{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:03:23Z","timestamp":1790139803874,"version":"4.0.1"},"reference-count":51,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fujian Provincial Department of agriculture"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Fungi","JoF"],"abstract":"<jats:p>Flammulina filiformis is one of the most important commercially cultivated species, and the assessment of strain quality is of paramount importance. The analysis measured physiological-biochemical indicators, morphological indicators, combined non-targeted metabolomics, and microbiomics in F. filiformis strains of different ages. The results indicate that, as the culture age increased, ergosterol content and catalase (CAT) activity declined continuously. The morphology of the mycelia gradually deteriorated, and yield continued to decrease. The relative content of lipids and lipid-like molecules decreased overall, while the proportion of organic acids and their derivatives increased; the oxidative phosphorylation pathway continued to be significantly enriched. The richness and diversity of the mycelium-associated bacterial community in the mycelia decreased significantly, and the microbial community structure changed. The community was dominated by the genus Acinetobacter from 15 to 60 days, whereas the genus Serratia was predominant in 90 days group. Correlation analysis revealed that the core differential signature metabolites MG 14:1_0:0_0:0, aspartic acid-threonine-aspartamide, and nicotinamide adenine dinucleotide (NAD+) were significantly correlated with multiple physiological-biochemical indicators. N-arachidonyl glycine showed significant correlations with 21 core bacterial genera; the dominant genera Acinetobacter and Serratia exhibited strong correlations with membrane homeostasis, core indicators of oxidative damage, and signature metabolites. These results indicate that the mycelial vitality of F. filiformis remains good within the first 15 days of cultivation, with significant ageing occurring after 60 days. These findings provide a theoretical basis for optimizing fungal strain preservation techniques and regulating mycelial ageing.<\/jats:p>","DOI":"10.3390\/jof12090708","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T11:09:35Z","timestamp":1790075375000},"page":"708","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Physio-Morphological Assessment and Multi-Omics Analysis of Flammulina filiformis Mycelial Ageing"],"prefix":"10.3390","volume":"12","author":[{"given":"Keming","family":"Zhu","sequence":"first","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zenan","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waner","family":"Lv","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingjie","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiying","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoran","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengzhen","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"},{"name":"Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Ningde 352200, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1147-3343","authenticated-orcid":false,"given":"Shujing","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China"},{"name":"Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Ningde 352200, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Li, Z.Y., Wen, J., Jing, Z.H., Li, H., Huang, J.H., Yuan, C.J., Xian, L.J., Gao, L.L., Zhu, J., and Xie, B.G. (2023). Low temperature, mechanical wound, and exogenous salicylic acid (SA) can stimulate the SA signaling molecule as well as its downstream pathway and the formation of fruiting bodies in Flammulina filiformis. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1197498"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"laxf039","DOI":"10.1093\/jambio\/lxaf039","article-title":"Transcriptional analysis provides molecular insights into degeneration of the edible fungus Flammulina filiformis","volume":"136","author":"Wang","year":"2025","journal-title":"J. Appl. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Feng, L.D., Wang, L.J., Lei, Y.X., Li, J., and Zhao, F.Y. (2025). Molecular mechanism during mycelium subculture degeneration of Volvariella volvacea. J. Fungi, 11.","DOI":"10.3390\/jof11010007"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Zhao, F.Y., Liu, X.X., Chen, C., Cheng, Z.H., Wang, W.P., and Yun, J.M. (2022). Successive mycelial subculturing decreased lignocellulase activity and increased ROS accumulation in Volvariella volvacea. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.997485"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"He, H., Cao, Z.F., Wang, T., Tang, C.Y., Li, Y.L., and Li, X.Z. (2024). Metabolomics combined with physiology and transcriptomics reveal the response of Samsoniella hepiali to key metabolic pathways and Its degradation mechanism during subculture. Antioxidants, 13.","DOI":"10.3390\/antiox13070780"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Zhao, F.Y., Wang, Q.L., An, X.M., Tan, Q.F., Yun, J.M., and Zhang, Y.B. (2023). Oxidative damage from repeated tissue isolation for subculturing causes degeneration in Volvariella volvacea. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1210496"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Zhu, W.W., Hu, J.B., Chi, J.L., Li, Y., Yang, B., Hu, W.L., Chen, F., Xu, C., Chai, L.S., and Bao, Y.M. (2020). Label-free proteomics reveals the molecular mechanism of subculture induced strain degeneration and discovery of indicativeindex for degeneration in Pleurotus ostreatus. Molecules, 25.","DOI":"10.3390\/molecules25214920"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/s42770-019-00165-4","article-title":"The NADPH oxidase in Volvariella volvacea and its differential expression in response to mycelial ageing and mechanical injury","volume":"51","author":"Yan","year":"2020","journal-title":"Braz. J. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Gao, Q., Fan, Y.Y., Wei, S., Song, S., Guo, Y., Wang, S.X., Liu, Y., and Yan, D. (2023). Insights into the global transcriptome response of Lentinula edodes mycelia during aging. J. Fungi, 9.","DOI":"10.3390\/jof9030379"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1002\/jsfa.6027","article-title":"Changes in reactive oxygen species production and antioxidant enzyme activity of Agaricus bisporus harvested at different stages of maturity","volume":"93","author":"Liu","year":"2013","journal-title":"J. Sci. Food Agric."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1093\/mmy\/myv058","article-title":"Novel in vivo observations on double acting points of luliconazole on Trichophyton rubrum: An ultrastructural study","volume":"53","author":"Yamada","year":"2015","journal-title":"Med. Mycol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1042\/BST0391488","article-title":"Mitochondrial quality control in aging and lifespan control of the fungal aging model Podospora anserina","volume":"39","author":"Osiewacz","year":"2011","journal-title":"Biochem. Soc. Trans."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"16593","DOI":"10.1021\/acs.jafc.3c04398","article-title":"The tissue browning and concomitant toughening of yellow Flammulina filiformis stipes is caused by oxidative damage-mediated metabolic disorder and cell wall glycan remodeling","volume":"71","author":"Deng","year":"2023","journal-title":"J. Agric. Food Chem."},{"key":"ref_14","first-page":"775","article-title":"Transcriptome sequencing on six agaricus bisporus strains at four developmental stages","volume":"34","author":"Shi","year":"2019","journal-title":"Fujian J. Agric. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Krause, K., Jung, E.-M., Lindner, J., Hardiman, I., Poetschner, J., Madhavan, S., Matth\u00e4us, C., Kai, M., Menezes, R.C., and Popp, J. (2020). Response of the wood-decay fungus Schizophyllum commune to co-occurring microorganisms. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0232145"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Chen, L., Yan, M., Qian, X., Yang, Z., Xu, Y., Wang, T., Cao, J., and Sun, S. (2022). Bacterial community composition in the growth process of Pleurotus eryngii and growth-promoting abilities of isolated bacteria. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.787628"},{"key":"ref_17","first-page":"50","article-title":"Key technical points for the factory cultivation of Flammulina filiformis","volume":"41","author":"Liu","year":"2019","journal-title":"Edible Fungi"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.ab.2015.03.024","article-title":"An accurate and sensitive coomassie brilliant blue G-250-based assay for protein determination","volume":"480","author":"Grintzalis","year":"2015","journal-title":"Anal. Biochem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"102986","DOI":"10.1016\/j.algal.2023.102986","article-title":"An improved phenol-sulfuric acid method for the quantitative measurement of total carbohydrates in algal biomass","volume":"70","author":"Chen","year":"2023","journal-title":"Algal Res."},{"key":"ref_20","first-page":"1","article-title":"Rapid determination of 3 components with different polarities in medicinal mushrooms by multistepmatrix solid-phase dispersion and high-performance liquid chromatography analysis","volume":"16","author":"Qian","year":"2021","journal-title":"Nat. Prod. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/S0168-9452(99)00197-1","article-title":"Oxidative stress and some antioxidant systems in acid rain-treated bean plants: Protective role of exogenous polyamines","volume":"151","author":"Velikova","year":"2000","journal-title":"Plant Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"111995","DOI":"10.1016\/j.foodres.2022.111995","article-title":"Determination of amino acid content, fatty acid profiles, and phenolic compounds in non-conventional edible fruits of seven species of palm trees (Arecaceae) native to the southern half of South America","volume":"162","author":"Rodrigues","year":"2022","journal-title":"Food Res. Int."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Cao, J.X., Sun, M.J., Yu, M.M., Xu, Y.F., Xie, J.C., Zhang, H.R., Chen, J.Y., Xu, T., Qian, X., and Sun, S.J. (2023). Transcriptome analysis reveals the function of a g-protein \u03b1 subunit gene in the growth and development of Pleurotus eryngii. J. Fungi, 9.","DOI":"10.3390\/jof9010069"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1194\/jlr.S120001025","article-title":"Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures","volume":"61","author":"Liebisch","year":"2020","journal-title":"J. Lipid Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Salzberg","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: Highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/ismej.2011.119","article-title":"Using network analysis to explore co-occurrence patterns in soil microbial communities","volume":"6","author":"Bates","year":"2012","journal-title":"ISME J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e217","DOI":"10.1002\/imt2.217","article-title":"Majorbio cloud 2024: Update single-cell and multiomics workflows","volume":"3","author":"Han","year":"2024","journal-title":"iMeta"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chen, X., Zhang, Z., Liu, X., Cui, B., Miao, W., Cheng, W., and Zhao, F. (2019). Characteristics analysis reveals the progress of Volvariella volvacea mycelium subculture degeneration. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02045"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Rangsinth, P., Sharika, R., Pattarachotanant, N., Duangjan, C., Wongwan, C., Sillapachaiyaporn, C., Nilkhet, S., Wongsirojkul, N., Prasansuklab, A., and Tencomnao, T. (2023). Potential beneficial effects and pharmacological properties of ergosterol, a common bioactive compound in edible mushrooms. Foods, 12.","DOI":"10.3390\/foods12132529"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Wang, Q., Zhu, J., Wang, Y., Yun, J., Zhang, Y., and Zhao, F. (2024). Serine rejuvenated degenerated Volvariella volvacea by enhancing ROS scavenging ability and mitochondrial function. J. Fungi, 10.","DOI":"10.3390\/jof10080540"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/s12934-023-02213-z","article-title":"The transcription factor GCN4 contributes to maintaining intracellular amino acid contents under nitrogen-limiting conditions in the mushroom Ganoderma lucidum","volume":"22","author":"Lian","year":"2023","journal-title":"Microb. Cell Factories"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1111\/nph.19400","article-title":"Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis","volume":"242","author":"Plett","year":"2024","journal-title":"New Phytol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"62","DOI":"10.4014\/jmb.1904.04006","article-title":"Zygosaccharomyces rouxii combats salt stress by maintaining cell membrane structure and functionality","volume":"30","author":"Wang","year":"2020","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.4014\/jmb.1807.07002","article-title":"Nove approaches for efficient antifungal drug action","volume":"28","author":"Lee","year":"2018","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_38","first-page":"117","article-title":"Amendments of antioxidant enzyme status in different skeletal muscle fibers under age induced oxidative stress conditions with reference to exercise training","volume":"22","author":"Korivi","year":"2008","journal-title":"Asian J. Exp. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"9860841","DOI":"10.1155\/2017\/9860841","article-title":"Pro- and antioxidant functions of the peroxisome-mitochondria connection and its impact on aging and disease","volume":"2017","author":"Proft","year":"2017","journal-title":"Oxid. Med. Cell Longev."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"360438","DOI":"10.1155\/2014\/360438","article-title":"Lipid peroxidation: Production, metabolism, and signaling mechanisms of malondialdehyde and 4-Hydroxy-2-Nonenal","volume":"2014","author":"Ayala","year":"2014","journal-title":"Oxid. Med. Cell Longev."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Jov\u00e9, M., Mota-Martorell, N., Pradas, I., Mart\u00edn-Gari, M., Ayala, V., and Pamplona, R. (2020). The advanced lipoxidation end-product malondialdehyde-Lysine in aging and longevity. Antioxidants, 9.","DOI":"10.3390\/antiox9111132"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1007\/s10126-023-10223-6","article-title":"Effects of dietary cystine and tyrosine supplementation on melanin synthesis in the pacific oyster (Crassostrea gigas)","volume":"25","author":"Li","year":"2023","journal-title":"Mar. Biotechnol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1083\/jcb.119.2.301","article-title":"Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction","volume":"119","author":"Takeshige","year":"1992","journal-title":"J. Cell Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/s10522-022-09958-x","article-title":"The role of NAD and NAD precursors on longevity and lifespan modulation in the budding yeast, Saccharomyces cerevisiae","volume":"23","author":"Odoh","year":"2022","journal-title":"Biogerontology"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Champigny, C.M., Cormier, R.P.J., Simard, C.J., St-Coeur, P.D., Fortin, S., and Pichaud, N. (2018). Omega-3 monoacylglyceride effects on longevity, mitochondrial metabolism and oxidative stress: Insights from Drosophila melanogaster. Mar. Drugs, 16.","DOI":"10.20944\/preprints201810.0563.v1"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1039\/C8FO00997J","article-title":"A combination of monoacylglycerol crystalline network and hydrophilic antioxidants synergistically enhances the oxidative stability of gelled algae oil","volume":"10","author":"Wang","year":"2019","journal-title":"Food Funct."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1007\/s00253-022-11826-0","article-title":"Glutathione production by Saccharomyces cerevisiae: Current state and perspectives","volume":"106","author":"Santos","year":"2022","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Diepold, K., Bomans, K., Wiedmann, M., Zimmermann, B., Petzold, A., Schlothauer, T., Mueller, R., Moritz, B., Stracke, J.O., and M\u00f8lh\u00f8j, M. (2012). Simultaneous assessment of asp isomerization and asn deamidation in recombinant antibodies by LC-MS following incubation at elevated temperatures. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030295"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Sun, S., Li, F., Xu, X., Liu, Y., Kong, X., Chen, J., Liu, T., and Chen, L. (2020). Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus. BMC Microbiol., 20.","DOI":"10.1186\/s12866-020-01998-y"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1615\/IntJMedMushrooms.2017024388","article-title":"Evaluation of fatty acid composition and antioxidant activity of wild-growing mushrooms from southwest China","volume":"19","author":"Luo","year":"2017","journal-title":"Int. J. Med. Mushrooms"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Mueller, E.A., and Schlievert, P.M. (2015). Non-aqueous glycerol monolaurate gel exhibits antibacterial and anti-biofilm activity against Gram-positive and Gram-negative pathogens. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0120280"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/9\/708\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T04:20:19Z","timestamp":1790137219000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/9\/708"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":51,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["jof12090708"],"URL":"https:\/\/doi.org\/10.3390\/jof12090708","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,21]]}}}