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For: Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420-8. [PMID: 22495754 DOI: 10.1093/bioinformatics/bts174] [Citation(s) in RCA: 2083] [Impact Index Per Article: 160.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Lee JS, Kao DJ, Worledge CS, Villamaria ZF, Wang RX, Welch NM, Kostelecky RE, Colgan SP. E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult. Gut Microbes 2025;17:2490211. [PMID: 40247632 PMCID: PMC12013446 DOI: 10.1080/19490976.2025.2490211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 12/27/2024] [Accepted: 04/03/2025] [Indexed: 04/19/2025]  Open
2
Yu Q, Hu X, Qian Y, Wang Y, Shi C, Qi R, Heděnec P, Nan Z, Li H. Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment. J Environ Sci (China) 2025;154:550-562. [PMID: 40049896 DOI: 10.1016/j.jes.2024.08.026] [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: 06/27/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 05/13/2025]
3
Zhang Y, Wang Q, Rogers MJ, He J. Autotrophic denitrification under anoxic conditions by newly discovered mixotrophic sulfide-oxidizing bacterium. BIORESOURCE TECHNOLOGY 2025;430:132553. [PMID: 40254100 DOI: 10.1016/j.biortech.2025.132553] [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: 02/18/2025] [Revised: 04/15/2025] [Accepted: 04/15/2025] [Indexed: 04/22/2025]
4
Li S, Ma K, Zhao Y, Zhou L, Zhang P, Liu H, Ye Y, Lin W, Winter JM, Wu G. Genome mining and characterization of bifunctional Clerodane Diterpene synthase from a fungus Myrothecium sp. Bioorg Chem 2025;161:108548. [PMID: 40315625 DOI: 10.1016/j.bioorg.2025.108548] [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: 02/24/2025] [Revised: 04/01/2025] [Accepted: 04/28/2025] [Indexed: 05/04/2025]
5
Kong L, Feng Y, Zheng R, Wu X, Mao Y, Sun J, Liu S. Interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria drives nitrogen loss. Nat Commun 2025;16:5078. [PMID: 40450007 DOI: 10.1038/s41467-025-60327-x] [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: 07/19/2024] [Accepted: 05/20/2025] [Indexed: 06/03/2025]  Open
6
Chen Y, Wang Y, Shaoyong W, He Y, Liu Y, Wei S, Gan Y, Sun L, Wang Y, Zong X, Xiang Y, Wang Y, Jin M. High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance. J Anim Sci Biotechnol 2025;16:73. [PMID: 40400039 PMCID: PMC12096716 DOI: 10.1186/s40104-025-01191-z] [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: 11/20/2024] [Accepted: 03/05/2025] [Indexed: 05/23/2025]  Open
7
Gast K, Baker S, Borges AL, Ward S, Banfield JF, Barrangou R. Metagenome-Derived CRISPR-Cas12a Mining and Characterization. CRISPR J 2025. [PMID: 40397663 DOI: 10.1089/crispr.2024.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025]  Open
8
Ge X, Wang J, Deng Z, Chai L, Cao W, Liu W, Zhang J, Yan C. Phylogenetic Analysis of the Family Lepidostomatidae (Trichoptera: Integripalpia) Using Whole Mitochondrial Genomes. INSECTS 2025;16:536. [PMID: 40429249 PMCID: PMC12111908 DOI: 10.3390/insects16050536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 05/15/2025] [Accepted: 05/16/2025] [Indexed: 05/29/2025]
9
Veseli I, Chen YT, Schechter MS, Vanni C, Fogarty EC, Watson AR, Jabri B, Blekhman R, Willis AD, Yu MK, Fernàndez-Guerra A, Füssel J, Eren AM. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. eLife 2025;12:RP89862. [PMID: 40377187 PMCID: PMC12084026 DOI: 10.7554/elife.89862] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]  Open
10
Vique G, Mendoza-Barberá E, Ramos-Barbero MD, Blanco-Picazo P, Sala-Comorera L, Quirós P, Atares S, Salaet I, Muniesa M, Rodríguez-Rubio L. Efficacy of Erwinia amylovora and Xanthomonas campestris pv campestris phages to control fire blight and black rot in vivo. Microbiol Spectr 2025:e0028025. [PMID: 40377312 DOI: 10.1128/spectrum.00280-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Accepted: 04/08/2025] [Indexed: 05/18/2025]  Open
11
Ji X, Yu X, Xu Y, Wu Q, Madadi M, Khaneghah AM. Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu. Int J Food Microbiol 2025;435:111182. [PMID: 40168753 DOI: 10.1016/j.ijfoodmicro.2025.111182] [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: 12/19/2024] [Revised: 02/10/2025] [Accepted: 03/25/2025] [Indexed: 04/03/2025]
12
Middlebrook E, Hathaway J, Pittis A, Abernathy G, Davenport K, Gleasner C, Mcmurry K, Kelliher J, Bartlow AW, Shakya M, Albright M, Kumar A, Hovde B, Youtsey B, Hanson B, Robinson A, Flynn M, Johnson S, Northup D, Dichosa AEK. Draft genome sequences of related Paeniglutamicibacter sp. isolates from two disparate cave systems. Microbiol Resour Announc 2025:e0012725. [PMID: 40298421 DOI: 10.1128/mra.00127-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 04/05/2025] [Indexed: 04/30/2025]  Open
13
Zhu X, Zheng C, Dong X, Tang Z, Wang Y, Yang R, Bu W. Native genetic structure of black bean bug Brachyplatys subaeneus: Implications for pest management. PEST MANAGEMENT SCIENCE 2025. [PMID: 40298072 DOI: 10.1002/ps.8854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 01/27/2025] [Accepted: 02/08/2025] [Indexed: 04/30/2025]
14
Sarkar P, Beebe M, Bhandari G, Wielinski J, Lowry GV, Gulliver D. Novel anaerobic selenium oxyanion reducers native to FGD wastewater for enhanced selenium removal. Appl Environ Microbiol 2025;91:e0122224. [PMID: 40084890 PMCID: PMC12016495 DOI: 10.1128/aem.01222-24] [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: 07/01/2024] [Accepted: 01/25/2025] [Indexed: 03/16/2025]  Open
15
Chen XY, Xiao XR, Zhang Y, Zhang ZC, Zhang DS, Liu Z, Lin XL. Comparative Mitogenomic Analyses of Psectrocladius (Diptera: Chironomidae). INSECTS 2025;16:420. [PMID: 40332987 PMCID: PMC12027813 DOI: 10.3390/insects16040420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Revised: 04/15/2025] [Accepted: 04/15/2025] [Indexed: 05/08/2025]
16
Guo M, Wang A, Zheng Y, Liu C, Shao Q, Deng Y, Li L, Wang Y, Wang X, Shen Y, Qian J, Zhou X, Fang Q. Cryo-EM structures of a Xanthomonas phage: Insights into viral architecture and implications for the model phage HK97. Structure 2025:S0969-2126(25)00133-9. [PMID: 40273907 DOI: 10.1016/j.str.2025.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 02/19/2025] [Accepted: 03/30/2025] [Indexed: 04/26/2025]
17
Dakal TC, Xu C, Kumar A. Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification. FRONTIERS IN MEDICAL TECHNOLOGY 2025;6:1434799. [PMID: 40303946 PMCID: PMC12037385 DOI: 10.3389/fmedt.2024.1434799] [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: 07/23/2024] [Accepted: 10/16/2024] [Indexed: 05/02/2025]  Open
18
Doorenspleet K, Mailli AA, van der Hoorn BB, Beentjes KK, De Backer A, Derycke S, Murk AJ, Reiss H, Nijland R. Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics. PeerJ 2025;13:e19158. [PMID: 40247828 PMCID: PMC12005195 DOI: 10.7717/peerj.19158] [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: 06/13/2024] [Accepted: 02/21/2025] [Indexed: 04/19/2025]  Open
19
Li Y, Liu Q, Chen Z, Liang L, Wang Z, Duan Y, Song F, Cai W, Ge J, Li H, Tian L. Turning lances into shields: flower mantids stretch their raptorial forelegs to avert and deflect predator attack. Proc Biol Sci 2025;292:20243081. [PMID: 40169024 PMCID: PMC11961251 DOI: 10.1098/rspb.2024.3081] [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: 12/25/2024] [Revised: 02/16/2025] [Accepted: 03/06/2025] [Indexed: 04/03/2025]  Open
20
Yang X, Tang S, Du C, Chen Y, Luo Z, Li M, Liu S, Duan M, Jiang D, Shen Y, Zhang Q, Du C. Insights into the mitochondrial genome structure and phylogenetic placement of Theileria velifera in comparison to other apicomplexan parasites. Sci Rep 2025;15:10637. [PMID: 40148485 PMCID: PMC11950482 DOI: 10.1038/s41598-025-92939-0] [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: 09/19/2024] [Accepted: 03/04/2025] [Indexed: 03/29/2025]  Open
21
Kantor RS, Kennedy LC, Miller SE, Favere J, Nelson KL. Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community. ACS ES&T ENGINEERING 2025;5:772-781. [PMID: 40109356 PMCID: PMC11915367 DOI: 10.1021/acsestengg.4c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 03/22/2025]
22
Cao H, Xu J, Wang H, Yi W, Yang D, Yang J, Sun J, Wang Y, Zhang F, Yan J, Li D. Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis. BMC Microbiol 2025;25:135. [PMID: 40075266 PMCID: PMC11905490 DOI: 10.1186/s12866-025-03853-4] [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: 10/02/2024] [Accepted: 02/28/2025] [Indexed: 03/14/2025]  Open
23
Li R, Chen J, Wu Y, Lu M, Cheng G, Jia P, Yu S, Xie X, Zhang G, Xu Y, Zhang L, Liu Y. Molecular and biological characteristics of two rare bloodstream Candida isolates: Candida nonsorbophila and Candida sonorensis. BMC Infect Dis 2025;25:348. [PMID: 40075268 PMCID: PMC11905472 DOI: 10.1186/s12879-025-10696-x] [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: 07/08/2024] [Accepted: 02/19/2025] [Indexed: 03/14/2025]  Open
24
Kioukis A, Camargo AP, Pavlidis P, Iliopoulos I, Kyrpides NC, Lagkouvardos I. Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg. Microorganisms 2025;13:598. [PMID: 40142491 PMCID: PMC11944491 DOI: 10.3390/microorganisms13030598] [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: 01/24/2025] [Revised: 02/27/2025] [Accepted: 02/28/2025] [Indexed: 03/28/2025]  Open
25
Zheng R, Kong L, Feng Y, Chen B, Gu Y, Wu X, Liu S. Siderophore-Mediated Cooperation in Anammox Consortia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025;59:4003-4013. [PMID: 39960253 DOI: 10.1021/acs.est.4c11142] [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: 03/05/2025]
26
Liu ZS, Wang KH, Wang XK, Cai M, Yang ML, Yang WK, Li DF, Liu SJ. Curvibacter soli sp. nov., Extensimonas soli sp. nov., Pseudarthrobacter naphthalenicus sp. nov. and Terripilifer ovatus gen. nov., sp. nov., four new species isolated from polluted soil. Int J Syst Evol Microbiol 2025;75:006698. [PMID: 40048583 PMCID: PMC11936349 DOI: 10.1099/ijsem.0.006698] [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: 03/12/2024] [Accepted: 02/16/2025] [Indexed: 03/27/2025]  Open
27
Hai C, Wang L, Wu D, Pei D, Yang Y, Liu X, Zhao Y, Bai C, Su G, Bao Z, Yang L, Li G. Loss of Myostatin leads to low production of CH4 by altering rumen microbiota and metabolome in cattle. Int J Biol Macromol 2025;294:139533. [PMID: 39761884 DOI: 10.1016/j.ijbiomac.2025.139533] [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: 01/19/2024] [Revised: 01/01/2025] [Accepted: 01/03/2025] [Indexed: 02/20/2025]
28
Braga CM, da Silva SP, Neto JPN, Medeiros DBDA, Cruz ACR, Nascimento BLSD, Pinheiro LRS, Martins LC. Viral metagenomics of hematophagous insects collected in the Carajas mining complex, Pará State, Brazil. Acta Trop 2025;263:107551. [PMID: 39938727 DOI: 10.1016/j.actatropica.2025.107551] [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: 12/19/2024] [Revised: 01/28/2025] [Accepted: 02/09/2025] [Indexed: 02/14/2025]
29
Wu S, Zhang W, Wang D, Balcazar JL, Wang G, Ye M, Chao H, Sun M, Hu F. Bacteriophage-Bacteria Interactions Promote Ecological Multifunctionality in Compost-Applied Soils. Environ Microbiol 2025;27:e70074. [PMID: 40109201 DOI: 10.1111/1462-2920.70074] [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: 10/06/2024] [Revised: 02/01/2025] [Accepted: 02/18/2025] [Indexed: 03/22/2025]
30
Frederico TD, Cunha-Ferreira IC, Vizzotto CS, de Sousa JF, Portugal MM, Tótola MR, Krüger RH, Peixoto J. Genomic and taxonomic characterization of the Comamonas sp. nov., a bacterium isolated from Brazilian Cerrado soil. Braz J Microbiol 2025;56:137-154. [PMID: 39576463 PMCID: PMC11885727 DOI: 10.1007/s42770-024-01566-w] [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: 09/12/2024] [Accepted: 11/06/2024] [Indexed: 03/09/2025]  Open
31
Santos CA, Morais MAB, Mandelli F, Lima EA, Miyamoto RY, Higasi PMR, Araujo EA, Paixão DAA, Junior JM, Motta ML, Streit RSA, Morão LG, Silva CBC, Wolf LD, Terrasan CRF, Bulka NR, Diogo JA, Fuzita FJ, Colombari FM, Santos CR, Rodrigues PT, Silva DB, Grisel S, Bernardes JS, Terrapon N, Lombard V, Filho AJC, Henrissat B, Bissaro B, Berrin JG, Persinoti GF, Murakami MT. A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion. Nature 2025;639:1076-1083. [PMID: 39939775 PMCID: PMC11946906 DOI: 10.1038/s41586-024-08553-z] [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: 06/05/2024] [Accepted: 12/19/2024] [Indexed: 02/14/2025]
32
Velazquez-Meza ME, Galarde-López M, Cornejo-Juárez P, Bobadilla-del-Valle M, Godoy-Lozano E, Aguilar-Vera E, Carrillo-Quiroz BA, Ponce de León-Garduño A, Velazquez Acosta C, Alpuche-Aranda CM. Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis. Int J Mol Sci 2025;26:2051. [PMID: 40076673 PMCID: PMC11900532 DOI: 10.3390/ijms26052051] [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: 01/08/2025] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/14/2025]  Open
33
Wu DG, Harris CR, Kalis KM, Bowen M, Biddle JF, Farag IF. Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments. Appl Environ Microbiol 2025;91:e0222924. [PMID: 39840973 PMCID: PMC11837501 DOI: 10.1128/aem.02229-24] [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: 11/08/2024] [Accepted: 12/19/2024] [Indexed: 01/23/2025]  Open
34
Liu C, Chen Z, Wang X, Deng Y, Tao L, Zhou X, Deng J. Response of Soil Phage Communities and Prokaryote-Phage Interactions to Long-Term Drought. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025;59:3054-3066. [PMID: 39919201 DOI: 10.1021/acs.est.4c08448] [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: 02/09/2025]
35
Chrzastek K, Seal BS, Kulkarni A, Kapczynski DR. Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification. Vet Sci 2025;12:162. [PMID: 40005922 PMCID: PMC11861695 DOI: 10.3390/vetsci12020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 01/30/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025]  Open
36
Veluz JT, Mallari LAN, Gloria PCT, Siringan MAT. Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes. Front Genet 2025;16:1522253. [PMID: 40028274 PMCID: PMC11868764 DOI: 10.3389/fgene.2025.1522253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 01/13/2025] [Indexed: 03/05/2025]  Open
37
Wu H, Shi C, Xu T, Dai X, Zhao D. Characterization and Optimization of Cellulose-Degrading Bacteria Isolated from Fecal Samples of Elaphurus davidianus Through Response Surface Methodology. Microorganisms 2025;13:348. [PMID: 40005715 PMCID: PMC11858180 DOI: 10.3390/microorganisms13020348] [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: 09/07/2024] [Revised: 11/07/2024] [Accepted: 11/18/2024] [Indexed: 02/27/2025]  Open
38
Prabhaharan D, Go YW, Kim H, Kang S, Sang BI. Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea. Sci Data 2025;12:198. [PMID: 39900940 PMCID: PMC11791102 DOI: 10.1038/s41597-024-04315-8] [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: 09/11/2024] [Accepted: 12/17/2024] [Indexed: 02/05/2025]  Open
39
Tian J, Gao Z, Li M, Bao E, Zhao J. Accurate assembly of full-length consensus for viral quasispecies. BMC Bioinformatics 2025;26:36. [PMID: 39893441 PMCID: PMC11787740 DOI: 10.1186/s12859-025-06045-z] [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: 07/24/2024] [Accepted: 01/10/2025] [Indexed: 02/04/2025]  Open
40
Qayyum H, Talib MS, Ali A, Kayani MUR. Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes. Heliyon 2025;11:e41938. [PMID: 39897886 PMCID: PMC11786835 DOI: 10.1016/j.heliyon.2025.e41938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 01/08/2025] [Accepted: 01/13/2025] [Indexed: 02/04/2025]  Open
41
Bechtold EK, Ellenbogen JB, Villa JA, de Melo Ferreira DK, Oliverio AM, Kostka JE, Rich VI, Varner RK, Bansal S, Ward EJ, Bohrer G, Borton MA, Wrighton KC, Wilkins MJ. Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands. Nat Commun 2025;16:944. [PMID: 39843444 PMCID: PMC11754854 DOI: 10.1038/s41467-025-56133-0] [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: 06/04/2024] [Accepted: 01/09/2025] [Indexed: 01/24/2025]  Open
42
He Z, Burckhardt D, Luo X, Xu R, Cai W, Song F. A Review of the Psyllid Genus Epipsylla (Hemiptera, Psyllidae) from the Chinese Mainland with Phylogenetic Considerations and the Description of a New Species. INSECTS 2025;16:99. [PMID: 39859680 PMCID: PMC11766207 DOI: 10.3390/insects16010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/13/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025]
43
Kashchenko G, Taldaev A, Adonin L, Smutin D. Investigating Aerobic Hive Microflora: Role of Surface Microbiome of Apis Mellifera. BIOLOGY 2025;14:88. [PMID: 39857318 PMCID: PMC11760457 DOI: 10.3390/biology14010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 01/06/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025]
44
Winn JN, Wedlock EA, McHugh EP, Monismith, Jr. D, Campbell JH, Campbell AG. Permanent draft genome sequences of cadmium-resistant isolates of Cupriavidus from soils within the Tar Creek Superfund site. Microbiol Resour Announc 2025;14:e0081824. [PMID: 39589146 PMCID: PMC11737155 DOI: 10.1128/mra.00818-24] [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: 07/23/2024] [Accepted: 10/28/2024] [Indexed: 11/27/2024]  Open
45
Song H, Tithi SS, Brown C, Aylward FO, Jensen R, Zhang L. Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation. PeerJ 2025;13:e18515. [PMID: 39807156 PMCID: PMC11727651 DOI: 10.7717/peerj.18515] [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: 06/17/2024] [Accepted: 10/21/2024] [Indexed: 01/16/2025]  Open
46
Ribeyre Z, Depardieu C, Prunier J, Pelletier G, Parent GJ, Mackay J, Droit A, Bousquet J, Nolet P, Messier C. De novo transcriptome assembly and discovery of drought-responsive genes in white spruce (Picea glauca). PLoS One 2025;20:e0316661. [PMID: 39752431 PMCID: PMC11698436 DOI: 10.1371/journal.pone.0316661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 12/13/2024] [Indexed: 01/06/2025]  Open
47
Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Singleton DM, Bambakidis T, Pelly A, Daly RA, Liu F, Freiburger A, Edirisinghe JN, Faria JP, Danczak R, Leleiwi I, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Good SP, Sullivan MB, Wood-Charlson EM, Miller CS, Ross MRV, Henry CS, Crump BC, Stegen JC, Wrighton KC. A functional microbiome catalogue crowdsourced from North American rivers. Nature 2025;637:103-112. [PMID: 39567690 PMCID: PMC11666465 DOI: 10.1038/s41586-024-08240-z] [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: 07/25/2023] [Accepted: 10/17/2024] [Indexed: 11/22/2024]
48
Hemeda AA, Zahran SA, Ali-Tammam M, Ewida MA, Kashef MT, Yassin AS, Mitra A, Youssef NH, Elshahed MS. Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges. J Ind Microbiol Biotechnol 2024;52:kuaf006. [PMID: 40036345 PMCID: PMC11905756 DOI: 10.1093/jimb/kuaf006] [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: 09/24/2024] [Accepted: 02/25/2025] [Indexed: 03/06/2025]
49
Chen B, Duan M, Liu S, Liu Y, Tang S, Jiang D, Gu W, Zhang Q, Yang X. The complete mitochondrial genome and phylogenetic implications of Paradoxopsyllus custodis and Stenischia montanis yunlongensis. Sci Rep 2024;14:31555. [PMID: 39738824 PMCID: PMC11685425 DOI: 10.1038/s41598-024-84175-9] [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: 10/01/2024] [Accepted: 12/20/2024] [Indexed: 01/02/2025]  Open
50
Song HY, Choi YJ, Lee DS, Choi HK, Choi KM, Yu KY, Cho N, Lee S. Identification and characterization of 17 novel polynucleotide microsatellite markers in Ocypode stimpsoni (Decapoda: Ocypodidae). BMC Res Notes 2024;17:396. [PMID: 39736772 DOI: 10.1186/s13104-024-07049-3] [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: 12/13/2023] [Accepted: 12/18/2024] [Indexed: 01/01/2025]  Open
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