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For: Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. ACTA ACUST UNITED AC 2013;29:1072-5. [PMID: 23422339 DOI: 10.1093/bioinformatics/btt086] [Citation(s) in RCA: 6436] [Impact Index Per Article: 536.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Number Cited by Other Article(s)
201
Simar SR, Tran TT, Rydell KB, Atterstrom RL, Sahasrabhojane PV, Dinh AQ, Schettino MG, Slanis HS, Deyanov AE, DeTranaltes AM, Axell-House DB, Miller WR, Munita JM, Tobys D, Seifert H, Biehl L, Zervos M, Suleyman G, Kaur J, Warzocha V, Cifuentes RO, Abbo LM, Shimose L, Liu C, Nguyen K, Miller A, Shelburne SA, Hanson BM, Arias CA. Clinical and Genomic Characterization of Recalcitrant Enterococcal Bacteremia: A Multicenter Prospective Cohort Study (VENOUS). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.01.645485. [PMID: 40236068 PMCID: PMC11996524 DOI: 10.1101/2025.04.01.645485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
202
González D, Bruna P, Contreras MJ, Leal K, Urrutia CV, Núñez-Montero K, Barrientos L. Genome Mining of Pseudarthrobacter sp. So.54, a Rhizospheric Bacteria from Colobanthus quitensis Antarctic Plant. Biomolecules 2025;15:534. [PMID: 40305262 PMCID: PMC12025171 DOI: 10.3390/biom15040534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Revised: 03/25/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025]  Open
203
Bakelli A, Dif G, Djemouai N, Bouri M, Şahin F. Plant Growth-Promoting Pseudomonas sp. TR47 Ameliorates Pepper (Capsicum annuum L. var. conoides Mill) Growth and Tolerance to Salt Stress. Curr Microbiol 2025;82:231. [PMID: 40184005 DOI: 10.1007/s00284-025-04217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 03/22/2025] [Indexed: 04/05/2025]
204
Chan V, Holcomb T, Kaspar JR, Shields RC. Characterization of MreCD in Streptococcus mutans. J Oral Microbiol 2025;17:2487643. [PMID: 40206099 PMCID: PMC11980242 DOI: 10.1080/20002297.2025.2487643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/11/2025]  Open
205
Gomes AC, Montgomery J, Araujo ALS, Morran S, Cutti L, Patterson E, Marques Hill S, Matzrafi M, Shrestha A, Merotto A, Abdollahi F, Nelson DR, Llaca V, Fengler K, de Pinho CF, Gaines TA. Chromosome-Level Assemblies of the Allohexaploid Genomes of Conyza sumatrensis and Conyza bonariensis. Genome Biol Evol 2025;17:evaf065. [PMID: 40181513 PMCID: PMC12008746 DOI: 10.1093/gbe/evaf065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/19/2025] [Accepted: 03/24/2025] [Indexed: 04/05/2025]  Open
206
Ly T, de Melo Teixeira M, Jofre-Rodriguez G, Blanchet D, Mc Donald S, Alvarado P, da Silva SHM, Sepúlveda VE, Zeb Q, Vreden S, Adenis A, Yegres F, Demar M, Buitrago MJS, Barker B, Nacher M, Matute DR. High genetic diversity of Histoplasma in the Amazon basin, 2006-2017. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.04.01.25324933. [PMID: 40236390 PMCID: PMC11998801 DOI: 10.1101/2025.04.01.25324933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
207
Samper-Cativiela C, Torre-Fuentes L, Diéguez-Roda B, Maex M, Ugarte-Ruiz M, Carrizo P, Hernández M, Höfle Ú, Sáez JL, de Frutos C, Agüero M, Moreno MÁ, Domínguez L, Herrera-León S, Alvarez J. Molecular epidemiology of Salmonella Enteritidis in humans and animals in Spain. Antimicrob Agents Chemother 2025;69:e0073824. [PMID: 40029002 PMCID: PMC11963599 DOI: 10.1128/aac.00738-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 01/11/2025] [Indexed: 03/05/2025]  Open
208
Zampieri A, Carraro L, Mohammadpour H, Rovere GD, Milan M, Fasolato L, Cardazzo B. Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods. Int J Food Microbiol 2025;433:111113. [PMID: 39987648 DOI: 10.1016/j.ijfoodmicro.2025.111113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 02/07/2025] [Accepted: 02/15/2025] [Indexed: 02/25/2025]
209
Terra LA, Klepa MS, Nogueira MA, Hungria M. Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic Bradyrhizobium. FRONTIERS IN PLANT SCIENCE 2025;16:1539151. [PMID: 40241821 PMCID: PMC12000093 DOI: 10.3389/fpls.2025.1539151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 03/10/2025] [Indexed: 04/18/2025]
210
Petersen ME, Khamas AB, Østergaard LJ, Jørgensen NP, Meyer RL. Combination therapy delays antimicrobial resistance after adaptive laboratory evolution of Staphylococcus aureus. Antimicrob Agents Chemother 2025;69:e0148324. [PMID: 40084881 PMCID: PMC11963546 DOI: 10.1128/aac.01483-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 02/17/2025] [Indexed: 03/16/2025]  Open
211
Duchez R, Vingadassalon N, Merda D, Van Nieuwenhuysen T, Byrne B, Kourtis C, Nia Y, Hennekinne JA, Cavaiuolo M. Genetic relatedness of Staphylococcus aureus isolates within food outbreaks by single nucleotide polymorphisms. Int J Food Microbiol 2025;433:111115. [PMID: 39993362 DOI: 10.1016/j.ijfoodmicro.2025.111115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 02/14/2025] [Accepted: 02/15/2025] [Indexed: 02/26/2025]
212
Deng Z, Yang W, Lin T, Wang Y, Hua X, Jiang X, Chen J, Liu D, Ye Z, Zhang Y, Lynch M, Long H, Pan J. Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study. Microbiol Spectr 2025;13:e0169224. [PMID: 40172189 PMCID: PMC12054067 DOI: 10.1128/spectrum.01692-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 02/11/2025] [Indexed: 04/04/2025]  Open
213
Sawhney SS, Thänert R, Thänert A, Hall-Moore C, Ndao IM, Mahmud B, Warner BB, Tarr PI, Dantas G. Gut microbiome evolution from infancy to 8 years of age. Nat Med 2025:10.1038/s41591-025-03610-0. [PMID: 40175737 DOI: 10.1038/s41591-025-03610-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 02/24/2025] [Indexed: 04/04/2025]
214
Garcia E, Soares F, Rodrigues C, Trovão J, Pothier JF, Camelo A, Santo CE, Dragnev D, Petrova E, Costa J, Bobev S. Expansion of the Host Range of Xanthomonas euroxanthea: First Occurrence in Sunflower in Bulgaria. PLANT DISEASE 2025;109:810-815. [PMID: 39504143 DOI: 10.1094/pdis-08-24-1691-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
215
Roberts WR, Alverson AJ. Three reference genomes for freshwater diatom ecology and evolution. JOURNAL OF PHYCOLOGY 2025;61:267-274. [PMID: 39930529 PMCID: PMC12044402 DOI: 10.1111/jpy.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/10/2025] [Accepted: 01/16/2025] [Indexed: 05/02/2025]
216
Jiang Y, Jiang M, Lu X, Yan M, Shi X, Hu Q, Kan B. Genomic epidemiology and antimicrobial resistance reveal local transmission dynamics of enteric fever in Shenzhen, one of the mega cities in China. J Infect 2025;90:106469. [PMID: 40058502 DOI: 10.1016/j.jinf.2025.106469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 02/10/2025] [Accepted: 03/04/2025] [Indexed: 03/20/2025]
217
Yu K, Huang Z, Liu X, Gao H, Bai X, Sun Z, Wang D. The spread of CTX-M-type extended-spectrum beta-lactamases in China: Epidemiology and evolutionary analyses. J Infect 2025;90:106457. [PMID: 40043815 DOI: 10.1016/j.jinf.2025.106457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 02/23/2025] [Accepted: 02/26/2025] [Indexed: 04/12/2025]
218
Bargheet A, Noordzij HT, Ponsero AJ, Jian C, Korpela K, Valles-Colomer M, Debelius J, Kurilshikov A, Pettersen VK. Dynamics of gut resistome and mobilome in early life: a meta-analysis. EBioMedicine 2025;114:105630. [PMID: 40048849 PMCID: PMC11929092 DOI: 10.1016/j.ebiom.2025.105630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/13/2025] [Accepted: 02/19/2025] [Indexed: 03/25/2025]  Open
219
Dziurzyński M, Nowak ME, Furman M, Okrasińska A, Pawłowska J, Fondi M. Insights into optimization of oleaginous fungi - genome-scale metabolic reconstruction and analysis of Umbelopsis sp. WA50703. Comput Struct Biotechnol J 2025;27:1431-1439. [PMID: 40242294 PMCID: PMC12002602 DOI: 10.1016/j.csbj.2025.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025]  Open
220
Gao W, Wang S, Jiang T, Hu H, Gao R, Zhou M, Wang G. Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa. HORTICULTURE RESEARCH 2025;12:uhaf012. [PMID: 40093378 PMCID: PMC11908830 DOI: 10.1093/hr/uhaf012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 01/05/2025] [Indexed: 03/19/2025]
221
Brangsch H, Marcordes S, Busch A, Weber M, Wolf SA, Semmler T, Höper D, Calvelage S, Linde J, Barth SA. Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs. PLoS One 2025;20:e0320499. [PMID: 40168336 PMCID: PMC11960956 DOI: 10.1371/journal.pone.0320499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 02/20/2025] [Indexed: 04/03/2025]  Open
222
Fernández-Palacios P, Vela-Fernández R, Capote FJ, Jurado-Tarifa E, Rodríguez-Iglesias MA, Galán-Sánchez F. Corynebacterium nuruki: A novel pathogen in human catheter-related bacteremia. New Microbes New Infect 2025;64:101574. [PMID: 40129855 PMCID: PMC11930726 DOI: 10.1016/j.nmni.2025.101574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 02/25/2025] [Accepted: 03/03/2025] [Indexed: 03/26/2025]  Open
223
Zhu X, Huang Y, Shi Y, Gao X, Chen D, Liu C, Cao S, Xue X, Li Y. Comparative genomic analysis of food-animal-derived and human-derived Clostridium perfringens isolates from markets in Shandong, China. Front Microbiol 2025;16:1543511. [PMID: 40236475 PMCID: PMC11996926 DOI: 10.3389/fmicb.2025.1543511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 03/05/2025] [Indexed: 04/17/2025]  Open
224
Frias-De-Diego A, Jara M, Lanzas C. Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens. Open Forum Infect Dis 2025;12:ofaf183. [PMID: 40212029 PMCID: PMC11983279 DOI: 10.1093/ofid/ofaf183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Accepted: 03/24/2025] [Indexed: 04/13/2025]  Open
225
Ariute JC, Coelho-Rocha ND, Dantas CWD, de Vasconcelos LAT, Profeta R, de Jesus Sousa T, de Souza Novaes A, Galotti B, Gomes LG, Gimenez EGT, Diniz C, Dias MV, de Jesus LCL, Jaiswal AK, Tiwari S, Carvalho R, Benko-Iseppon AM, Brenig B, Azevedo V, Barh D, Martins FS, Aburjaile F. Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties. Probiotics Antimicrob Proteins 2025;17:500-515. [PMID: 37804433 DOI: 10.1007/s12602-023-10170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
226
Chu C, Li D, Gu L, Yang S, Liu C. Evidence for the Existence of Mating Subtypes Within the Schizophyllum commune: Mating Behavior and Genetic Divergence. J Fungi (Basel) 2025;11:277. [PMID: 40278098 PMCID: PMC12028200 DOI: 10.3390/jof11040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/27/2025] [Accepted: 03/31/2025] [Indexed: 04/26/2025]  Open
227
Caron T, Crequer E, Le Piver M, Le Prieur S, Brunel S, Snirc A, Cueff G, Roueyre D, Place M, Chassard C, Simon A, de la Vega RCR, Coton M, Coton E, Foulongne-Oriol M, Branca A, Giraud T. Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti. PLoS Genet 2025;21:e1011669. [PMID: 40233118 PMCID: PMC12047768 DOI: 10.1371/journal.pgen.1011669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/02/2025] [Accepted: 03/28/2025] [Indexed: 04/17/2025]  Open
228
Harrigian F, LeBlanc N, Eriksen RL, Bush E, Salamanca LR, Salgado-Salazar C. Uncovering the Fungus Responsible for Stem and Root Rot of False Indigo: Pathogen Identification, New Disease Description, and Genome Analyses. PLANT DISEASE 2025;109:921-930. [PMID: 39504142 DOI: 10.1094/pdis-07-24-1396-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
229
Laufer Halpin A, Mathers AJ, Walsh TR, Zingg W, Okeke IN, McDonald LC, Elkins CA, Harbarth S, Peacock SJ, Srinivasan A, Bell M, Pittet D, Cardo D. A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens. THE LANCET. INFECTIOUS DISEASES 2025;25:e235-e244. [PMID: 39832513 DOI: 10.1016/s1473-3099(24)00729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 10/09/2024] [Accepted: 10/22/2024] [Indexed: 01/22/2025]
230
Pipponzi S, Primisser S, Antonielli L, Stefani E, Compant S, Sessitsch A, Kostic T. Lettuce fortification through vitamin B12-producing bacteria - proof of concept study. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2025;105:3343-3354. [PMID: 39831556 PMCID: PMC11949862 DOI: 10.1002/jsfa.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 10/02/2024] [Accepted: 12/09/2024] [Indexed: 01/22/2025]
231
Nothdurfter S, Linde J, Sting R, Tomaso H, Heuner K, Meincke M, Brockmann SO, Wagner-Wiening C. Epidemiology of Tularemia among Humans and Animals, Baden-Wuerttemberg, Germany, 2012-2022. Emerg Infect Dis 2025;31:678-688. [PMID: 40133006 PMCID: PMC11950275 DOI: 10.3201/eid3104.240414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]  Open
232
Dirks AC, Methven AS, Miller AN, Orozco-Quime M, Maurice S, Bonito G, Van Wyk J, Ahrendt S, Kuo A, Andreopoulos W, Riley R, Lipzen A, Chovatia M, Savage E, Barry K, Grigoriev IV, Bradshaw AJ, Martin FM, Arnold AE, James TY. Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota). Mol Phylogenet Evol 2025;205:108286. [PMID: 39788220 DOI: 10.1016/j.ympev.2025.108286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 11/21/2024] [Accepted: 01/05/2025] [Indexed: 01/12/2025]
233
Arathi S, Samji A, Eashwarlal K, Gokulkrishnan S, Muthubhavani M, Yasini NP, Uma Maheswari G, Warrier RR. Transcriptome sequencing on different ages of Saraca asoca bark: Insights from tannin biosynthetic pathways and EST-SSR marker design. Fitoterapia 2025;182:106459. [PMID: 40023231 DOI: 10.1016/j.fitote.2025.106459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 02/21/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
234
Nilsen HK, Olsen AB, Birkbeck TH, Manji F, Colquhoun DJ, Gulla S. Reclassification of Pasteurella skyensis as Phocoenobacter skyensis comb. nov. and description of Phocoenobacter atlanticus sp. nov. isolated from diseased Atlantic salmon (Salmo salar) and lumpfish (Cyclopterus lumpus), with subdivision into Phocoenobacter atlanticus subspecies atlanticus subsp. nov. and Phocoenobacter atlanticus subspecies cyclopteri subsp. nov. Int J Syst Evol Microbiol 2025;75. [PMID: 40202776 DOI: 10.1099/ijsem.0.006729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2025]  Open
235
Iranzadeh A, Alisoltani A, Kiran AM, Breiman RF, Chaguza C, Peno C, Cornick JE, Everett DB, Mulder N. Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity. Microb Genom 2025;11. [PMID: 40232949 DOI: 10.1099/mgen.0.001370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]  Open
236
Oberti H, Sessa L, Oliveira-Rizzo C, Di Paolo A, Sanchez-Vallet A, Seidl MF, Abreo E. Novel genomic features in entomopathogenic fungus Beauveria bassiana ILB308: accessory genomic regions and putative virulence genes involved in the infection process of soybean pest Piezodorus guildinii. PEST MANAGEMENT SCIENCE 2025;81:2323-2336. [PMID: 39797536 DOI: 10.1002/ps.8631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 12/12/2024] [Accepted: 12/16/2024] [Indexed: 01/13/2025]
237
Mills EG, Hewlett K, Smith AB, Griffith MP, Pless L, Sundermann AJ, Harrison LH, Zackular JP, Van Tyne D. Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. Nat Microbiol 2025;10:871-881. [PMID: 40119148 PMCID: PMC11964922 DOI: 10.1038/s41564-025-01958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 02/14/2025] [Indexed: 03/24/2025]
238
Bhanse P, Singh L, Qureshi A. Functional and Genomic Potential of Burkholderia contaminans PB_AQ24 Isolate for Boosting the Growth of Bamboo Seedlings in Heavy Metal Contaminated Soils. Appl Biochem Biotechnol 2025;197:2437-2456. [PMID: 39754688 DOI: 10.1007/s12010-024-05156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2024] [Indexed: 01/06/2025]
239
Biasizzo M, Henigman U, Avberšek J, Jamnikar-Ciglenečki U, Vadnjal S. Clostridioides difficile in raw mechanically separated poultry meat and pasteurized product made from contaminated meat. Anaerobe 2025;92:102946. [PMID: 40010486 DOI: 10.1016/j.anaerobe.2025.102946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Revised: 02/07/2025] [Accepted: 02/23/2025] [Indexed: 02/28/2025]
240
Jensen EL, Marchisio C, Ochoa A, Gray R, Parra V, Miller JM, Çilingir FG, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecol Evol 2025;15:e71358. [PMID: 40290375 PMCID: PMC12032190 DOI: 10.1002/ece3.71358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/26/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025]  Open
241
Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J, Xiang H, Fang L, Tang Z, Liao Y, Yi G. Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2413023. [PMID: 40009528 PMCID: PMC12021115 DOI: 10.1002/advs.202413023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/29/2025] [Indexed: 02/28/2025]
242
Kim IE, Fola AA, Puig E, Maina TK, Hui ST, Ma H, Zuckerman K, Agwati EO, Leonetti A, Crudale R, Luftig MA, Moormann AM, Oduor C, Bailey JA. Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma. Sci Rep 2025;15:10970. [PMID: 40164811 PMCID: PMC11958722 DOI: 10.1038/s41598-025-94737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 03/17/2025] [Indexed: 04/02/2025]  Open
243
Chen R, Chen J, Powell OR, Outram MA, Arndell T, Gajendiran K, Wang YL, Lubega J, Xu Y, Ayliffe MA, Blundell C, Figueroa M, Sperschneider J, Vanhercke T, Kanyuka K, Tang D, Zhong G, Gardener C, Yu G, Gourdoupis S, Jaremko Ł, Matny O, Steffenson BJ, Boshoff WHP, Meyer WB, Arold ST, Dodds PN, Wulff BBH. A wheat tandem kinase activates an NLR to trigger immunity. Science 2025;387:1402-1408. [PMID: 40146821 DOI: 10.1126/science.adp5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 11/26/2024] [Accepted: 02/14/2025] [Indexed: 03/29/2025]
244
Mahmud MN, Momoshed M, Ahamed Talukder MF, Ferdous J, Koly FA, Islam S. Exploring the occurrence of Pseudomonas aeruginosa and comprehensive whole genome analysis of the bcsir_p4_s20 strain from municipal wastewater in Chattogram. World J Microbiol Biotechnol 2025;41:112. [PMID: 40148700 DOI: 10.1007/s11274-025-04328-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 03/17/2025] [Indexed: 03/29/2025]
245
Davis LJ, Krunić A, Alexander KL, Khin M, Wood JS, Earp C, Rangel-Grimaldo M, Eustáquio AS, Burdette JE, Williamson RT, Oberlies NH, Orjala J. Menominin A and B: Cytotoxic Cyclodepsipeptides from the Freshwater Sponge-Associated Cyanobacterium Nostoc sp. UIC 10607. JOURNAL OF NATURAL PRODUCTS 2025;88:732-746. [PMID: 39977243 PMCID: PMC11952978 DOI: 10.1021/acs.jnatprod.4c01445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
246
Patra M, Pandey AK, Dubey SK. Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences. World J Microbiol Biotechnol 2025;41:114. [PMID: 40148599 DOI: 10.1007/s11274-025-04323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 03/13/2025] [Indexed: 03/29/2025]
247
Kiraz D, Özcan A. Comparative genome analysis of 15 Streptococcus thermophilus strains isolated from Turkish traditional yogurt. Antonie Van Leeuwenhoek 2025;118:64. [PMID: 40153053 DOI: 10.1007/s10482-025-02070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 02/27/2025] [Indexed: 03/30/2025]
248
Romyasamit C, Surachat K, Pattaranggoon NC, Suksabay P, Permpoon U, Nam TG, Sornsenee P. Phenotypic and Genomic Insights into Schleiferilactobacillus harbinensis WU01, a Candidate Probiotic with Broad-Spectrum Antimicrobial Activity Against ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) Pathogens. Foods 2025;14:1161. [PMID: 40238333 PMCID: PMC11989002 DOI: 10.3390/foods14071161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/18/2025]  Open
249
Vinskienė J, Tamošiūnė I, Andriūnaitė E, Gelvonauskienė D, Rugienius R, Hakim MF, Stanys V, Buzaitė O, Baniulis D. Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets. PLANTS (BASEL, SWITZERLAND) 2025;14:1045. [PMID: 40219113 PMCID: PMC11990893 DOI: 10.3390/plants14071045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/14/2025]
250
Martín-Díaz A, de Vega C, Martín-Hernanz S, Aparicio A, Albaladejo RG. De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms. Sci Data 2025;12:515. [PMID: 40148317 PMCID: PMC11950303 DOI: 10.1038/s41597-025-04888-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 03/24/2025] [Indexed: 03/29/2025]  Open
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