Almeida-Santos AC, Novais C, Peixe L, Freitas AR (2021) Enterococcus spp. as a producer and target of bacteriocins: a double-edged sword in the antimicrobial resistance crisis context. Antibiotics 10(10):1215

CAS  PubMed  PubMed Central  Google Scholar 

Ameri R, García JL, Derenfed AB, Pradel N, Neifar S, Mhiri S, Mezghanni M, Jaouadi NZ, Barriuso J, Bejar S (2022) Genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of the thermophilic Caldicoprobacter algeriensis TH7C1T. Microb Cell Fact 21(1):91

CAS  PubMed  PubMed Central  Google Scholar 

Aswal M, Singhal N, Kumar M (2023) Comprehensive genomic analysis of hypocholesterolemic probiotic Enterococcus faecium LR13 reveals unique proteins involved in cholesterol-assimilation. Front Nutr 10:1082566

PubMed  PubMed Central  Google Scholar 

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477

CAS  PubMed  PubMed Central  Google Scholar 

Ben Braïek O, Smaoui S (2019) Enterococci: between emerging pathogens and potential probiotics. Biomed Res Int 1:5938210

Google Scholar 

Bhardwaj A, Gupta H, Kapila S, Kaur G, Vij S, Malik RK (2010) Safety assessment and evaluation of probiotic potential of bacteriocinogenic Enterococcus faecium KH 24 strain under in vitro and in vivo conditions. Int J Food Microbiol 141(3):156–164

PubMed  Google Scholar 

Blin K, Shaw S, Vader L, Szenei J, Reitz ZL, Augustijn HE, Cediel-Becerra JD, de Crécy-Lagard V, Koetsier RA, Williams SE, Cruz-Morales P (2025) antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation. Nucleic Acids Res 53(W1):W32-W38

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

CAS  PubMed  PubMed Central  Google Scholar 

Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491–3500

CAS  PubMed  PubMed Central  Google Scholar 

Bustamante MI, Elfar K, Eskalen A (2022) Evaluation of the antifungal activity of endophytic and rhizospheric bacteria against grapevine trunk pathogens. Microorganisms 10(10):2035

CAS  PubMed  PubMed Central  Google Scholar 

Camprubí-Font C, Lopez-Siles M, Ferrer-Guixeras M, Niubó-Carulla L, Abellà-Ametller C, Garcia-Gil LJ, Martinez-Medina M (2018) Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. Sci Rep 8(1):2695. https://doi.org/10.1038/s41598-018-20843-x

CAS  PubMed  PubMed Central  Google Scholar 

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895–3903

PubMed  PubMed Central  Google Scholar 

Chatterjee A, Rajarshi K, Ghosh H, Singh MK, Roy OP, Ray S (2020) Molecular chaperones in protein folding and stress management in cyanobacteria. In: Advances in cyanobacterial biology. Academic Press, pp 119–128

Google Scholar 

Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33(suppl_1):D325-D328. https://doi.org/10.1093/nar/gki008

Chugh B, Kamal-Eldin A (2020) Bioactive compounds produced by probiotics in food products. Curr Opin Food Sci 32:76–82

Google Scholar 

Costa OY, De Hollander M, Pijl A, Liu B, Kuramae EE (2020) Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. Microbiome 8:1–19

Google Scholar 

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EP, Vergnaud G, Gautheret D, Pourcel C (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46(W1):W246–W251

CAS  PubMed  PubMed Central  Google Scholar 

Cumsille A, Durán RE, Rodríguez-Delherbe A, Saona-Urmeneta V, Cámara B, Seeger M, Araya M, Jara N, Buil-Aranda C (2023) GenoVi, an open-source automated circular genome visualizer for bacteria and archaea. PLoS Comput Biol 19(4):e1010998

CAS  PubMed  PubMed Central  Google Scholar 

Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5(6):e11147

PubMed  PubMed Central  Google Scholar 

Dimidi E, Cox SR, Rossi M, Whelan K (2019) Fermented foods: definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease. Nutrients 11(8):1806

CAS  PubMed  PubMed Central  Google Scholar 

Duan X, Yang H, Tian Y, Wang R, Liu C, Zhou H (2019) Complete genome sequence of bacteriocin-producing Enterococcus faecium HY07. Microbiol Resour Announc 8(38). https://doi.org/10.1128/mra.00276-19

El Oirdi S, Lakhlifi T, Bahar AA, Yatim M, Rachid Z, Belhaj A (2021) Isolation and identification of Lactobacillus plantarum 4F, a strain with high antifungal activity, fungicidal effect, and biopreservation properties of food. J Food Process Preserv 45(6):e15517

Google Scholar 

Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:1–14

CAS  Google Scholar 

Feng Y, Zou S, Chen H, Yu Y, Ruan Z (2021) BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. Nucleic Acids Res 49(D1):D644–D650

CAS  PubMed  Google Scholar 

Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(suppl_2):W29–W37

CAS  PubMed  PubMed Central  Google Scholar 

García Alegría A, Anduro Corona I, Perez Martinez C, Corella M, Rascón-Durán M, Garcia H (2020) Quantification of DNA through the NanoDrop spectrophotometer: methodological validation using standard reference material and Sprague Dawley rat and human DNA. Int J Analytical Chem 2020:1–9. https://doi.org/10.1155/2020/8896738

CAS  Google Scholar 

Gato E, Vázquez-Ucha JC, Rumbo-Feal S, Álvarez-Fraga L, Vallejo JA, Martínez-Guitián M, Beceiro A, Ramos Vivas J, Sola Campoy PJ, Pérez-Vázquez M (2020) Kpi, a chaperone-usher pili system associated with the worldwide-disseminated high-risk clone Klebsiella pneumoniae ST-15. Proc Natl Acad Sci 117(29):17249–17259

CAS  PubMed  PubMed Central  Google Scholar 

Hanchi H, Mottawea W, Sebei K, Hammami R (2018) The genus Enterococcus: between probiotic potential and safety concerns—an update. Front Microbiol 9:1791

PubMed  PubMed Central  Google Scholar 

Hasnat S, Hoque MN, Mahbub MM, Sakif TI, Shahinuzzaman A, Islam T (2024a) Pantothenate kinase: a promising therapeutic target against pathogenic Clostridium species. Heliyon 10(14):e34544. https://doi.org/10.1016/j.heliyon.2024.e34544

CAS  PubMed  PubMed Central  Google Scholar 

Hasnat S, Rahman MM, Yeasmin F, Jubair M, Helmy YA, Islam T, Hoque MN (2024b) Natural bacteriocins as potential drug candidates targeting core proteins in mastitis pathogens of dairy cattle. bioRxiv:2024.11.05.622021. https://doi.org/10.1101/2024.11.05.622021

Hasnat S, Rahman MM, Yeasmin F, Jubair M, Helmy YA, Islam T, Hoque MN (2025) Genomic and computational analysis unveils bacteriocin based therapeutics against clinical mastitis pathogens in dairy cows. Probiotics Antimicrob Proteins 2025:1–21. https://doi.org/10.1007/s12602-025-10563-w

Google Scholar 

Holzapfel W, Arini A, Aeschbacher M, Coppolecchia R, Pot B (2018) Enterococcus faecium SF68 as a model for efficacy and safety evaluation of pharmaceutical probiotics. Beneficial Microbes 9(3):375–388

CAS  PubMed  Google Scholar 

Hong SW, Kim J-H, Cha HA, Chung KS, Bae HJ, Park WS, Ham J-S, Park B-Y, Oh M-H (2022) Identification and characterization of a bacteriocin from the newly isolated Bacillus subtilis HD15 with inhibitory effects against Bacillus cereus. J Microbiol Biotechnol 32(11):1462

CAS  PubMed  PubMed Central  Google Scholar 

Hoque MN, Das ZC, Talukder AK, Alam MS, Rahman ANMA (2015) Different screening tests and milk somatic cell count for the prevalence of subclinical bovine mastitis in Bangladesh. Trop Anim Health Prod 47:79–86

PubMed  Google Scholar 

Hoque M, Das Z, Rahman A, Hoque M (2016) Effect of administration of vitamin E, selenium and antimicrobial therapy on incidence of mastitis, productive and reproductive performances in dairy cows. Int J Vet Sci Med 4(2):63–70

CAS  PubMed  PubMed Central  Google Scholar 

Hoque MN, Istiaq A, Clement RA, Gibson KM, Saha O, Islam OK, Abir RA, Sultana M, Siddiki AZ, Crandall KA (2020) Insights into the resistome of bovine clinical mastitis microbiome, a key factor in disease complication. Front Microbiol 11:860

PubMed  PubMed Central  Google Scholar 

Hoque MN, Talukder AK, Saha O, Hasan MM, Sultana M, Rahman AA, Das ZC (2022) Antibiogram and virulence profiling reveals multidrug resistant Staphylococcus aureus as the predominant aetiology of subclinical mastitis in riverine buffaloes. Vet Med Sci 8(6):2631–2645

CAS  PubMed  PubMed Central  Google Scholar 

Hoque MN, Jerin S, Faisal GM, Das ZC, Islam T, Rahman ANMA (2023) Whole-genome sequence of multidrug-resistant Escherichia coli strains isolated from mice with mastitis. Microbiol Resour Announc 12(7):e00320–e00323

PubMed  PubMed Central  Google Scholar 

Hoque MN, Faisal G