{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T14:02:18Z","timestamp":1790863338277,"version":"4.1.0"},"reference-count":33,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad T\u00e9cnica del Norte","award":["InvestigaUTN-2024-1432"],"award-info":[{"award-number":["InvestigaUTN-2024-1432"]}],"id":[{"id":"https:\/\/ror.org\/03f0t8b71","id-type":"ROR","asserted-by":"crossref"}]},{"award":["InvestigaUTN-2024-1432"],"award-info":[{"award-number":["InvestigaUTN-2024-1432"]}],"id":[{"id":"https:\/\/ror.org\/03f0t8b71","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Lactiplantibacillus plantarum exhibits substantial strain-level genomic diversity that may contribute to variation in stress tolerance and functional properties. Five isolates recovered from spontaneously fermented red coffee cherries were analyzed by whole-genome resequencing and phenotypic characterization. Single-nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels) were identified and functionally annotated. SNPs predominated, ranging from 16,865 to 20,280 per isolate, with CATR21 showing the highest SNP and InDel counts. Synonymous variants were the most frequent predicted consequence, followed by upstream and missense variants, whereas high-impact variants were uncommon. Selected isolate-specific missense variants affected atpF and atpB in CATR7, mobQ in CATR14, ptsP in CATR21, and glf and epsC in TYPR1. Phenotypic responses were strain- and condition-dependent. CATR21 exhibited the highest viability at pH 2.5 and the highest 24-h autoaggregation among the coffee-derived isolates. CATR7 showed the highest viability under 1% NaCl and the highest numerical viability under 4% NaCl. Genome-wide variant counts did not show a consistent relationship with the evaluated phenotypic traits. Overall, the combined genomic and phenotypic analyses demonstrated substantial strain-level variability among the coffee-derived L. plantarum isolates across the evaluated conditions.<\/jats:p>","DOI":"10.3390\/ijms27188307","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:18:26Z","timestamp":1790860706000},"page":"8307","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Variation and Phenotypic Diversity of Coffee-Derived Lactiplantibacillus plantarum Isolates"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7819-9679","authenticated-orcid":false,"given":"Gabriela N.","family":"Tenea","sequence":"first","affiliation":[{"name":"Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad T\u00e9cnica del Norte, Av. 17 de Julio s-21 y Jos\u00e9 Mar\u00eda C\u00f3rdova, Ibarra 100150, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Victor","family":"Cifuentes","sequence":"additional","affiliation":[{"name":"Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad T\u00e9cnica del Norte, Av. 17 de Julio s-21 y Jos\u00e9 Mar\u00eda C\u00f3rdova, Ibarra 100150, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Jazmin","family":"Hidalgo","sequence":"additional","affiliation":[{"name":"Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad T\u00e9cnica del Norte, Av. 17 de Julio s-21 y Jos\u00e9 Mar\u00eda C\u00f3rdova, Ibarra 100150, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Anumudu, C.K., Miri, T., and Onyeaka, H. (2024). Multifunctional applications of lactic acid bacteria: Enhancing safety, quality, and nutritional value in foods and fermented beverages. Foods, 13.","DOI":"10.3390\/foods13233714"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e14392","DOI":"10.1111\/1751-7915.14392","article-title":"Novel Lactobacillaceae strains and consortia to produce propionate-containing fermentates as biopreservatives","volume":"17","year":"2024","journal-title":"Microb. Biotechnol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"4974","DOI":"10.1111\/1462-2920.13455","article-title":"Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats","volume":"18","author":"Martino","year":"2016","journal-title":"Environ. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Mao, B., Yin, R., Li, X., Cui, S., Zhang, H., Zhao, J., and Chen, W. (2021). Comparative genomic analysis of Lactiplantibacillus plantarum isolated from different niches. Genes, 12.","DOI":"10.3390\/genes12020241"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1111\/1751-7915.13871","article-title":"Strain diversity of plant-associated Lactiplantibacillus plantarum","volume":"14","author":"Yu","year":"2021","journal-title":"Microb. Biotechnol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Garc\u00eda-Gonz\u00e1lez, N., Bottacini, F., van Sinderen, D., Gahan, C.G.M., and Corsetti, A. (2022). Comparative genomics of Lactiplantibacillus plantarum: Insights into probiotic markers in strains isolated from the human gastrointestinal tract and fermented foods. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.854266"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Tenea, G.N. (2022). Decoding the gene variants of two native probiotic Lactiplantibacillus plantarum strains through whole-genome resequencing: Insights into bacterial adaptability to stressors and antimicrobial strength. Genes, 13.","DOI":"10.3390\/genes13030443"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"105551","DOI":"10.1016\/j.jfca.2023.105551","article-title":"Transformation of organic acids and sugars in the mucilage and coffee beans during prolonged fermentation","volume":"123","author":"Osorio","year":"2023","journal-title":"J. Food Compos. Anal."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Kim, S.-G., Abbas, A., and Moon, G.-S. (2024). Improved functions of fermented coffee by lactic acid bacteria. Appl. Sci., 14.","DOI":"10.3390\/app14177596"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"L\u00f3pez-Palestino, A., G\u00f3mez-Vargas, R., Su\u00e1rez-Quiroz, M., Gonz\u00e1lez-R\u00edos, O., Hern\u00e1ndez-Estrada, Z.J., Castellanos-Onorio, O.P., Alonso-Villegas, R., Estrada-Beltr\u00e1n, A.E., and Figueroa-Hern\u00e1ndez, C.Y. (2025). Probiotic potential of lactic acid bacteria and yeast isolated from cocoa and coffee bean fermentation: A review. Fermentation, 11.","DOI":"10.3390\/fermentation11020095"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"107381","DOI":"10.1016\/j.jff.2026.107381","article-title":"Coffee-derived lactic acid bacteria postbiotics: Strain-specific antimicrobial, redox and Caco-2 immunomodulation readouts","volume":"143","author":"Tenea","year":"2026","journal-title":"J. Funct. Foods"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e201912475","DOI":"10.1085\/jgp.201912475","article-title":"ATP synthase: Evolution, energetics, and membrane interactions","volume":"152","author":"Nirody","year":"2020","journal-title":"J. Gen. Physiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1007\/s10068-024-01582-4","article-title":"Acid tolerance responses and their mechanisms in Lactiplantibacillus plantarum LM1001","volume":"33","author":"Lee","year":"2024","journal-title":"Food Sci. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Cui, Y., Wang, M., Zheng, Y., Miao, K., and Qu, X. (2021). The carbohydrate metabolism of Lactiplantibacillus plantarum. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222413452"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Zhao, X., Liang, Q., Song, X., and Zhang, Y. (2023). Whole genome sequence of Lactiplantibacillus plantarum MC5 and comparative analysis of eps gene clusters. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1146566"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1007\/s44154-022-00072-z","article-title":"Methionine addition improves the acid tolerance of Lactiplantibacillus plantarum by altering cellular metabolic flux, energy distribution, and lipid composition","volume":"2","author":"Meng","year":"2022","journal-title":"Stress Biol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Sun, Y., Zhang, S., Li, H., Zhu, J., Liu, Z., Hu, X., and Yi, J. (2022). Assessments of probiotic potentials of Lactiplantibacillus plantarum strains isolated from Chinese traditional fermented food: Phenotypic and genomic analysis. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.895132"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"105007","DOI":"10.1016\/j.fbio.2024.105007","article-title":"Natural aggregation of Lactobacillus: Mechanisms and influencing factors","volume":"62","author":"Wang","year":"2024","journal-title":"Food Biosci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"15288","DOI":"10.1038\/s41598-021-94776-3","article-title":"Rhizospheric Lactobacillus plantarum (Lactiplantibacillus plantarum) strains exhibit bile salt hydrolysis, hypocholesterolemic and probiotic capabilities in vitro","volume":"11","author":"Singhal","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e030","DOI":"10.48130\/animadv-0025-0026","article-title":"Non-pasteurized milk enhances early colonization and persistence of Lactobacillus species in dairy calves promoting a stable hindgut microbiome","volume":"2","author":"Qiu","year":"2025","journal-title":"Anim. Adv."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e028","DOI":"10.48130\/animadv-0025-0024","article-title":"Effects of yeast-derived postbiotic in different energy diets on growth performance, immunity, antioxidant status, and intestinal microbiota in growing pigs","volume":"2","author":"Li","year":"2025","journal-title":"Anim. Adv."},{"key":"ref_22","unstructured":"Andrews, S. (2026, August 31). FastQC: A Quality Control Tool for High-Throughput Sequence Data. Babraham Bioinformatics. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1128\/JB.01159-10","article-title":"Complete genome sequence of the probiotic Lactobacillus plantarum ST-III","volume":"193","author":"Wang","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short-read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single-nucleotide polymorphisms, SnpEff","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"103677","DOI":"10.1016\/j.micpath.2019.103677","article-title":"Inhibition of Escherichia coli adhesion to human intestinal Caco-2 cells by probiotic candidate Lactobacillus plantarum strain L15","volume":"136","author":"Noshad","year":"2019","journal-title":"Microb. Pathog."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3060","DOI":"10.1128\/AEM.71.6.3060-3067.2005","article-title":"Survival of probiotic lactobacilli in acidic environments is enhanced in the presence of metabolizable sugars","volume":"71","author":"Corcoran","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Liang, L., Meng, Z., Zhang, F., Jianguo, Z., Fang, S., Hu, Q., Tang, X., and Li, Y. (2023). Lactobacillus gasseri LG08 and Leuconostoc mesenteroides LM58 exert preventive effects on the development of hyperuricemia by repairing the antioxidant system and intestinal flora balance. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1211831"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Borcard, D., Gillet, F., and Legendre, P. (2018). Numerical Ecology with R, Springer International Publishing. [2nd ed.].","DOI":"10.1007\/978-3-319-71404-2"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/S0022-2275(20)36896-6","article-title":"Determination of cholesterol using o-phthalaldehyde","volume":"14","author":"Rudel","year":"1973","journal-title":"J. Lipid Res."},{"key":"ref_33","first-page":"380316","article-title":"Cholesterol assimilation by Lactobacillus probiotic bacteria: An in vitro investigation","volume":"2014","author":"Saha","year":"2014","journal-title":"BioMed Res. Int."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8307\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:24:19Z","timestamp":1790861059000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8307"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":33,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188307"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188307","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,18]]}}}