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For: Van Goethem MW, Osborn AR, Bowen BP, Andeer PF, Swenson TL, Clum A, Riley R, He G, Koriabine M, Sandor L, Yan M, Daum CG, Yoshinaga Y, Makhalanyane TP, Garcia-Pichel F, Visel A, Pennacchio LA, O'Malley RC, Northen TR. Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Commun Biol 2021;4:1302. [PMID: 34795375 DOI: 10.1038/s42003-021-02809-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]  Open
Number Cited by Other Article(s)
1
Dinglasan JLN, Otani H, Doering DT, Udwary D, Mouncey NJ. Microbial secondary metabolites: advancements to accelerate discovery towards application. Nat Rev Microbiol 2025;23:338-354. [PMID: 39824928 DOI: 10.1038/s41579-024-01141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2024] [Indexed: 01/20/2025]
2
Medeiros W, Kralova S, Oliveira V, Ziemert N, Sehnal L. Antarctic bacterial natural products: from genomic insights to drug discovery. Nat Prod Rep 2025;42:774-787. [PMID: 39996333 DOI: 10.1039/d4np00045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
3
Salamzade R, Kalan LR. Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution. mSystems 2025;10:e0153824. [PMID: 39992097 PMCID: PMC11915812 DOI: 10.1128/msystems.01538-24] [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] [Indexed: 02/25/2025]  Open
4
Barber DG, Child HT, Joslin GR, Wierzbicki L, Tennant RK. Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics. Sci Rep 2024;14:28934. [PMID: 39578630 PMCID: PMC11584900 DOI: 10.1038/s41598-024-80584-y] [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: 07/10/2024] [Accepted: 11/19/2024] [Indexed: 11/24/2024]  Open
5
Smith GJ, van Alen TA, van Kessel MA, Lücker S. Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly. PeerJ 2024;12:e18132. [PMID: 39529629 PMCID: PMC11552494 DOI: 10.7717/peerj.18132] [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: 09/18/2023] [Accepted: 08/29/2024] [Indexed: 11/16/2024]  Open
6
Cansdale A, Chong JPJ. MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes. MICROBIOME 2024;12:226. [PMID: 39490992 PMCID: PMC11533350 DOI: 10.1186/s40168-024-01949-z] [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: 12/19/2023] [Accepted: 10/13/2024] [Indexed: 11/05/2024]
7
Barrett SE, Mitchell DA. Advances in lasso peptide discovery, biosynthesis, and function. Trends Genet 2024;40:950-968. [PMID: 39218755 PMCID: PMC11537843 DOI: 10.1016/j.tig.2024.08.002] [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: 06/03/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
8
Kazantseva E, Donmez A, Frolova M, Pop M, Kolmogorov M. Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing. Nat Methods 2024;21:2034-2043. [PMID: 39327484 DOI: 10.1038/s41592-024-02424-1] [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: 11/22/2023] [Accepted: 08/22/2024] [Indexed: 09/28/2024]
9
Andreani-Gerard CM, Cambiazo V, González M. Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert. mSphere 2024;9:e0019224. [PMID: 39287428 PMCID: PMC11520301 DOI: 10.1128/msphere.00192-24] [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: 03/05/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024]  Open
10
Sanguineti D, Zampieri G, Treu L, Campanaro S. Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads. mSystems 2024;9:e0021324. [PMID: 38980053 PMCID: PMC11338496 DOI: 10.1128/msystems.00213-24] [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: 02/14/2024] [Accepted: 06/15/2024] [Indexed: 07/10/2024]  Open
11
Gao Y, Zhong Z, Zhang D, Zhang J, Li YX. Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining. MICROBIOME 2024;12:94. [PMID: 38790030 PMCID: PMC11118758 DOI: 10.1186/s40168-024-01807-y] [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: 11/11/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
12
Zhang Z, Zhang L, Zhang L, Chu H, Zhou J, Ju F. Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes. mSystems 2024;9:e0126323. [PMID: 38470142 PMCID: PMC11019929 DOI: 10.1128/msystems.01263-23] [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: 11/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024]  Open
13
Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024;48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024]  Open
14
Rosenzweig AF, Burian J, Brady SF. Present and future outlooks on environmental DNA-based methods for antibiotic discovery. Curr Opin Microbiol 2023;75:102335. [PMID: 37327680 PMCID: PMC11076179 DOI: 10.1016/j.mib.2023.102335] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
15
Garcia-Pichel F. The Microbiology of Biological Soil Crusts. Annu Rev Microbiol 2023;77:149-171. [PMID: 37068777 DOI: 10.1146/annurev-micro-032521-015202] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
16
Mukherjee A, Tikariha H, Bandla A, Pavagadhi S, Swarup S. Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes. mSystems 2023;8:e0038723. [PMID: 37409823 PMCID: PMC10469690 DOI: 10.1128/msystems.00387-23] [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: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023]  Open
17
Huang R, Wang Y, Liu D, Wang S, Lv H, Yan Z. Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites. Microbiol Spectr 2023;11:e0150123. [PMID: 37409950 PMCID: PMC10434046 DOI: 10.1128/spectrum.01501-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]  Open
18
Dow L, Gallart M, Ramarajan M, Law SR, Thatcher LF. Streptomyces and their specialised metabolites for phytopathogen control - comparative in vitro and in planta metabolic approaches. FRONTIERS IN PLANT SCIENCE 2023;14:1151912. [PMID: 37389291 PMCID: PMC10301723 DOI: 10.3389/fpls.2023.1151912] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
19
Bhattacharjee A, Sarma S, Sen T, Devi MV, Deka B, Singh AK. Genome mining to identify valuable secondary metabolites and their regulation in Actinobacteria from different niches. Arch Microbiol 2023;205:127. [PMID: 36944761 DOI: 10.1007/s00203-023-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
20
Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges. Mar Drugs 2022;21:md21010029. [PMID: 36662202 PMCID: PMC9864124 DOI: 10.3390/md21010029] [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: 11/22/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]  Open
21
Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem. mSystems 2022;7:e0063222. [PMID: 36445112 PMCID: PMC9765116 DOI: 10.1128/msystems.00632-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
22
Sofiev M, Sofieva S, Palamarchuk J, Šaulienė I, Kadantsev E, Atanasova N, Fatahi Y, Kouznetsov R, Kuula J, Noreikaite A, Peltonen M, Pihlajamäki T, Saarto A, Svirskaite J, Toiviainen L, Tyuryakov S, Šukienė L, Asmi E, Bamford D, Hyvärinen AP, Karppinen A. Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign. ENVIRONMENTAL RESEARCH 2022;214:113798. [PMID: 35810819 DOI: 10.1016/j.envres.2022.113798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
23
Mackelprang R, Vaishampayan P, Fisher K. Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities. mSystems 2022;7:e0141921. [PMID: 35852333 PMCID: PMC9426607 DOI: 10.1128/msystems.01419-21] [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: 11/29/2021] [Accepted: 06/30/2022] [Indexed: 12/24/2022]  Open
24
Djemiel C, Dequiedt S, Karimi B, Cottin A, Horrigue W, Bailly A, Boutaleb A, Sadet-Bourgeteau S, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L, Terrat S. Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production. Front Microbiol 2022;13:889788. [PMID: 35847063 PMCID: PMC9280627 DOI: 10.3389/fmicb.2022.889788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023]  Open
25
Dulić T, Svirčev Z, Palanački Malešević T, Faassen EJ, Savela H, Hao Q, Meriluoto J. Assessment of Common Cyanotoxins in Cyanobacteria of Biological Loess Crusts. Toxins (Basel) 2022;14:toxins14030215. [PMID: 35324712 PMCID: PMC8953721 DOI: 10.3390/toxins14030215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/27/2022] [Accepted: 03/11/2022] [Indexed: 12/23/2022]  Open
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