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For: Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. Microbiome 2022;10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Number Cited by Other Article(s)
1
Arend M, Paulitz E, Hsieh YE, Nikoloski Z. Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms. Metab Eng 2025;90:67-77. [PMID: 40081464 DOI: 10.1016/j.ymben.2025.02.015] [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: 09/20/2024] [Revised: 02/11/2025] [Accepted: 02/25/2025] [Indexed: 03/16/2025]
2
Delgado-Baquerizo M, Singh BK, Liu YR, Sáez-Sandino T, Coleine C, Muñoz-Rojas M, Bastida F, Trivedi P. Integrating ecological and evolutionary frameworks for SynCom success. THE NEW PHYTOLOGIST 2025;246:1922-1933. [PMID: 40177999 DOI: 10.1111/nph.70112] [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: 10/25/2024] [Accepted: 03/11/2025] [Indexed: 04/05/2025]
3
Li D, Li Z, Xu B, Chen T, Sun J, Hou J, Liu S. Microbial denitrification responses to elevated CO2 in lake-shore sediments under different flooding conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025;386:125835. [PMID: 40381298 DOI: 10.1016/j.jenvman.2025.125835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Revised: 04/25/2025] [Accepted: 05/13/2025] [Indexed: 05/20/2025]
4
Song X, Wang Y, Wang Y, Zhao K, Tong D, Gao R, Lv X, Kong D, Ruan Y, Wang M, Tang X, Li F, Luo Y, Zhu Y, Xu J, Ma B. Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation. Nat Commun 2025;16:4048. [PMID: 40307209 PMCID: PMC12044158 DOI: 10.1038/s41467-025-58695-5] [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: 09/07/2024] [Accepted: 03/26/2025] [Indexed: 05/02/2025]  Open
5
Chesneau G, Herpell J, Wolf SM, Perin S, Hacquard S. MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions. Nat Commun 2025;16:3310. [PMID: 40210863 PMCID: PMC11985495 DOI: 10.1038/s41467-025-58530-x] [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: 11/11/2024] [Accepted: 03/25/2025] [Indexed: 04/12/2025]  Open
6
Wang Q, Zhang J, Liang J, Wang Y, Ren C, Chen X, Cheng D, Zhang H, Liu H. Genomic Insights into Selenate Reduction by Anaerobacillus Species. Microorganisms 2025;13:659. [PMID: 40142551 PMCID: PMC11944866 DOI: 10.3390/microorganisms13030659] [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: 02/18/2025] [Revised: 03/11/2025] [Accepted: 03/11/2025] [Indexed: 03/28/2025]  Open
7
Delgado-Baquerizo M, Eldridge DJ, Liu YR, Liu ZW, Coleine C, Trivedi P. Soil biodiversity and function under global change. PLoS Biol 2025;23:e3003093. [PMID: 40146744 DOI: 10.1371/journal.pbio.3003093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2025] [Indexed: 03/29/2025]  Open
8
Zheng X, Li J, Ouyang Y, Wu G, He X, Wang D, Zhang XX. Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes. WATER RESEARCH 2024;267:122491. [PMID: 39353343 DOI: 10.1016/j.watres.2024.122491] [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: 06/02/2024] [Revised: 08/15/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024]
9
Li Z, Li D, Liu S, Zhao H, Li B, Shan S, Zhu Y, Sun J, Hou J. Impact of elevated CO2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;954:176481. [PMID: 39341255 DOI: 10.1016/j.scitotenv.2024.176481] [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: 04/03/2024] [Revised: 08/14/2024] [Accepted: 09/21/2024] [Indexed: 09/30/2024]
10
Peng X, Wang S, Wang M, Feng K, He Q, Yang X, Hou W, Li F, Zhao Y, Hu B, Zou X, Deng Y. Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks. Nat Commun 2024;15:8166. [PMID: 39289365 PMCID: PMC11408653 DOI: 10.1038/s41467-024-52532-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: 03/08/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]  Open
11
Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024;32:858-873. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [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: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
12
Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024;16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
13
Hsieh YE, Tandon K, Verbruggen H, Nikoloski Z. Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ Syst Biol Appl 2024;10:54. [PMID: 38783065 PMCID: PMC11116368 DOI: 10.1038/s41540-024-00384-y] [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: 01/06/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]  Open
14
Williams A, Sinanaj B, Hoysted GA. Plant-microbe interactions through a lens: tales from the mycorrhizosphere. ANNALS OF BOTANY 2024;133:399-412. [PMID: 38085925 PMCID: PMC11006548 DOI: 10.1093/aob/mcad191] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 04/12/2024]
15
Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024;48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]  Open
16
Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024;18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [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: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
17
Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota. Nat Commun 2023;14:8274. [PMID: 38092730 PMCID: PMC10719396 DOI: 10.1038/s41467-023-43688-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]  Open
18
Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023;18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
19
Tian Y, Liu Y, Uwaremwe C, Zhao X, Yue L, Zhou Q, Wang Y, Tran LSP, Li W, Chen G, Sha Y, Wang R. Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention. PLANT CELL REPORTS 2023;42:1757-1776. [PMID: 37674059 DOI: 10.1007/s00299-023-03060-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023]
20
Yuan J, Zhao K, Tan X, Xue R, Zeng Y, Ratti C, Trivedi P. Perspective on the development of synthetic microbial community (SynCom) biosensors. Trends Biotechnol 2023;41:1227-1236. [PMID: 37183053 DOI: 10.1016/j.tibtech.2023.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
21
Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023;24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]  Open
22
Cao Y, Du P, Zhang J, Ji J, Xu J, Liang B. Dopamine alleviates cadmium stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed by high-throughput sequencing and soil metabolomics. HORTICULTURE RESEARCH 2023;10:uhad112. [PMID: 37577402 PMCID: PMC10419553 DOI: 10.1093/hr/uhad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 08/15/2023]
23
Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023;18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
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