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(2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p &lt; 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p &lt; 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p &lt; 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein\u2013protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function.<\/jats:p>","DOI":"10.3390\/ijms262311397","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T15:29:47Z","timestamp":1764084587000},"page":"11397","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Lacticaseibacillus rhamnosus MS27 Potentially Prevents Ulcerative Colitis Through Modulation of Gut Microbiota"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5010-0833","authenticated-orcid":false,"given":"Jie","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Public Health, North China University of Science and Technology, Tangshan 063210, China"},{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiakun","family":"Shen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linbao","family":"Ji","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Tan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4374-4867","authenticated-orcid":false,"given":"Chunchen","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Public Health, North China University of Science and Technology, Tangshan 063210, China"},{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiujun","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Public Health, North China University of Science and Technology, Tangshan 063210, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4562-9331","authenticated-orcid":false,"given":"Xi","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Public Health, North China University of Science and Technology, Tangshan 063210, China"},{"name":"State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/S0140-6736(12)60150-0","article-title":"Ulcerative colitis","volume":"380","author":"Eckmann","year":"2012","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1001\/jama.2023.23814","article-title":"What is ulcerative colitis?","volume":"331","author":"Voelker","year":"2024","journal-title":"JAMA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"69","DOI":"10.5217\/ir.2019.00084","article-title":"5-Aminosalicylic acid intolerance is associated with a risk of adverse clinical outcomes and dysbiosis in patients with ulcerative colitis","volume":"18","author":"Mizuno","year":"2020","journal-title":"Intest. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1159\/000527452","article-title":"Significance of 5-Aminosalicylic acid intolerance in the clinical management of ulcerative colitis","volume":"104","author":"Mikami","year":"2023","journal-title":"Digestion"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2088","DOI":"10.1002\/art.42646","article-title":"2022 American college of rheumatology guideline for the prevention and treatment of glucocorticoid-induced osteoporosis","volume":"75","author":"Humphrey","year":"2023","journal-title":"Arthritis Rheumatol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/S2468-1253(21)00062-5","article-title":"Discontinuation of infliximab in patients with ulcerative colitis in remission (HAYABUSA): A multicentre, open-label, randomised controlled trial","volume":"6","author":"Kobayashi","year":"2021","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1053\/j.gastro.2023.10.015","article-title":"AGA clinical practice guideline on the management of pouchitis and inflammatory pouch disorders","volume":"166","author":"Barnes","year":"2024","journal-title":"Gastroenterology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3748\/wjg.v24.i1.5","article-title":"Relationship between intestinal microbiota and ulcerative colitis: Mechanisms and clinical application of probiotics and fecal microbiota transplantation","volume":"24","author":"Shen","year":"2018","journal-title":"World J. Gastroenterol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2179","DOI":"10.4049\/jimmunol.2100102","article-title":"Lacticaseibacillus rhamnosus GG promotes early B lineage development and IgA production in the Lamina propria in piglets","volume":"207","author":"Jin","year":"2021","journal-title":"J. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e29499","DOI":"10.1016\/j.heliyon.2024.e29499","article-title":"Unlocking the genetic potential of Lacticaseibacillus rhamnosus strains: Medical applications of a promising probiotic for human and animal health","volume":"10","author":"Wonglapsuwan","year":"2024","journal-title":"Heliyon"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Ali, M., Amin, A., and Zaigham, A. (2025). Efficacy of Lacticaseibacillus rhamnosus probiotic strains in treating chromate induced dermatitis. Sci. Rep., 15.","DOI":"10.1038\/s41598-025-93732-9"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Leser, T., and Baker, A. (2024). Molecular Mechanisms of Lacticaseibacillus rhamnosus, LGG\u00ae Probiotic Function. Microorganisms, 12.","DOI":"10.20944\/preprints202402.1631.v1"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Lao, J., Chen, M., Yan, S., Gong, H., Wen, Z.H., Yong, Y.H., Jia, D., Lv, S.T., Zou, W.L., and Li, J.M. (2025). Lacticaseibacillus rhamnosus G7 alleviates DSS-induced ulcerative colitis by regulating the intestinal microbiota. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-03904-w"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e174910","DOI":"10.1172\/JCI174910","article-title":"Lacticaseibacillus rhamnosus GG induces STING-dependent IL-10 in intestinal monocytes and alleviates inflammatory colitis in mice","volume":"135","author":"Si","year":"2025","journal-title":"J. Clin. Invest."},{"key":"ref_15","first-page":"249","article-title":"Lacticaseibacillus rhamnosus strain GG is a potential probiotic for calves","volume":"68","author":"Ewaschuk","year":"2004","journal-title":"Can. J. Vet. Res. J."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Huang, X., Ai, F., Ji, C., Tu, P.C., Gao, Y.F., Wu, Y.L., Yan, F.J., and Yu, T. (2021). A rapid screening method of candidate probiotics for inflammatory bowel diseases and the anti-inflammatory effect of the selected strain bacillus smithii XY1. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.760385"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3121\/cmr.2.1.37","article-title":"Rapid molecular diagnosis of Lacticaseibacillus bacteremia by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene","volume":"2","author":"Christensen","year":"2004","journal-title":"Clin. Med. Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2145843","DOI":"10.1080\/19490976.2022.2145843","article-title":"Lacticaseibacillus johnsonii alleviates colitis by TLR1\/2-STAT3 mediated CD206+ macrophages IL-10 activation","volume":"14","author":"Jia","year":"2022","journal-title":"Gut Microbes"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1093\/ibd\/izy359","article-title":"Difference in pathomechanism between crohn\u2019s disease and ulcerative colitis revealed by colon transcriptome","volume":"25","author":"Yang","year":"2019","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1002\/ueg2.12636","article-title":"Efficacy and safety of probiotics in IBD: An overview of systematic reviews and updated meta-analysis of randomized controlled trials","volume":"12","author":"Estevinho","year":"2024","journal-title":"United Eur. Gastroenterol. J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1016\/j.cell.2019.07.045","article-title":"Therapeutic opportunities in inflammatory bowel disease: Mechanistic dissection of host-microbiome relationships","volume":"178","author":"Plichta","year":"2019","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Huang, C., Hao, W., Wang, X.Y., Zhou, R.M., and Lin, Q. (2023). Probiotics for the treatment of ulcerative colitis: A review of experimental research from 2018 to 2022. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1211271"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"164","DOI":"10.4161\/gmic.1.3.12127","article-title":"Safety assessment of probiotics for human use","volume":"1","author":"Sanders","year":"2010","journal-title":"Gut Microbes"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Kwon, H., Nam, E.H., Hayoung, K., Haneul, J., Won, Y.B., Minjee, L., Hyeonmin, S., Dana, K., Jeongho, K., and Hyejin, K. (2024). Effect of Lacticaseibacillus rhamnosus IDCC 3201 on irritable bowel syndrome with constipation: A randomized, double-blind, and placebo-controlled trial. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-72887-x"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Zhu, Y., Chen, B., Zhang, X., Akbar, M.T., Wu, T., Zhang, Y., Zhi, L., and Shen, Q. (2024). Exploration of the Muribaculaceae family in the gut microbiota: Diversity, metabolism, and function. Nutrients, 16.","DOI":"10.3390\/nu16162660"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41579-024-01106-1","article-title":"Akkermansia muciniphila: Biology, microbial ecology, host interactions and therapeutic potential","volume":"23","author":"Ioannou","year":"2025","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Ma, X., Tian, M., Yu, X.P., Liu, M., Li, B., Ren, D.Y., and Wang, W. (2024). Characterization and preliminary safety evaluation of Akkermansia muciniphila PROBIO. Foods, 13.","DOI":"10.3390\/foods13030442"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Mu, Q., Tavella, V.J., and Luo, X.M. (2018). Role of Limosilactobacillus reuteri in human health and diseases. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00757"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"115212","DOI":"10.1016\/j.foodres.2024.115212","article-title":"Limosilactobacillus reuteri or Lacticaseibacillus rhamnosus GG intervention facilitates gut barrier function, decreases corticosterone and ameliorates social behavior in LPS-exposed offspring","volume":"197","author":"Wang","year":"2024","journal-title":"Food Res. Int."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Abuqwider, J., Altamimi, M., and Mauriello, G. (2022). LimosiLimosilactobacillus reuteri in health and disease. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030522"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/ismej.2015.148","article-title":"The initial state of the human gut microbiome determines its reshaping by antibiotics","volume":"10","author":"Raymond","year":"2016","journal-title":"ISME J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3669","DOI":"10.1038\/s41467-023-39403-7","article-title":"Gut microbiota Turicibacter strains differentially modify bile acids and host lipids","volume":"14","author":"Lynch","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.chom.2024.02.001","article-title":"Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia","volume":"32","author":"Xu","year":"2024","journal-title":"Cell Host Microbe."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1007\/s00253-020-11051-7","article-title":"Selection and characterization of a SpaCBA pilus-secreting food-grade derivative of Lacticaseibacillus rhamnosus GG","volume":"105","author":"Tytgat","year":"2021","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"8280","DOI":"10.4049\/jimmunol.180.12.8280","article-title":"Flagellin treatment protects against chemicals, bacteria, viruses, and radiation","volume":"180","author":"Aitken","year":"2008","journal-title":"J. Immunol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Micallef, P., Vuji\u010di\u0107, M., Wu, Y.L., Eduard, P., Wang, Y., Bel\u00e9n, C., Anders, S., Susanna, L.C., and Ingrid, W.A. (2022). C1QTNF3 is upregulated during subcutaneous adipose tissue remodeling and stimulates macrophage chemotaxis and M1-like polarization. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.914956"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e201900478","DOI":"10.26508\/lsa.201900478","article-title":"Enhanced carbonyl stress induces irreversible multimerization of CRMP2 in schizophrenia pathogenesis","volume":"2","author":"Toyoshima","year":"2019","journal-title":"Life Sci. Alliance"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"j3076","DOI":"10.1136\/bmj.j3076","article-title":"US medical groups denounce Senate health repeal bill","volume":"357","author":"McCarthy","year":"2017","journal-title":"BMJ"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1111\/jcpt.13548","article-title":"Efficacy and safety of dexmedetomidine in sepsis patients requiring mechanical ventilation: A systematic review and meta-analysis","volume":"47","author":"Liu","year":"2022","journal-title":"J. Clin. Pharm. Ther."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1146\/annurev-immunol-042617-053119","article-title":"Nonclassical monocytes in health and disease","volume":"37","author":"Narasimhan","year":"2019","journal-title":"Annu. Rev. Immunol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1016\/j.immuni.2022.08.002","article-title":"Liver macrophages in health and disease","volume":"55","author":"Guilliams","year":"2022","journal-title":"Immunity"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"5157","DOI":"10.1021\/acs.jafc.8b01253","article-title":"Dietary Clostridium butyricum induces a phased shift in fecal microbiota structure and increases the acetic acid-producing bacteria in a weaned piglet model","volume":"66","author":"Zhang","year":"2018","journal-title":"J. Agric. Food Chem."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Zhang, H., Shen, G., Lu, H.L., Jiang, C.K., Hu, W.J., Jiang, Q.H., Xiang, X.W., Wang, Z.X., and Chen, L. (2024). Psidium guajava seed oil reduces the severity of colitis induced by dextran sulfate sodium by modulating the intestinal microbiota and restoring the intestinal barrier. Foods, 13.","DOI":"10.3390\/foods13172668"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/jb.173.2.697-703.1991","article-title":"16S ribosomal DNA amplification for phylogenetic study","volume":"173","author":"Weisburg","year":"1991","journal-title":"J. Bacteriol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Shen, J., Zhang, J., Zhao, Y., Lin, Z.S., Ji, L.B., and Ma, X. (2022). Tibetan pig-derived probiotic Lacticaseibacillus amylovorus SLZX20-1 Improved Intestinal Function via Producing Enzymes and Regulating Intestinal Microflora. Front. Nutr., 9.","DOI":"10.3389\/fnut.2022.846991"},{"key":"ref_46","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_47","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_48","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_49","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1099\/00207713-44-4-846","article-title":"Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology","volume":"44","author":"Stackebrandt","year":"1994","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref_50","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_51","doi-asserted-by":"crossref","unstructured":"Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., and Robinson, C.J. (2009). Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75.","DOI":"10.1128\/AEM.01541-09"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W.S., and Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biol., 12.","DOI":"10.1186\/gb-2011-12-6-r60"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","article-title":"DEGseq: An R package for identifying differentially expressed genes from RNA-seq data","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/23\/11397\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T10:50:59Z","timestamp":1764931859000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/23\/11397"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,25]]},"references-count":57,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["ijms262311397"],"URL":"https:\/\/doi.org\/10.3390\/ijms262311397","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,25]]}}}