{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T19:34:32Z","timestamp":1769801672137,"version":"3.49.0"},"reference-count":168,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:00:00Z","timestamp":1769558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FCT","award":["UIDB\/04035\/2025"],"award-info":[{"award-number":["UIDB\/04035\/2025"]}]},{"name":"Competitiveness and Internationalization Operational Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Fermentation"],"abstract":"<jats:p>The food industry generates large volumes of nutrient-rich by-products that remain underutilised despite their considerable biochemical potential. These materials originate predominantly from the fruit and vegetable, dairy, meat, and fish and seafood sectors and represent a substantial opportunity for sustainable valorisation. Fermentation has emerged as a powerful platform for converting such by-products into high-value ingredients, including bioactive compounds, functional metabolites, enzymes, antimicrobials, and nutritionally enriched fractions. This review synthesises recent advances in microbial fermentation strategies\u2014spanning lactic acid bacteria, filamentous fungi, yeasts, and mixed microbial consortia\u2014and highlights their capacity to enhance the bioavailability, stability, and functionality of recovered compounds across diverse substrate streams. Key technological enablers, including substrate pre-treatments, precision fermentation, omics-guided strain selection and improvement, and bioprocess optimisation, are examined within the broader framework of circular bioeconomy integration. Despite significant scientific progress, major challenges remain, particularly related to substrate heterogeneity, process scalability, regulatory alignment, safety assessment, and consumer acceptance. The review identifies critical research gaps and future directions, emphasising the need for standardised analytical frameworks, harmonised compositional databases, AI-driven fermentation control, integrated biorefinery concepts, and pilot-scale validation. Overall, the evidence indicates that integrated fermentation-based approaches\u2014especially those combining complementary by-product streams, tailored microbial consortia, and system-level process integration\u2014represent the most promising pathway toward the scalable, sustainable, and economically viable valorisation of food industry by-products.<\/jats:p>","DOI":"10.3390\/fermentation12020073","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T17:40:22Z","timestamp":1769622022000},"page":"73","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fermenting the Unused: Microbial Biotransformation of Food Industry By-Products for Circular Bioeconomy Valorisation"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5814-0490","authenticated-orcid":false,"given":"Elsa M.","family":"Gon\u00e7alves","sequence":"first","affiliation":[{"name":"UEISTSA\u2014Unidade Estrat\u00e9gica de Investiga\u00e7\u00e3o e Servi\u00e7os de Tecnologia e Seguran\u00e7a Alimentar, Instituto Nacional de Investiga\u00e7\u00e3o Veterin\u00e1ria e Agr\u00e1ria, Av. da Rep\u00fablica, Quinta do Marqu\u00eas, 2780-157 Oeiras, Portugal"},{"name":"GeoBiotec\u2014GeoBioTec Research Institute, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3772-8877","authenticated-orcid":false,"given":"Jos\u00e9 M.","family":"Pestana","sequence":"additional","affiliation":[{"name":"LEAF\u2014Linking Landscape, Environment, Agriculture and Food Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal"},{"name":"Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal"},{"name":"CiTUR\u2014Centro de Investiga\u00e7\u00e3o, Desenvolvimento e Inova\u00e7\u00e3o em Turismo\u2014Polo Estoril, Escola Superior de Hotelaria e Turismo do Estoril, Av. Condes de Barnecola N. 808, 2769-510 Estoril, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0625-0687","authenticated-orcid":false,"given":"Nuno","family":"Alvarenga","sequence":"additional","affiliation":[{"name":"UEISTSA\u2014Unidade Estrat\u00e9gica de Investiga\u00e7\u00e3o e Servi\u00e7os de Tecnologia e Seguran\u00e7a Alimentar, Instituto Nacional de Investiga\u00e7\u00e3o Veterin\u00e1ria e Agr\u00e1ria, Av. da Rep\u00fablica, Quinta do Marqu\u00eas, 2780-157 Oeiras, Portugal"},{"name":"GeoBiotec\u2014GeoBioTec Research Institute, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.wasman.2015.06.008","article-title":"Food Waste Generation and Industrial Uses: A Review","volume":"45","author":"Girotto","year":"2015","journal-title":"Waste Manag."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1021\/acsenvironau.2c00050","article-title":"A Review on the Challenges and Choices for Food Waste Valorization: Environmental and Economic Impacts","volume":"3","author":"Roy","year":"2023","journal-title":"ACS Environ. 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