{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T01:15:19Z","timestamp":1792113319192,"version":"4.4.0"},"reference-count":42,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002888","name":"R&D Program of Beijing Municipal Education Commission","doi-asserted-by":"publisher","award":["KM202310011004"],"award-info":[{"award-number":["KM202310011004"]}],"id":[{"id":"10.13039\/501100002888","id-type":"DOI","asserted-by":"publisher"}]},{"award":["KM202310011004"],"award-info":[{"award-number":["KM202310011004"]}],"id":[{"id":"https:\/\/ror.org\/04bpn6s66","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["52300027"],"award-info":[{"award-number":["52300027"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["52300027"],"award-info":[{"award-number":["52300027"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Strawberry preservation remains a critical challenge due to rapid postharvest microbial spoilage. This study investigated the preservative efficacy of Cinnamomum cassia and Punica granatum peel aqueous extracts, prepared via spray drying, on strawberries over 5 days of storage, with a specific focus on their regulatory impact on the fruit surface microbiome. Preservation tests demonstrated that the C. cassia extract was more effective in reducing visible mold development. High-throughput sequencing revealed that the C. cassia treatment reshaped microbial community structures, decreasing the relative abundance of spoilage-associated bacteria and the primary pathogenic fungus Botrytis (94.37%), while enriching potentially beneficial or antagonistic genera such as Sphingobium (28.72%), Sphingomonas (9.52%), and Cladosporium (0.62%). Using a probability threshold of 0.7, 121 compounds were identified as potential active candidates from a library of 675 C. cassia constituents. These compounds predominantly have a molecular weight between 100 and 250 and are characterized by prevalent functional groups including alkene (49.60%), hydroxyl (38.80%), and benzene rings (36.40%). In vitro antibacterial assays confirmed the inhibitory activity of vanillin and its isomers, validating the reliability of the computational predictions. These findings suggest that the preservative mechanism of C. cassia is likely mediated by the collective action of a multi-component matrix that modulates the microecological balance on the fruit surface, rather than the isolated effect of a single compound. This integrated approach provides an effective framework for developing plant-derived preservation strategies by combining microbiome dynamics with machine learning.<\/jats:p>","DOI":"10.3390\/foods15112005","type":"journal-article","created":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T07:36:28Z","timestamp":1780558588000},"page":"2005","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Deep Learning and Microbiome Analysis Reveal the Preservation Mechanism of Cinnamomum cassia for Strawberry"],"prefix":"10.3390","volume":"15","author":[{"given":"Shanxue","family":"Jiang","sequence":"first","affiliation":[{"name":"School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haishu","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihan","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"117442","DOI":"10.1016\/j.lwt.2025.117442","article-title":"Development of Predictive Models for Shelf-Life of Sweet Cherry under Different Storage Temperatures","volume":"217","author":"Xing","year":"2025","journal-title":"LWT"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"115895","DOI":"10.1016\/j.foodres.2025.115895","article-title":"Comprehensive Characterization of Biodegradable Edible Films Activated with Rose and Marigold Extracts and Application of Active Edible Coatings to Extend the Postharvest Storage Life of Guava","volume":"203","author":"Lekshmi","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1038\/s43016-022-00523-w","article-title":"High-Throughput Coating with Biodegradable Antimicrobial Pullulan Fibres Extends Shelf Life and Reduces Weight Loss in an Avocado Model","volume":"3","author":"Chang","year":"2022","journal-title":"Nat. Food"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"101026","DOI":"10.1016\/j.fpsl.2023.101026","article-title":"Cinnamon: An Antimicrobial Ingredient for Active Packaging","volume":"35","author":"Yilmaz","year":"2023","journal-title":"Food Packag. Shelf Life"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"101416","DOI":"10.1016\/j.fochx.2024.101416","article-title":"Recent Advances in Characterizing the Physical and Functional Properties of Active Packaging Films Containing Pomegranate Peel","volume":"22","author":"Soleimanzadeh","year":"2024","journal-title":"Food Chem. X"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"132312","DOI":"10.1016\/j.foodchem.2022.132312","article-title":"Antimicrobial Mechanisms of Spice Essential Oils and Application in Food Industry","volume":"382","author":"Li","year":"2022","journal-title":"Food Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"100262","DOI":"10.1016\/j.prmcm.2023.100262","article-title":"Antifungal Natural Products and Their Derivatives: A Review of Their Activity and Mechanism of Actions","volume":"7","author":"Zhang","year":"2023","journal-title":"Pharmacol. Res. Mod. Chin. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"100924","DOI":"10.1016\/j.fpsl.2022.100924","article-title":"Botanic Antimicrobial Agents, Their Antioxidant Properties, Application and Safety Issue","volume":"34","author":"Myint","year":"2022","journal-title":"Food Packag. Shelf Life"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"120125","DOI":"10.1016\/j.indcrop.2024.120125","article-title":"Purification of Bioactive Compounds from Rosemary By-Products for Innovative Solutions in Food Industry","volume":"223","author":"Ziani","year":"2025","journal-title":"Ind. Crops Prod."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"103377","DOI":"10.1016\/j.fochx.2025.103377","article-title":"Antimicrobial EU@Ag-MOF\/PLA Composite Films Enhance Postharvest Quality of Strawberries by Mitigating Oxidative Stress and Modulating Microbial Communities","volume":"32","author":"Qin","year":"2025","journal-title":"Food Chem. 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Technol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"102849","DOI":"10.1016\/j.fochx.2025.102849","article-title":"Biological Control of Postharvest Spoilage and Diseases in Apples Caused by Pathogens, Using Plant Extracts in Collaboration with a Chitosan-Based Coating","volume":"29","author":"Shokri","year":"2025","journal-title":"Food Chem. X"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1093\/femsre\/fuy008","article-title":"Bacterial\u2013Fungal Interactions: Ecology, Mechanisms and Challenges","volume":"42","author":"Deveau","year":"2018","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/s41592-024-02503-3","article-title":"Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning","volume":"22","author":"Chitra","year":"2025","journal-title":"Nat. Methods"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/s42256-024-00966-9","article-title":"A Unified Evolution-Driven Deep Learning Framework for Virus Variation Driver Prediction","volume":"7","author":"Nie","year":"2025","journal-title":"Nat. Mach. Intell."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s41564-024-01907-3","article-title":"Explainable Deep Learning and Virtual Evolution Identifies Antimicrobial Peptides with Activity against Multidrug-Resistant Human Pathogens","volume":"10","author":"Wang","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/s41586-023-06887-8","article-title":"Discovery of a Structural Class of Antibiotics with Explainable Deep Learning","volume":"626","author":"Wong","year":"2024","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"118842","DOI":"10.1016\/j.indcrop.2024.118842","article-title":"Galla chinensis Extract Based Membranes with Effective Antibacterial Performance","volume":"217","author":"Jiang","year":"2024","journal-title":"Ind. Crops Prod."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"141643","DOI":"10.1016\/j.foodchem.2024.141643","article-title":"Biodegradable Antimicrobial Films Prepared in a Continuous Way by Melt Extrusion Using Plant Extracts as Effective Components","volume":"464","author":"Jiang","year":"2025","journal-title":"Food Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"144246","DOI":"10.1016\/j.foodchem.2025.144246","article-title":"Unraveling the Antimicrobial Performance and Mechanisms of Syzygium aromaticum and Myristica fragrans Extracts-Based Coatings in Strawberries Storage","volume":"483","author":"Sun","year":"2025","journal-title":"Food Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1111\/jfpp.12584","article-title":"Optimization of Phosphate and Anionic Polyacrylamide Flocculant (APF) Level for Sugar Cane Juice Clarification Using Central Composite Design","volume":"40","author":"Mohammed","year":"2016","journal-title":"J. Food Process. Preserv."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"119157","DOI":"10.1016\/j.lwt.2026.119157","article-title":"An Integrated Experimental and Deep Learning Modeling Approach to Harness Plant-Derived Antimicrobials for Biodegradable Food Packaging Films","volume":"243","author":"Jiang","year":"2026","journal-title":"LWT"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"117222","DOI":"10.1016\/j.foodres.2025.117222","article-title":"Unraveling the Spoilage Characteristics and Mechanism of Bacillus spizizenii in Spiced Beef: Insights from in-Situ and Metabolomics Analysis","volume":"221","author":"Pan","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"101622","DOI":"10.1016\/j.fpsl.2025.101622","article-title":"New Insights into the Growth Characteristics, Bacterial Interaction and Spoilage Contribution of Pseudomonas Species in Vacuum Skin Packaged Beef","volume":"52","author":"Yang","year":"2025","journal-title":"Food Packag. Shelf Life"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1111\/j.1364-3703.2009.00542.x","article-title":"Pantoea ananatis: An Unconventional Plant Pathogen","volume":"10","author":"Coutinho","year":"2009","journal-title":"Mol. Plant Pathol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.resmic.2016.10.003","article-title":"Spore-Forming Bacteria Responsible for Food Spoilage","volume":"168","author":"Vallaeys","year":"2017","journal-title":"Res. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e00599-23","DOI":"10.1128\/mbio.00599-23","article-title":"Tomato Root-Associated Sphingobium Harbors Genes for Catabolizing Toxic Steroidal Glycoalkaloids","volume":"14","author":"Nakayasu","year":"2023","journal-title":"mBio"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Luo, Y., Wang, F., Huang, Y., Zhou, M., Gao, J., Yan, T., Sheng, H., and An, L. (2019). Sphingomonas Sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana under Drought Stress. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01221"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3122","DOI":"10.1080\/14786419.2022.2142220","article-title":"Control of Fungal Spoilage in Strawberries Using Crude Plant Extracts against the Fungus Botrytis cinerea","volume":"37","year":"2023","journal-title":"Nat. Prod. Res."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Fang, Y., Wang, J., Qin, Y., Li, Y., Lu, K., Wu, W., and Zhang, M. (J. Futur. Foods, 2025). Inhibition Effect of Graphene Quantum Dots against Alternaria alternate and Botrytis cinerea and Their Potential Application in Strawberry Preservation, J. Futur. Foods, in press.","DOI":"10.1016\/j.jfutfo.2025.02.014"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Jiang, L., Lee, M.H., Kim, C.Y., Kim, S.W., Kim, P.I., Min, S.R., and Lee, J. (2021). Plant Growth Promotion by Two Volatile Organic Compounds Emitted From the Fungus Cladosporium halotolerans NGPF1. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.794349"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"103715","DOI":"10.1016\/j.fm.2020.103715","article-title":"Spoilage Potential of Bacillus subtilis in a Neutral-PH Dairy Dessert","volume":"95","author":"Moschonas","year":"2021","journal-title":"Food Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"106280","DOI":"10.1016\/j.idairyj.2025.106280","article-title":"High Spoilage Potential and Multidrug Resistance of P. aeruginosa Strains Isolated from Sheep Milk","volume":"167","author":"Bruzaroski","year":"2025","journal-title":"Int. Dairy J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1002\/jsfa.9357","article-title":"Plant Antimicrobial Polyphenols as Potential Natural Food Preservatives","volume":"99","author":"Degraeve","year":"2019","journal-title":"J. Sci. Food Agric."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"115132","DOI":"10.1016\/j.foodres.2024.115132","article-title":"Synergistic Antimicrobial Action of Chlorogenic Acid and Ultraviolet-A (365 Nm) Irradiation; Mechanisms and Effects on DNA Integrity","volume":"196","author":"Kang","year":"2024","journal-title":"Food Res. Int."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"251","DOI":"10.3390\/medicines2030251","article-title":"Modes of Action of Herbal Medicines and Plant Secondary Metabolites","volume":"2","author":"Wink","year":"2015","journal-title":"Medicines"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0168-1605(02)00233-7","article-title":"Food Spoilage\u2014Interactions between Food Spoilage Bacteria","volume":"78","author":"Gram","year":"2002","journal-title":"Int. J. Food Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1039\/C9NP00011A","article-title":"Synergy and Antagonism in Natural Product Extracts: When 1 + 1 Does Not Equal 2","volume":"36","author":"Caesar","year":"2019","journal-title":"Nat. Prod. Rep."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Hyldgaard, M., Mygind, T., and Meyer, R.L. (2012). Essential Oils in Food Preservation: Mode of Action, Synergies, and Interactions with Food Matrix Components. Front. Microbiol., 3.","DOI":"10.3389\/fmicb.2012.00012"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.ijfoodmicro.2004.03.022","article-title":"Essential Oils: Their Antibacterial Properties and Potential Applications in Foods\u2014A Review","volume":"94","author":"Burt","year":"2004","journal-title":"Int. J. Food Microbiol."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/11\/2005\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T07:59:30Z","timestamp":1780559970000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/11\/2005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,4]]},"references-count":42,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["foods15112005"],"URL":"https:\/\/doi.org\/10.3390\/foods15112005","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,4]]}}}