{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T07:13:40Z","timestamp":1787987620793,"version":"build-2784847793"},"reference-count":42,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010978","name":"Wallonie-Bruxelles International","doi-asserted-by":"publisher","award":["BOU\/PaD\/CC\/PVB\/sd-eab\/LD 2024-2025\/WBI.IN"],"award-info":[{"award-number":["BOU\/PaD\/CC\/PVB\/sd-eab\/LD 2024-2025\/WBI.IN"]}],"id":[{"id":"10.13039\/501100010978","id-type":"DOI","asserted-by":"publisher"}]},{"award":["BOU\/PaD\/CC\/PVB\/sd-eab\/LD 2024-2025\/WBI.IN"],"award-info":[{"award-number":["BOU\/PaD\/CC\/PVB\/sd-eab\/LD 2024-2025\/WBI.IN"]}],"id":[{"id":"https:\/\/ror.org\/008vsyy18","id-type":"ROR","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon Europe research and innovation programme","award":["101059232"],"award-info":[{"award-number":["101059232"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Here we report the draft genome sequences of three Enterococcus faecalis strains, LAB1, LAB10, and LAB11, isolated from the pond water of a tilapia (Oreochromis niloticus) aquaculture farm at the University Nangui Abrogoua, Abidjan, Ivory Coast. These strains were previously characterised for their probiotic, plant growth-promoting (PGP), and nitrifying properties. All three strains were assigned to sequence type ST19 by multilocus sequence typing (MLST). The draft genomes of LAB1, LAB10, and LAB11 consist of 34, 35, and 34 contigs, totalling 2.94 Mb each (GC content 37.40%). Prokka annotation predicted 2872, 2873, and 2875 protein-coding sequences (CDS) for LAB1, LAB10, and LAB11, respectively. Genomic screening revealed no vancomycin resistance genes; however, tet(M) and lsa(A) resistance determinants were identified in all three strains, located on a repUS43-type plasmid replicon. Fourteen virulence factor homologs conserved in the E. faecalis reference strain V583 were detected, including Ebp pili, gelatinase (gelE), Fsr quorum-sensing system, and capsule biosynthesis genes, but no cytolysin operon was identified. Genes associated with stress tolerance (katA, sodA), bile salt hydrolysis (cbh), siderophore transport (fepC, fhuD), and ethanolamine nitrogen metabolism (eutB\/eutC) were identified in all three genomes. Pan-genome analysis with the E. faecalis reference strain revealed 551 core gene clusters and 279 gene clusters exclusive to the three aquaculture isolates. Despite their high genomic similarity, we report the three genomes as distinct isolates due to observed differences in their expressed phenotypic properties. These sequences provide a genomic resource supporting the development of multifunctional probiotic consortia for integrated aquaponic systems.<\/jats:p>","DOI":"10.3390\/microorganisms14081653","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T08:16:52Z","timestamp":1785313012000},"page":"1653","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genome Sequences of Three Enterococcus faecalis Strains (LAB1, LAB10, and LAB11) with Probiotic, Plant Growth-Promoting, and Nitrifying Properties"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0734-686X","authenticated-orcid":false,"given":"Muiz Oluwatosin","family":"Akinyemi","sequence":"first","affiliation":[{"name":"Leeds Institute of Health Sciences, University of Leeds, Leeds LS2 9LN, UK"},{"name":"Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6189-0316","authenticated-orcid":false,"given":"Wahauwou\u00e9l\u00e9 Hermann","family":"Coulibaly","sequence":"additional","affiliation":[{"name":"Food Science and Technology Formation and Research Unit, Biotechnology and Food Microbiology Laboratory, Nangui Abrogoua University, Abidjan P.O. Box 801 02, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tano Marie-Ange","family":"Sakia Mian","sequence":"additional","affiliation":[{"name":"Agroforestery Trainning and Research Unit, Agro-Valorization Laboratory, Jean Lorougnon Gu\u00e9d\u00e9 University, Daloa BP-150, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9096-2232","authenticated-orcid":false,"given":"Paul-Alexandru","family":"Popescu","sequence":"additional","affiliation":[{"name":"University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59 Marasti Blvd., District 1, 011464 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bassey","family":"Ebenso","sequence":"additional","affiliation":[{"name":"Leeds Institute of Health Sciences, University of Leeds, Leeds LS2 9LN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4757-7072","authenticated-orcid":false,"given":"Hary","family":"Razafindralambo","sequence":"additional","affiliation":[{"name":"Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liege, UMRt 1158 BioEcoAgro, Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium"},{"name":"ProBioLab, 5004 Namur, Belgium"},{"name":"Faculty of Agricultural and Natural Resources, An Giang University, Vietnam National University, 18 Ung Van Khiem Street, Long Xuyen, An Giang 90000, Vietnam"},{"name":"Ing\u00e9nierie et Technologie Emergentes, Universit\u00e9 de Vakinankaratra, Campus Vatofotsy, Antsirabe 110 BP 108, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"836","DOI":"10.3390\/su6020836","article-title":"Sustainable treatment of aquaculture effluents\u2014What can we learn from the past for the future?","volume":"6","author":"Turcios","year":"2014","journal-title":"Sustainability"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.vetpar.2005.07.005","article-title":"Disease and health management in Asian aquaculture","volume":"132","author":"Subasinghe","year":"2005","journal-title":"Vet. Parasitol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1208\/s12248-015-9722-z","article-title":"Does the Recent Growth of Aquaculture Create Antibiotic Resistance Threats Different from those Associated with Land Animal Production in Agriculture?","volume":"17","author":"Done","year":"2015","journal-title":"AAPS J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","article-title":"The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic","volume":"11","author":"Hill","year":"2014","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_5","first-page":"1","article-title":"Developments in the use of probiotics for disease control in aquaculture","volume":"431","author":"Austin","year":"2014","journal-title":"Aquaculture"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1007\/s11160-014-9361-y","article-title":"Application of vaccines and dietary supplements in aquaculture: Possibilities and challenges","volume":"24","author":"Olsen","year":"2014","journal-title":"Rev. Fish. Biol. Fish."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1111\/raq.12209","article-title":"Beneficial roles of feed additives as immunostimulants in aquaculture: A review","volume":"10","author":"Dawood","year":"2018","journal-title":"Rev. Aquac."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.ijfoodmicro.2011.08.014","article-title":"Enterococci as probiotics and their implications in food safety","volume":"151","author":"Franz","year":"2011","journal-title":"Int. J. Food Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Ring\u00f8, E., Hoseinifar, S.H., Ghosh, K., Doan, H.V., Beck, B.R., and Song, S.K. (2018). Lactic acid bacteria in finfish\u2014An update. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01818"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"EFSA Panel on Additives and Products or Substances Used in Animal Feed (FEEDAP) (2012). Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. EFSA J., 10, 2740.","DOI":"10.2903\/j.efsa.2012.2740"},{"key":"ref_11","unstructured":"Coulibaly, W.H., Mian, T.M.-A.S., Tohoyessou, M.G., Akinyemi, M.O., Ebenso, B., Yao, A.P., Meex, C., Popescu, P.-A., Fievez, T., and Maesen, P. (Microorganisms, 2026). Relevant Probiotic and Functional Properties of Lactic Acid Bacteria Isolated from Aquaculture Environments in Ivory Coast for Potential Aquaponic Applications, Microorganisms, under review."},{"key":"ref_12","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_13","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"10872","DOI":"10.1038\/s41598-018-28948-z","article-title":"GOATOOLS: A Python library for Gene Ontology analyses","volume":"8","author":"Klopfenstein","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_18","first-page":"000685","article-title":"Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","article-title":"DFAST: A flexible prokaryotic genome annotation pipeline for faster genome publication","volume":"34","author":"Tanizawa","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Bharat, A., Petkau, A., Avery, B.P., Chen, J.C., Folster, J.P., Carson, C.A., Kearney, A., Nadon, C., Mabon, P., and Thiessen, J. (2022). Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020292"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Patz, S., Gautam, A., Becker, M., Ruppel, S., Rodr\u00edguez-Palenzuela, P., and Huson, D.H. (2021). PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. BioRxiv.","DOI":"10.1101\/2021.12.13.472471"},{"key":"ref_22","first-page":"000748","article-title":"ResFinder\u2014An open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa","year":"2022","journal-title":"Microb. Genom."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: A general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e70025","DOI":"10.1002\/mnfr.70025","article-title":"ProbML: A Machine Learning-Based Genome Classifier for Identifying Probiotic Organisms","volume":"69","author":"Mudgal","year":"2025","journal-title":"Mol. Nutr. Food Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"895","DOI":"10.3390\/toxins5050895","article-title":"Structure, function, and biology of the Enterococcus faecalis cytolysin","volume":"5","author":"Martin","year":"2013","journal-title":"Toxins"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Tang, J., Li, Y., Zhang, L., Mu, J., Jiang, Y., Fu, H., Zhang, Y., Cui, H., Yu, X., and Ye, Z. (2023). Biosynthetic pathways and functions of indole-3-acetic acid in microorganisms. Microorganisms, 11.","DOI":"10.3390\/microorganisms11082077"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1126\/science.1080613","article-title":"Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis","volume":"299","author":"Paulsen","year":"2003","journal-title":"Science"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e00058-18","DOI":"10.1128\/CMR.00058-18","article-title":"The Enterococcus: A Model of Adaptability to Its Environment","volume":"32","author":"Rice","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Hussain, N., Muccee, F., Mirza, A.F., Ashraf, N.M., and Al Haddad, A.H. (2026). Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture. Front. Vet. Sci., 13.","DOI":"10.3389\/fvets.2026.1778532"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1128\/JCM.41.6.2569-2576.2003","article-title":"Comparative Study Using Type Strains and Clinical and Food Isolates To Examine Hemolytic Activity and Occurrence of the cyl Operon in Enterococci","volume":"41","author":"Semedo","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Elnar, A.G., and Kim, G.-B. (2025). Probiotic potential and safety assessment of bacteriocinogenic Enterococcus faecalis CAUM157. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1563444"},{"key":"ref_33","first-page":"mgen000880","article-title":"Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents","volume":"8","author":"Sanderson","year":"2022","journal-title":"Microb. Genom."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1128\/AAC.46.6.1845-1850.2002","article-title":"An Enterococcus faecalis ABC Homologue (Lsa) Is Required for the Resistance of This Species to Clindamycin and Quinupristin-Dalfopristin","volume":"46","author":"Singh","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3851","DOI":"10.1021\/jf200251k","article-title":"Coexpression of the Superoxide Dismutase and the Catalase Provides Remarkable Oxidative Stress Resistance in Lactobacillus rhamnosus","volume":"59","author":"An","year":"2011","journal-title":"J. Agric. Food Chem."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Huang, F., Yang, N., Zhang, Q., Luo, C., Wang, J., Yang, Y., Yue, B., Chen, P., and Zhang, X. (2025). Marine-Derived Enterococcus faecalis HY0110 as a Next-Generation Functional Food Probiotic: Comprehensive In Vitro and In Vivo Bioactivity Evaluation and Synergistic Fermentation of Periplaneta americana Extract Powder. Foods, 14.","DOI":"10.3390\/foods14071181"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.1128\/AEM.72.3.1729-1738.2006","article-title":"Bile Salt Hydrolase Activity in Probiotics","volume":"72","author":"Begley","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Dong, Z., Yang, S., Tang, C., Li, D., Kan, Y., and Yao, L. (2025). New insights into microbial bile salt hydrolases: From physiological roles to potential applications. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1513541"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"5530","DOI":"10.1038\/s41598-022-09263-0","article-title":"Bacteriocinogenic probiotic bacteria isolated from an aquatic environment inhibit the growth of food and fish pathogens","volume":"12","author":"Pereira","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"R94","DOI":"10.1016\/j.cub.2015.12.021","article-title":"The nitrogen cycle","volume":"26","author":"Stein","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Lu, S., Liu, X., Liu, C., Cheng, G., Zhou, R., and Li, Y. (2021). A review of ammonia-oxidizing archaea and anaerobic ammonia-oxidizing bacteria in the aquaculture pond environment in China. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.775794"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1007\/s00248-020-01498-6","article-title":"Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss)","volume":"80","author":"Neissi","year":"2020","journal-title":"Microb. Ecol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1653\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T08:35:56Z","timestamp":1785314156000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1653"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,29]]},"references-count":42,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["microorganisms14081653"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14081653","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,29]]}}}