title":"Bleaching causes loss of disease resistance within the threatened coral species Acropora cervicornis","volume":"7","author":"Muller","journal-title":"eLife"},{"key":"2025122707061844500_ref88","doi-asserted-by":"publisher","first-page":"e0129841","DOI":"10.1371\/journal.pone.0129841","article-title":"Contrasting lesion dynamics of white syndrome among the scleractinian corals Porites spp","volume":"10","author":"Lozada-Misa","year":"2015","journal-title":"PLoS One"},{"key":"2025122707061844500_ref89","doi-asserted-by":"publisher","first-page":"575927","DOI":"10.3389\/fevo.2020.575927","article-title":"Deciphering coral disease dynamics: integrating host, microbiome, and the changing environment","volume":"8","author":"Vega Thurber","year":"2020","journal-title":"Front Ecol Evol"},{"key":"2025122707061844500_ref90","doi-asserted-by":"publisher","first-page":"20161938","DOI":"10.1098\/rspb.2016.1938","article-title":"Symbiodinium biogeography tracks environmental patterns rather than host genetics in a key Caribbean reef-builder","volume":"283","author":"Kennedy","year":"2016","journal-title":"Orbicella annularis Proc Biol Sci"},{"key":"2025122707061844500_ref91","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1080\/09670262.2015.1025857","article-title":"Symbiodinium necroappetens sp. nov. (Dinophyceae): an opportunist \u2018zooxanthella\u2019 found in bleached and diseased tissues of Caribbean reef corals","volume":"50","author":"LaJeunesse","year":"2015","journal-title":"Eur J Phycol"},{"key":"2025122707061844500_ref92","doi-asserted-by":"publisher","first-page":"711","DOI":"10.3390\/jmse9070711","article-title":"A review of marine viruses in coral ecosystem","volume":"9","author":"Ambalavanan","year":"2021","journal-title":"J Mar Sci Eng"},{"key":"2025122707061844500_ref93","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1038\/s41579-024-01015-3","article-title":"The coral microbiome in sickness, in health and in a changing world","volume":"22","author":"Voolstra","year":"2024","journal-title":"Nat Rev Microbiol"},{"key":"2025122707061844500_ref94","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.2217\/fmb.10.102","article-title":"Leptospira as an emerging pathogen: A review of its biology, pathogenesis and host immune responses","volume":"5","author":"Evangelista","year":"2010","journal-title":"Future Microbiol"},{"key":"2025122707061844500_ref95","doi-asserted-by":"publisher","first-page":"e0146636","DOI":"10.1371\/journal.pone.0146636","article-title":"Genetic signature of resistance to white band disease in the Caribbean staghorn coral Acropora cervicornis","volume":"11","author":"Libro","year":"2016","journal-title":"PLoS One"},{"key":"2025122707061844500_ref96","doi-asserted-by":"publisher","first-page":"e81821","DOI":"10.1371\/journal.pone.0081821","article-title":"RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease","volume":"8","author":"Libro","year":"2013","journal-title":"PLoS One"},{"key":"2025122707061844500_ref97","doi-asserted-by":"publisher","first-page":"341","DOI":"10.3389\/fmicb.2017.00341","article-title":"Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience","volume":"8","author":"Peixoto","year":"2017","journal-title":"Front Microbiol"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycaf226\/65572288\/ycaf226.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/5\/1\/ycaf226\/65572288\/ycaf226.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/5\/1\/ycaf226\/65572288\/ycaf226.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,27]],"date-time":"2025-12-27T12:06:25Z","timestamp":1766837185000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycaf226\/8346043"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1]]},"references-count":97,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,17]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycaf226","relation":{},"ISSN":["2730-6151"],"issn-type":[{"value":"2730-6151","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2025,1]]},"article-number":"ycaf226"}}