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For: Liu F, Mao J, Kong W, Hua Q, Feng Y, Bashir R, Lu T. Interaction variability shapes succession of synthetic microbial ecosystems. Nat Commun 2020;11:309. [PMID: 31949154 PMCID: PMC6965111 DOI: 10.1038/s41467-019-13986-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 12/09/2019] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Huang X, Li R, Xu J, Kang J, Chen X, Han B, Xue Y. Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome. Food Res Int 2025;208:116061. [PMID: 40263874 DOI: 10.1016/j.foodres.2025.116061] [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: 07/12/2024] [Revised: 01/08/2025] [Accepted: 02/22/2025] [Indexed: 04/24/2025]
2
Huang X, Kang J, Zhang Y, Chen X, Han B. Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor Baijiu. Food Chem X 2025;25:101982. [PMID: 39801587 PMCID: PMC11721831 DOI: 10.1016/j.fochx.2024.101982] [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: 08/04/2024] [Revised: 11/01/2024] [Accepted: 11/06/2024] [Indexed: 01/16/2025]  Open
3
Choudhary R, Mahadevan R. DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities. Biophys J 2024;123:2974-2995. [PMID: 38733081 PMCID: PMC11427784 DOI: 10.1016/j.bpj.2024.05.006] [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: 01/27/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]  Open
4
Qi J, Gao T, Zhou Q, Huang S, Lin J, Xu R, Tang CY, Meng F. Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39078411 DOI: 10.1021/acs.est.4c03038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
5
Kang J, Huang X, Li R, Zhang Y, Chen XX, Han BZ. Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review. Food Res Int 2024;188:114497. [PMID: 38823877 DOI: 10.1016/j.foodres.2024.114497] [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: 12/28/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
6
Wang J, Appidi MR, Burdick LH, Abraham PE, Hettich RL, Pelletier DA, Doktycz MJ. Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition. mSystems 2024;9:e0000624. [PMID: 38470038 PMCID: PMC11019790 DOI: 10.1128/msystems.00006-24] [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: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/13/2024]  Open
7
Hedin KA, Mirhakkak MH, Vaaben TH, Sands C, Pedersen M, Baker A, Vazquez-Uribe R, Schäuble S, Panagiotou G, Wellejus A, Sommer MOA. Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities. THE ISME JOURNAL 2024;18:wrae212. [PMID: 39488793 PMCID: PMC11631509 DOI: 10.1093/ismejo/wrae212] [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: 08/30/2024] [Revised: 10/17/2024] [Accepted: 11/01/2024] [Indexed: 11/04/2024]
8
Wang X, Teng Y, Wang X, Xu Y, Li R, Sun Y, Dai S, Hu W, Wang H, Li Y, Fang Y, Luo Y. Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation. THE ISME JOURNAL 2023;17:2169-2181. [PMID: 37775536 PMCID: PMC10689768 DOI: 10.1038/s41396-023-01522-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
9
Syed Z, Sogani M, Rajvanshi J, Sonu K. Microbial Biofilms for Environmental Bioremediation of Heavy Metals: a Review. Appl Biochem Biotechnol 2023;195:5693-5711. [PMID: 36576654 DOI: 10.1007/s12010-022-04276-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 12/29/2022]
10
Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023;21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
11
Zhang C, Mu Y, Li T, Jin FJ, Jin CZ, Oh HM, Lee HG, Jin L. Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere". Front Microbiol 2023;14:1181967. [PMID: 37138608 PMCID: PMC10150012 DOI: 10.3389/fmicb.2023.1181967] [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: 03/08/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023]  Open
12
Moon TS. SynMADE: synthetic microbiota across diverse ecosystems. Trends Biotechnol 2022;40:1405-1414. [PMID: 36117027 DOI: 10.1016/j.tibtech.2022.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 01/21/2023]
13
Nagarajan K, Ni C, Lu T. Agent-Based Modeling of Microbial Communities. ACS Synth Biol 2022;11:3564-3574. [PMID: 36315012 PMCID: PMC10129392 DOI: 10.1021/acssynbio.2c00411] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
14
Ni C, Lu T. Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations. ACS Synth Biol 2022;11:3714-3723. [PMID: 36336839 PMCID: PMC10129442 DOI: 10.1021/acssynbio.2c00322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
15
Yang D, Kato H, Kawatsu K, Osada Y, Azuma T, Nagata Y, Kondoh M. Reconstruction of a Soil Microbial Network Induced by Stress Temperature. Microbiol Spectr 2022;10:e0274822. [PMID: 35972265 PMCID: PMC9602341 DOI: 10.1128/spectrum.02748-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023]  Open
16
Yu Z, Huang Y, Gan Z, Meng Y, Meng F. State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022;56:12765-12777. [PMID: 35943816 DOI: 10.1021/acs.est.2c02844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
17
Huang X, Xin Y, Lu T. A systematic, complexity-reduction approach to dissect the kombucha tea microbiome. eLife 2022;11:76401. [PMID: 35950909 PMCID: PMC9371603 DOI: 10.7554/elife.76401] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/03/2022] [Indexed: 12/14/2022]  Open
18
Jiang W, Yang X, Gu F, Li X, Wang S, Luo Y, Qi Q, Liang Q. Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion. ACS Synth Biol 2022;11:538-546. [PMID: 35044170 DOI: 10.1021/acssynbio.1c00354] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
19
Liao YL, Niu FX, Liu JZ. Recent Progress in Microbial Biosynthesis by Coculture Engineering. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
20
Venturi V, Bez C. A call to arms for cell-cell interactions between bacteria in the plant microbiome. TRENDS IN PLANT SCIENCE 2021;26:1126-1132. [PMID: 34334316 DOI: 10.1016/j.tplants.2021.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 05/17/2023]
21
A light tunable differentiation system for the creation and control of consortia in yeast. Nat Commun 2021;12:5829. [PMID: 34611168 PMCID: PMC8492667 DOI: 10.1038/s41467-021-26129-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]  Open
22
Gupta G, Ndiaye A, Filteau M. Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. Front Microbiol 2021;12:700752. [PMID: 34646243 PMCID: PMC8503676 DOI: 10.3389/fmicb.2021.700752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022]  Open
23
Yuan S, Xu R, Wang D, Lin Q, Zhou S, Lin J, Xia L, Fu Y, Gan Z, Meng F. Ecological Linkages between a Biofilm Ecosystem and Reactor Performance: The Specificity of Biofilm Development Phases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021;55:11948-11960. [PMID: 34415760 DOI: 10.1021/acs.est.1c02486] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
24
The spatial organization of microbial communities during range expansion. Curr Opin Microbiol 2021;63:109-116. [PMID: 34329942 DOI: 10.1016/j.mib.2021.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/26/2021] [Accepted: 07/05/2021] [Indexed: 12/28/2022]
25
Wu S, Xu C, Liu J, Liu C, Qiao J. Vertical and horizontal quorum-sensing-based multicellular communications. Trends Microbiol 2021;29:1130-1142. [PMID: 34020859 DOI: 10.1016/j.tim.2021.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
26
Wang J, Carper DL, Burdick LH, Shrestha HK, Appidi MR, Abraham PE, Timm CM, Hettich RL, Pelletier DA, Doktycz MJ. Formation, characterization and modeling of emergent synthetic microbial communities. Comput Struct Biotechnol J 2021;19:1917-1927. [PMID: 33995895 PMCID: PMC8079826 DOI: 10.1016/j.csbj.2021.03.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023]  Open
27
Diender M, Parera Olm I, Sousa DZ. Synthetic co-cultures: novel avenues for bio-based processes. Curr Opin Biotechnol 2021;67:72-79. [PMID: 33517194 DOI: 10.1016/j.copbio.2021.01.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
28
Rain-Franco A, de Moraes GP, Beier S. Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities. Front Microbiol 2021;11:597653. [PMID: 33584565 PMCID: PMC7877341 DOI: 10.3389/fmicb.2020.597653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/30/2020] [Indexed: 11/25/2022]  Open
29
Ursell T. Structured environments foster competitor coexistence by manipulating interspecies interfaces. PLoS Comput Biol 2021;17:e1007762. [PMID: 33412560 PMCID: PMC7790539 DOI: 10.1371/journal.pcbi.1007762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023]  Open
30
Yuan S, Yu Z, Pan S, Huang J, Meng F. Deciphering the succession dynamics of dominant and rare genera in biofilm development process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020;739:139961. [PMID: 32540665 DOI: 10.1016/j.scitotenv.2020.139961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
31
Regularized S-Map Reveals Varying Bacterial Interactions. Appl Environ Microbiol 2020;86:AEM.01615-20. [PMID: 32801185 DOI: 10.1128/aem.01615-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022]  Open
32
Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments. Sci Rep 2020;10:8383. [PMID: 32433471 PMCID: PMC7239927 DOI: 10.1038/s41598-020-64921-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/23/2020] [Indexed: 01/17/2023]  Open
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