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Microbiome-based approaches have attracted attention as a promising avenue to enhance the resilience and recovery of these organisms. Over the past decade, diverse marine probiotic microbes have been isolated and shown to positively influence key host life functions, including growth, development, reproduction, responses to environmental stressors, and pathogen defence. However, current research remains confined to laboratory settings, with few practical field applications tested or utilised, likely driven by practical and technological challenges and lacking communication between science and policy. To help close this gap, we propose a set of risk and success assessment criteria for microbiome-assisted restoration. This framework is built around four pillars: (1) ensuring environmental compatibility of candidate probiotics, (2) establishing scientific validation for their mechanisms of action, (3) securing legal clarity before application, and (4) implementing mandatory in situ monitoring to evaluate ecological outcomes. By integrating these pillars into a cycle of risk assessment, monitoring, and adaptive management, microbiome-assisted restoration could progress from an experimental concept to a practical application complementing existing conservation tools, strengthening the resilience of these ecosystems.<\/jats:p>","DOI":"10.1093\/femsre\/fuag044","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T14:22:52Z","timestamp":1787754172000},"source":"Crossref","is-referenced-by-count":0,"title":["From holobionts to habitats: opportunities and limitations of microbiome-assisted restoration strategies of marine ecosystem engineers"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-4032-6194","authenticated-orcid":false,"given":"Sofie","family":"Peeters","sequence":"first","affiliation":[{"name":"Phycology Research Group, Department of Biology, Ghent University , 9000 Ghent 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University of Wuppertal , 42119 Wuppertal ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Quiroga-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Zoological Department III, Natural History Museum Vienna , 1010 Vienna ,","place":["Austria"]},{"name":"University of Vienna Department of Functional and Evolutionary Ecology, , 1030 Vienna ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9579-9606","authenticated-orcid":false,"given":"Aschwin H","family":"Engelen","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias do Mar do Algarve (CCMAR\/CIMAR LA), Universidade do Algarve , 8005-139 Faro 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