{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T16:40:20Z","timestamp":1792600820829,"version":"4.5.0"},"reference-count":106,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":273,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Stony coral tissue loss disease (SCTLD) is widespread within the Caribbean and affects at least 22 species of reef-building coral. Bacteria have been implicated in the etiology of SCTLD, but the community of bacteria and archaea may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to SCTLD resistance, we sequenced metagenomes from 41 colonies of the threatened coral, Orbicella faveolata, in the lower Florida Keys. All colonies were fate-tracked for 4 to 5 years, treated with amoxicillin if needed to prevent SCTLD-related mortality, and categorized into 4 health status categories following the monitoring period: never diseased (20%), diseased before sampling but recovered (10%), apparently healthy during sampling but eventually diseased (22%), and diseased (49%). Within the coral microbiome, diseased and yet-to-be diseased colonies exhibited higher variability in functional genes. In contrast, corals that remained unaffected or recovered had less variable microbiomes with greater abundances of vitamin and antibiotic biosynthesis, secretion system, and quorum-sensing genes that may support host health and resilience to pathogens. Despite repeated antibiotic treatments on some colonies, there was no effect on the diversity of beta-lactamases, antibiotic resistance genes that may confer amoxicillin resistance. Additional potentially probiotic gene clusters for the production of antimicrobial and bioactive compounds were present in many colonies regardless of fate. Taken together, we find significant putative probiotic functions in the coral microbiome to armor host O. faveolata corals against SCTLD infection, which may underpin intraspecific variation in stony coral tissue loss disease resilience and susceptibility.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag278","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T12:01:33Z","timestamp":1790769693000},"source":"Crossref","is-referenced-by-count":0,"title":["Markers of resilience to stony coral tissue loss disease and putative probiotic functions in the microbiomes of the coral,\n                    <i>Orbicella faveolata<\/i>"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7174-2306","authenticated-orcid":false,"given":"Cynthia C","family":"Becker","sequence":"first","affiliation":[{"name":"Department of Soil, Water, and Ecosystem Sciences, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida , Gainesville, FL 32611,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6684-5765","authenticated-orcid":false,"given":"Allison R","family":"Cauvin","sequence":"additional","affiliation":[{"name":"School of Natural Resources and Environment, University of Florida , Gainesville, FL 32611,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0934-3256","authenticated-orcid":false,"given":"Karen L","family":"Neely","sequence":"additional","affiliation":[{"name":"National Coral Reef Institute, Nova Southeastern University , Ft. Lauderdale, FL 33328,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2216-7925","authenticated-orcid":false,"given":"Caroline E","family":"Dennison","sequence":"additional","affiliation":[{"name":"Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami , Miami, FL 33149,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7866-2587","authenticated-orcid":false,"given":"Andrew C","family":"Baker","sequence":"additional","affiliation":[{"name":"Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami , Miami, FL 33149,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8385-7066","authenticated-orcid":false,"given":"Brian K","family":"Walker","sequence":"additional","affiliation":[{"name":"National Coral Reef Institute, Nova Southeastern University , Ft. Lauderdale, FL 33328,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3382-3321","authenticated-orcid":false,"given":"Julie L","family":"Meyer","sequence":"additional","affiliation":[{"name":"Department of Soil, Water, and Ecosystem Sciences, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida , Gainesville, FL 32611,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"2026102111532699800_ref1","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":"2026102111532699800_ref2","doi-asserted-by":"publisher","first-page":"323","DOI":"10.3389\/fmars.2018.00323","article-title":"Impacts of a regional, multi-year, multi-species coral disease outbreak in Southeast Florida","volume":"5","author":"Walton","year":"2018","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref3","doi-asserted-by":"publisher","first-page":"31374","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":"2026102111532699800_ref4","doi-asserted-by":"publisher","first-page":"656515","DOI":"10.3389\/fmars.2021.656515","article-title":"Rapid population decline of the pillar coral Dendrogyra cylindrus along the Florida reef tract","volume":"8","author":"Neely","year":"2021","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref5","doi-asserted-by":"publisher","first-page":"1276400","DOI":"10.3389\/fmars.2023.1276400","article-title":"Stony coral tissue loss disease accelerated shifts in coral composition and declines in reef accretion potential in the Florida keys","volume":"10","author":"Toth","year":"2023","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref6","doi-asserted-by":"crossref","DOI":"10.3133\/tm19I1","volume-title":"Stony Coral Tissue Loss Disease (SCTLD) Case Definition for Wildlife","author":"Hawthorn","year":"2024"},{"key":"2026102111532699800_ref7","doi-asserted-by":"publisher","first-page":"e0241871","DOI":"10.1371\/journal.pone.0241871","article-title":"Evaluating the small-scale epidemiology of the stony-coral-tissue-loss-disease in the middle Florida keys","volume":"15","author":"Sharp","year":"2020","journal-title":"PLoS One"},{"key":"2026102111532699800_ref8","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.3389\/fmars.2021.675349","article-title":"Short- and long-term effectiveness of coral disease treatments","volume":"8","author":"Neely","year":"2021","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref9","doi-asserted-by":"publisher","first-page":"1649646","DOI":"10.3389\/fmars.2025.1649646","article-title":"Survival and reinfection rates of SCTLD-affected corals treated in situ with amoxicillin","volume":"12","author":"Neely","year":"2025","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3354\/meps243001","article-title":"Diversity and distribution of coral-associated bacteria","volume":"243","author":"Rohwer","year":"2002","journal-title":"Mar Ecol Prog Ser"},{"key":"2026102111532699800_ref11","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":"2026102111532699800_ref12","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3389\/fmars.2017.00009","article-title":"On the importance of the microbiome and pathobiome in coral health and disease","volume":"4","author":"Sweet","year":"2017","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref13","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1016\/j.tim.2015.03.008","article-title":"Nitrogen cycling in corals: the key to understanding holobiont functioning?","volume":"23","author":"R\u00e4decker","year":"2015","journal-title":"Trends Microbiol"},{"key":"2026102111532699800_ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3755\/galaxea.11.1","article-title":"Coral symbiotic complex: hypothesis through vitamin B12 for a new evaluation","volume":"11","author":"Agostini","year":"2009","journal-title":"Galaxea (Tokyo)"},{"key":"2026102111532699800_ref15","doi-asserted-by":"publisher","first-page":"1","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":"2026102111532699800_ref16","doi-asserted-by":"publisher","first-page":"113286","DOI":"10.1016\/j.isci.2025.113286","article-title":"A coral peptide with bactericidal activity against a global marine pathogen, vibrio coralliilyticus","volume":"28","author":"Aoyama","year":"2025","journal-title":"iScience"},{"key":"2026102111532699800_ref17","doi-asserted-by":"publisher","first-page":"618","DOI":"10.3389\/fmicb.2017.00618","article-title":"Comparative metagenomics of the polymicrobial black band disease of corals","volume":"8","author":"Meyer","year":"2017","journal-title":"Front Microbiol"},{"key":"2026102111532699800_ref18","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1111\/j.1462-2920.2012.02746.x","article-title":"Ciliate and bacterial communities associated with white syndrome and brown band disease in reef-building corals","volume":"14","author":"Sweet","year":"2012","journal-title":"Environ Microbiol"},{"key":"2026102111532699800_ref19","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1111\/1462-2920.15718","article-title":"Microbial bioindicators of stony coral tissue loss disease identified in corals and overlying waters using a rapid field-based sequencing approach","volume":"24","author":"Becker","year":"2022","journal-title":"Environ Microbiol"},{"key":"2026102111532699800_ref20","doi-asserted-by":"crossref","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":"2026102111532699800_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":"2026102111532699800_ref22","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 Commun"},{"key":"2026102111532699800_ref23","doi-asserted-by":"publisher","first-page":"1","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 Commun"},{"key":"2026102111532699800_ref24","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":"2026102111532699800_ref25","doi-asserted-by":"publisher","first-page":"569354","DOI":"10.3389\/fmicb.2020.569354","article-title":"Disease diagnostics and potential coinfections by Vibrio coralliilyticus during an ongoing coral disease outbreak in Florida","volume":"11","author":"Ushijima","year":"2020","journal-title":"Front Microbiol"},{"key":"2026102111532699800_ref26","doi-asserted-by":"publisher","first-page":"2393","DOI":"10.1002\/ece3.642","article-title":"Nutrient cycling in early coral life stages: Pocillopora damicornis larvae provide their algal symbiont (Symbiodinium) with nitrogen acquired from bacterial associates","volume":"3","author":"Ceh","year":"2013","journal-title":"Ecol Evol"},{"key":"2026102111532699800_ref27","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.syapm.2011.09.001","article-title":"Multilocus sequence analysis provides basis for fast and reliable identification of Vibrio harveyi-related species and reveals previous misidentification of important marine pathogens","volume":"34","author":"Cano-Gomez","year":"2011","journal-title":"Syst Appl Microbiol"},{"key":"2026102111532699800_ref28","doi-asserted-by":"publisher","first-page":"9908","DOI":"10.1038\/s41598-024-60505-9","article-title":"Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species","volume":"14","author":"Leunda-Esnaola","year":"2024","journal-title":"Sci Rep"},{"key":"2026102111532699800_ref29","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":"2026102111532699800_ref30","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":"2026102111532699800_ref31","doi-asserted-by":"publisher","first-page":"ycaf226","DOI":"10.1093\/ismeco\/ycaf226","article-title":"Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD)","volume":"5","author":"Nandi","year":"2025","journal-title":"ISME Commun"},{"key":"2026102111532699800_ref32","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1186\/s40168-022-01382-0","article-title":"Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species","volume":"10","author":"McIlroy","year":"2022","journal-title":"Microbiome"},{"key":"2026102111532699800_ref33","doi-asserted-by":"publisher","first-page":"422","DOI":"10.3389\/fmicb.2014.00422","article-title":"The engine of the reef: photobiology of the coral-algal symbiosis","volume":"5","author":"Roth","year":"2014","journal-title":"Front Microbiol"},{"key":"2026102111532699800_ref34","doi-asserted-by":"publisher","first-page":"1090","DOI":"10.3389\/fmars.2020.576013","article-title":"Stony coral tissue loss disease in Florida is associated with disruption of host\u2013zooxanthellae physiology","volume":"7","author":"Landsberg","year":"2020","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref35","doi-asserted-by":"publisher","first-page":"1128","DOI":"10.3389\/fmars.2020.597643","article-title":"3D photogrammetry reveals dynamics of stony coral tissue loss disease (SCTLD) lesion progression across a thermal stress event","volume":"7","author":"Meiling","year":"2020","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref36","doi-asserted-by":"publisher","first-page":"422","DOI":"10.3389\/fmars.2021.631776","article-title":"Fine scale temporal and spatial dynamics of the stony coral tissue loss disease outbreak within the lower Florida keys","volume":"8","author":"Williams","year":"2021","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref37","doi-asserted-by":"publisher","first-page":"22261","DOI":"10.1038\/s41598-025-06322-0","article-title":"Elevated temperature decreases stony coral tissue loss disease transmission, with little effect of nutrients","volume":"15","author":"Palacio-Castro","year":"2025","journal-title":"Sci Rep"},{"key":"2026102111532699800_ref38","article-title":"The role of algal symbionts (genus Breviolum) in the susceptibility of corals to stony coral tissue loss disease in South Florida","author":"Dennison"},{"key":"2026102111532699800_ref39","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":"2026102111532699800_ref40","article-title":"SCTLD resistance research consortium summary report through May 2023","author":"Walker BK"},{"key":"2026102111532699800_ref41","doi-asserted-by":"publisher","first-page":"1287457","DOI":"10.3389\/fmars.2024.1287457","article-title":"Algal symbiont genera but not coral host genotypes correlate to stony coral tissue loss disease susceptibility among Orbicella faveolata colonies in South Florida","volume":"11","author":"Klein","year":"2024","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref42","doi-asserted-by":"publisher","first-page":"20141725","DOI":"10.1098\/rspb.2014.1725","article-title":"Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change","volume":"282","author":"Cunning","year":"2015","journal-title":"Proc Biol Sci"},{"key":"2026102111532699800_ref43","volume-title":"Lophelia Metagenome Extraction Protocol","author":"Galkiewicz","year":"2019"},{"key":"2026102111532699800_ref44","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026102111532699800_ref45","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":"2026102111532699800_ref46","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":"2026102111532699800_ref47","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2026102111532699800_ref48","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1101\/gr.228429.117","article-title":"Genome-reconstruction for eukaryotes from complex natural microbial communities","volume":"28","author":"West","year":"2018","journal-title":"Genome Res"},{"key":"2026102111532699800_ref49","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2026102111532699800_ref50","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026102111532699800_ref51","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":"2026102111532699800_ref52","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"key":"2026102111532699800_ref53","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026102111532699800_ref54","doi-asserted-by":"publisher","first-page":"btaf147","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"CoverM: read alignment statistics for metagenomics","volume":"41","author":"Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"2026102111532699800_ref55","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":"2026102111532699800_ref56","first-page":"125031","author":"Oksanen J","year":"2024"},{"key":"2026102111532699800_ref57","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1214\/19-aoas1283","article-title":"Modeling microbial abundances and dysbiosis with beta-binomial regression","volume":"14","author":"Martin","year":"2020","journal-title":"Ann Appl Stat"},{"key":"2026102111532699800_ref58","doi-asserted-by":"publisher","volume-title":"KEGGREST: Client-Side REST Access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)","author":"Tenenbaum","DOI":"10.18129\/B9.bioc.KEGGREST"},{"key":"2026102111532699800_ref59","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1111\/biom.12332","article-title":"Estimating diversity via frequency ratios: estimating diversity via ratios","volume":"71","author":"Willis","year":"2015","journal-title":"Biometrics"},{"key":"2026102111532699800_ref60","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1111\/rssc.12206","article-title":"Improved detection of changes in species richness in high diversity microbial communities","volume":"66","author":"Willis","year":"2017","journal-title":"J R Stat Soc Ser C Appl Stat"},{"key":"2026102111532699800_ref61","doi-asserted-by":"publisher","first-page":"17121","DOI":"10.1038\/nmicrobiol.2017.121","article-title":"Stress and stability: applying the Anna Karenina principle to animal microbiomes","volume":"2","author":"Zaneveld","year":"2017","journal-title":"Nat Microbiol"},{"key":"2026102111532699800_ref62","doi-asserted-by":"publisher","first-page":"100606","DOI":"10.1016\/j.crsus.2025.100606","article-title":"Longitudinal microbiomes of coral and near-coral seawater are influenced by disease phase","volume":"3","author":"Bloomberg","year":"2026","journal-title":"Cell Rep Sustain"},{"key":"2026102111532699800_ref63","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.3390\/microorganisms12051005","article-title":"Pre-bleaching coral microbiome is enriched in beneficial taxa and functions","volume":"12","author":"Lima","year":"2024","journal-title":"Microorganisms"},{"key":"2026102111532699800_ref64","doi-asserted-by":"publisher","first-page":"2477","DOI":"10.1111\/mec.15494","article-title":"Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance","volume":"29","author":"Claar","year":"2020","journal-title":"Mol Ecol"},{"key":"2026102111532699800_ref65","doi-asserted-by":"crossref","first-page":"24319","DOI":"10.1038\/s41598-024-70121-2","article-title":"Bacterial and Symbiodiniaceae communities\u2019 variation in corals with distinct traits and geographical distribution","volume":"14","author":"Villela","year":"2024","journal-title":"Sci Rep"},{"key":"2026102111532699800_ref66","doi-asserted-by":"publisher","first-page":"wraf189","DOI":"10.1093\/ismejo\/wraf189","article-title":"Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host","volume":"19","author":"McCauley","year":"2025","journal-title":"ISME J"},{"key":"2026102111532699800_ref67","doi-asserted-by":"publisher","first-page":"e0032722","DOI":"10.1128\/msystems.00327-22","article-title":"Cultured bacteria provide insight into the functional potential of the coral-associated microbiome","volume":"7","author":"Li","year":"2022","journal-title":"mSystems"},{"key":"2026102111532699800_ref68","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1007\/s44289-025-00110-4","article-title":"Symbiodiniaceae-Roseibium exhibit synergistic growth effects without B12 supplementation","volume":"2","author":"Aguirre","year":"2025","journal-title":"Discov Ocean"},{"key":"2026102111532699800_ref69","doi-asserted-by":"publisher","first-page":"e0114324","DOI":"10.1128\/aem.01143-24","article-title":"Quorum sensing regulates virulence factors in the coral pathogen Vibrio coralliilyticus","volume":"91","author":"Lydick","year":"2025","journal-title":"Appl Environ Microbiol"},{"key":"2026102111532699800_ref70","doi-asserted-by":"publisher","first-page":"117221","DOI":"10.1016\/j.envres.2023.117221","article-title":"Interactions between quorum sensing\/quorum quenching and virulence genes may affect coral health by regulating symbiotic bacterial community","volume":"238","author":"Xu","year":"2023","journal-title":"Environ Res"},{"key":"2026102111532699800_ref71","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1007\/978-3-319-15630-9_4","volume-title":"Molecular and Integrative Toxicology","author":"Engin","year":"2015"},{"key":"2026102111532699800_ref72","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/s43705-022-00184-7","article-title":"Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs","volume":"2","author":"Weber","year":"2022","journal-title":"ISME Commun"},{"key":"2026102111532699800_ref73","doi-asserted-by":"publisher","first-page":"1764","DOI":"10.1038\/ismej.2014.261","article-title":"Chemotaxis by natural populations of coral reef bacteria","volume":"9","author":"Tout","year":"2015","journal-title":"ISME J"},{"key":"2026102111532699800_ref74","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.3390\/microorganisms10071349","article-title":"Marine Actinomycetes associated with stony corals: a potential hotspot for specialized metabolites","volume":"10","author":"Siro","year":"2022","journal-title":"Microorganisms"},{"key":"2026102111532699800_ref75","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1038\/s42003-018-0189-1","article-title":"Coral metabolite gradients affect microbial community structures and act as a disease cue","volume":"1","author":"Ochsenk\u00fchn","year":"2018","journal-title":"Commun Biol"},{"key":"2026102111532699800_ref76","doi-asserted-by":"publisher","first-page":"14987","DOI":"10.1038\/s41598-026-44748-2","article-title":"Frequent coral disease interventions reduces tissue loss","volume":"16","author":"Kozachuk","year":"2026","journal-title":"Sci Rep"},{"key":"2026102111532699800_ref77","doi-asserted-by":"publisher","first-page":"859740","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":"2026102111532699800_ref78","doi-asserted-by":"publisher","first-page":"1302697","DOI":"10.3389\/fmars.2023.1302697","article-title":"Broadscale coral disease interventions elicit efficiencies in endemic disease response","volume":"10","author":"Toth","year":"2024","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref79","doi-asserted-by":"publisher","first-page":"746","DOI":"10.3389\/fmars.2021.666224","article-title":"Optimizing stony coral tissue loss disease (SCTLD) intervention treatments on Montastraea cavernosa in an endemic zone","volume":"8","author":"Walker","year":"2021","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref80","doi-asserted-by":"publisher","first-page":"883062","DOI":"10.3389\/fmars.2022.883062","article-title":"Management responses in Belize and Honduras, as stony coral tissue loss disease expands its prevalence in the Mesoamerican reef","volume":"9","author":"Lee Hing","year":"2022","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref81","volume-title":"Amoxicillin Occurrence and Toxicity in the Aquatic Environment and Mechanisms of Resistance: A Review","author":"Salda\u00f1a","year":"2024"},{"key":"2026102111532699800_ref82","doi-asserted-by":"publisher","first-page":"1460163","DOI":"10.3389\/fmars.2024.1460163","article-title":"The effects of disease lesions and amoxicillin treatment on the physiology of SCTLD-affected corals","volume":"11","author":"Neely","year":"2024","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref83","doi-asserted-by":"publisher","first-page":"1369222","DOI":"10.3389\/fmars.2024.1369222","article-title":"Southeast Florida large Orbicella faveolata are highly fecund without evident disease intervention effects","volume":"11","author":"Renegar","year":"2024","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref84","doi-asserted-by":"publisher","first-page":"1445735","DOI":"10.3389\/fmars.2024.1445735","article-title":"The impact of stony coral tissue loss disease and amoxicillin treatments on coral gametogenesis","volume":"11","author":"Mazurek","year":"2025","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref85","doi-asserted-by":"publisher","first-page":"5394","DOI":"10.1111\/mec.17110","article-title":"Stony coral tissue loss disease intervention with amoxicillin leads to a reversal of disease-modulated gene expression pathways","volume":"32","author":"Studivan","year":"2023","journal-title":"Mol Ecol"},{"key":"2026102111532699800_ref86","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1007\/s00338-026-02832-z","article-title":"Assessment of antimicrobial resistance genes in Caribbean corals, including those treated with amoxicillin","volume":"45","author":"Neely","year":"2026","journal-title":"Coral Reefs"},{"key":"2026102111532699800_ref87","doi-asserted-by":"publisher","first-page":"xtaf004","DOI":"10.1093\/femsmc\/xtaf004","article-title":"Psychrotrophic Antarctic marine bacteria as potential reservoirs for novel antimicrobial genes","volume":"6","author":"Hwengwere","year":"2025","journal-title":"FEMS Microbes"},{"key":"2026102111532699800_ref88","doi-asserted-by":"publisher","first-page":"e2275","DOI":"10.7717\/peerj.2275","article-title":"Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals","volume":"4","author":"Raina","year":"2016","journal-title":"PeerJ"},{"key":"2026102111532699800_ref89","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1016\/j.tree.2009.02.008","article-title":"How feasible is the biological control of coral diseases?","volume":"24","author":"Teplitski","year":"2009","journal-title":"Trends Ecol Evol"},{"key":"2026102111532699800_ref90","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3354\/meps322001","article-title":"Regulation of microbial populations by coral surface mucus and mucus-associated bacteria","volume":"322","author":"Ritchie","year":"2006","journal-title":"Mar Ecol Prog Ser"},{"key":"2026102111532699800_ref91","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1021\/acs.jnatprod.1c01110","article-title":"Metabolomics approaches to dereplicate natural products from coral-derived bioactive bacteria","volume":"85","author":"Deutsch","year":"2022","journal-title":"J Nat Prod"},{"key":"2026102111532699800_ref92","doi-asserted-by":"publisher","first-page":"1480966","DOI":"10.3389\/fmars.2025.1480966","article-title":"Evaluating the effectiveness of field-based probiotic treatments for stony coral tissue loss disease in Southeast Florida, USA","volume":"12","author":"Pitts","year":"2025","journal-title":"Front Mar Sci"},{"key":"2026102111532699800_ref93","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1021\/jo00085a006","article-title":"Structure of curacin A, a novel antimitotic, antiproliferative and brine shrimp toxic natural product from the marine Cyanobacterium Lyngbya majuscula","volume":"59","author":"Gerwick","year":"1994","journal-title":"J Org Chem"},{"key":"2026102111532699800_ref94","doi-asserted-by":"publisher","first-page":"6573","DOI":"10.1128\/AEM.01800-16","article-title":"Lack of overt genome reduction in the bryostatin-producing bryozoan symbiont \u2018Candidatus Endobugula sertula\u2019","volume":"82","author":"Miller","year":"2016","journal-title":"Appl Environ Microbiol"},{"key":"2026102111532699800_ref95","doi-asserted-by":"publisher","first-page":"237","DOI":"10.3109\/13880209.2013.804100","article-title":"Marine natural products: bryostatins in preclinical and clinical studies","volume":"52","author":"Koll\u00e1r","year":"2014","journal-title":"Pharm Biol"},{"key":"2026102111532699800_ref96","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1021\/np060361d","article-title":"Identification of the putative bryostatin polyketide synthase gene cluster from \u2018Candidatus Endobugula sertula\u2019, the uncultivated microbial symbiont of the marine bryozoan Bugula neritina","volume":"70","author":"Sudek","year":"2007","journal-title":"J Nat Prod"},{"key":"2026102111532699800_ref97","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1021\/ja045749e","article-title":"Polytheonamides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei","volume":"127","author":"Hamada","year":"2005","journal-title":"J Am Chem Soc"},{"key":"2026102111532699800_ref98","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature12959","article-title":"An environmental bacterial taxon with a large and distinct metabolic repertoire","volume":"506","author":"Wilson","year":"2014","journal-title":"Nature"},{"key":"2026102111532699800_ref99","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.cbpa.2015.11.002","article-title":"Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated \u2018Entotheonella\u2019 bacteria","volume":"31","author":"Freeman","year":"2016","journal-title":"Curr Opin Chem Biol"},{"key":"2026102111532699800_ref100","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1128\/AEM.02650-14","article-title":"Role of secondary metabolites in establishment of the mutualistic partnership between Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae","volume":"81","author":"Singh","year":"2015","journal-title":"Appl Environ Microbiol"},{"key":"2026102111532699800_ref101","doi-asserted-by":"publisher","first-page":"e0018521","DOI":"10.1128\/AEM.00185-21","article-title":"Toyoncin, a novel leaderless bacteriocin that is produced by Bacillus toyonensis Xin-YC13 and specifically targets B. cereus and Listeria monocytogenes","volume":"87","author":"Wang","year":"2021","journal-title":"Appl Environ Microbiol"},{"key":"2026102111532699800_ref102","doi-asserted-by":"publisher","first-page":"123","DOI":"10.7164\/antibiotics.56.123","article-title":"YM-266183 and YM-266184, novel thiopeptide antibiotics produced by Bacillus cereus isolated from a marine sponge. I. Taxonomy, fermentation, isolation, physico-chemical properties and biological properties","volume":"56","author":"Nagai","year":"2003","journal-title":"J Antibiot (Tokyo)"},{"key":"2026102111532699800_ref103","doi-asserted-by":"publisher","first-page":"2571","DOI":"10.1128\/AEM.00257-07","article-title":"A complex ergovaline gene cluster in Epichlo\u00eb endophytes of grasses","volume":"73","author":"Fleetwood","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"2026102111532699800_ref104","doi-asserted-by":"publisher","first-page":"3940","DOI":"10.1038\/s41467-018-06202-4","article-title":"Strobilurin biosynthesis in Basidiomycete fungi","volume":"9","author":"Nofiani","year":"2018","journal-title":"Nat Commun"},{"key":"2026102111532699800_ref105","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.3390\/microorganisms8071093","article-title":"New insight into antimicrobial compounds from food and marine-sourced Carnobacterium species through phenotype and genome analyses","volume":"8","author":"Begrem","year":"2020","journal-title":"Microorganisms"},{"key":"2026102111532699800_ref106","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1038\/s41396-018-0323-6","article-title":"Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation","volume":"13","author":"Rosado","year":"2019","journal-title":"ISME J"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycag278\/71560548\/ycag278.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag278\/71560548\/ycag278.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag278\/71560548\/ycag278.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T15:53:41Z","timestamp":1792598021000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag278\/8859178"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":106,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycag278","relation":{},"ISSN":["2730-6151"],"issn-type":[{"value":"2730-6151","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2026,1]]},"article-number":"ycag278"}}