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For: Dubinkina V, Fridman Y, Pandey PP, Maslov S. Multistability and regime shifts in microbial communities explained by competition for essential nutrients. eLife 2019;8:e49720. [PMID: 31756158 PMCID: PMC6874476 DOI: 10.7554/elife.49720] [Citation(s) in RCA: 29] [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: 06/27/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Silverstein MR, Bhatnagar JM, Segrè D. Metabolic complexity drives divergence in microbial communities. Nat Ecol Evol 2024:10.1038/s41559-024-02440-6. [PMID: 38956426 DOI: 10.1038/s41559-024-02440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
2
Hu Y, Cai J, Song Y, Li G, Gong Y, Jiang X, Tang X, Shao K, Gao G. Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake. MICROBIAL ECOLOGY 2024;87:68. [PMID: 38722447 PMCID: PMC11082002 DOI: 10.1007/s00248-024-02365-4] [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: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 05/12/2024]
3
Ng E, Tay JRH, Mattheos N, Bostanci N, Belibasakis GN, Seneviratne CJ. A Mapping Review of the Pathogenesis of Peri-Implantitis: The Biofilm-Mediated Inflammation and Bone Dysregulation (BIND) Hypothesis. Cells 2024;13:315. [PMID: 38391928 PMCID: PMC10886485 DOI: 10.3390/cells13040315] [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: 12/07/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]  Open
4
Qiao Y, Huang Q, Guo H, Qi M, Zhang H, Xu Q, Shen Q, Ling N. Nutrient status changes bacterial interactions in a synthetic community. Appl Environ Microbiol 2024;90:e0156623. [PMID: 38126758 PMCID: PMC10807438 DOI: 10.1128/aem.01566-23] [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: 09/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]  Open
5
Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023;87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023]  Open
6
Skwara A, Gowda K, Yousef M, Diaz-Colunga J, Raman AS, Sanchez A, Tikhonov M, Kuehn S. Statistically learning the functional landscape of microbial communities. Nat Ecol Evol 2023;7:1823-1833. [PMID: 37783827 PMCID: PMC11088814 DOI: 10.1038/s41559-023-02197-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/11/2023] [Indexed: 10/04/2023]
7
George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023;17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
8
Revel-Muroz A, Akulinin M, Shilova P, Tyakht A, Klimenko N. Stability of human gut microbiome: Comparison of ecological modelling and observational approaches. Comput Struct Biotechnol J 2023;21:4456-4468. [PMID: 37745638 PMCID: PMC10511340 DOI: 10.1016/j.csbj.2023.08.030] [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: 06/20/2023] [Revised: 08/27/2023] [Accepted: 08/27/2023] [Indexed: 09/26/2023]  Open
9
Lee CY, Diegel J, France MT, Ravel J, Arnold KB. Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy. PLoS Comput Biol 2023;19:e1011295. [PMID: 37566641 PMCID: PMC10446192 DOI: 10.1371/journal.pcbi.1011295] [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: 01/30/2023] [Revised: 08/23/2023] [Accepted: 06/23/2023] [Indexed: 08/13/2023]  Open
10
Schäfer M, Pacheco AR, Künzler R, Bortfeld-Miller M, Field CM, Vayena E, Hatzimanikatis V, Vorholt JA. Metabolic interaction models recapitulate leaf microbiota ecology. Science 2023;381:eadf5121. [PMID: 37410834 DOI: 10.1126/science.adf5121] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
11
Zeng X, Zou Y, Zheng J, Qiu S, Liu L, Wei C. Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives. Microbiol Res 2023;273:127414. [PMID: 37236065 DOI: 10.1016/j.micres.2023.127414] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
12
Moore ER, Suazo D, Babilonia J, Montoya KN, Gallegos-Graves LV, Sevanto S, Dunbar J, Albright MBN. Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities. mSystems 2023:e0122022. [PMID: 37133282 DOI: 10.1128/msystems.01220-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]  Open
13
Newton DP, Ho PY, Huang KC. Modulation of antibiotic effects on microbial communities by resource competition. Nat Commun 2023;14:2398. [PMID: 37100773 PMCID: PMC10133249 DOI: 10.1038/s41467-023-37895-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 04/28/2023]  Open
14
Moore ER, Suazo D, Babilonia J, Montoya KN, Gallegos-Graves LV, Sevanto S, Dunbar J, Albright MBN. Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities. mSystems 2023:e0122022. [PMID: 38990008 DOI: 10.1128/msystems.01220-22-test] [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: 12/09/2022] [Accepted: 03/07/2023] [Indexed: 07/12/2024]  Open
15
Liu YY. Controlling the human microbiome. Cell Syst 2023;14:135-159. [PMID: 36796332 PMCID: PMC9942095 DOI: 10.1016/j.cels.2022.12.010] [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: 06/06/2022] [Revised: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
16
George AB, Korolev KS. Ecological landscapes guide the assembly of optimal microbial communities. PLoS Comput Biol 2023;19:e1010570. [PMID: 36626403 PMCID: PMC9831326 DOI: 10.1371/journal.pcbi.1010570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023]  Open
17
Lux J, Xie Z, Sun X, Wu D, Scheu S. Changes in microbial community structure and functioning with elevation are linked to local soil characteristics as well as climatic variables. Ecol Evol 2022;12:e9632. [PMID: 36590334 PMCID: PMC9797387 DOI: 10.1002/ece3.9632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022]  Open
18
Gu Y, Banerjee S, Dini-Andreote F, Xu Y, Shen Q, Jousset A, Wei Z. Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations. THE ISME JOURNAL 2022;16:2448-2456. [PMID: 35869387 PMCID: PMC9478146 DOI: 10.1038/s41396-022-01290-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]
19
Li Y, Zhang Y, Xue S. pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs. Front Microbiol 2022;13:952285. [PMID: 36187958 PMCID: PMC9515653 DOI: 10.3389/fmicb.2022.952285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022]  Open
20
Li Y, Liu B, Chen J, Yue X. Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals. ACS OMEGA 2022;7:22671-22681. [PMID: 35811862 PMCID: PMC9260939 DOI: 10.1021/acsomega.2c02126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 06/03/2023]
21
van den Berg NI, Machado D, Santos S, Rocha I, Chacón J, Harcombe W, Mitri S, Patil KR. Ecological modelling approaches for predicting emergent properties in microbial communities. Nat Ecol Evol 2022;6:855-865. [PMID: 35577982 PMCID: PMC7613029 DOI: 10.1038/s41559-022-01746-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/23/2022] [Indexed: 12/20/2022]
22
Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics. Proc Natl Acad Sci U S A 2022;119:e2116954119. [PMID: 35394868 PMCID: PMC9169654 DOI: 10.1073/pnas.2116954119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Garcia Lorenzana G, Altieri A. Well-mixed Lotka-Volterra model with random strongly competitive interactions. Phys Rev E 2022;105:024307. [PMID: 35291125 DOI: 10.1103/physreve.105.024307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
24
Zaoli S, Grilli J. A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome. SCIENCE ADVANCES 2021;7:eabj2882. [PMID: 34669476 PMCID: PMC8528411 DOI: 10.1126/sciadv.abj2882] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
25
Batista-Tomás AR, De Martino A, Mulet R. Path-integral solution of MacArthur's resource-competition model for large ecosystems with random species-resources couplings. CHAOS (WOODBURY, N.Y.) 2021;31:103113. [PMID: 34717338 DOI: 10.1063/5.0046972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
26
Kareva I, Brown JS. Estrogen as an Essential Resource and the Coexistence of ER+ and ER– Cancer Cells. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.673082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
27
Gralka M, Szabo R, Stocker R, Cordero OX. Trophic Interactions and the Drivers of Microbial Community Assembly. Curr Biol 2021;30:R1176-R1188. [PMID: 33022263 DOI: 10.1016/j.cub.2020.08.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
28
Altieri A, Roy F, Cammarota C, Biroli G. Properties of Equilibria and Glassy Phases of the Random Lotka-Volterra Model with Demographic Noise. PHYSICAL REVIEW LETTERS 2021;126:258301. [PMID: 34241496 DOI: 10.1103/physrevlett.126.258301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/06/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
29
Estrela S, Sánchez Á, Rebolleda-Gómez M. Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology. Front Microbiol 2021;12:657467. [PMID: 33897672 PMCID: PMC8062719 DOI: 10.3389/fmicb.2021.657467] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022]  Open
30
Liu F, Giometto A, Wu M. Microfluidic and mathematical modeling of aquatic microbial communities. Anal Bioanal Chem 2021;413:2331-2344. [PMID: 33244684 PMCID: PMC7990691 DOI: 10.1007/s00216-020-03085-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 01/27/2023]
31
Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. PLoS Comput Biol 2020;16:e1008135. [PMID: 32810127 PMCID: PMC7480867 DOI: 10.1371/journal.pcbi.1008135] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 09/09/2020] [Accepted: 07/09/2020] [Indexed: 01/03/2023]  Open
32
Li Z, Liu B, Li SHJ, King CG, Gitai Z, Wingreen NS. Modeling microbial metabolic trade-offs in a chemostat. PLoS Comput Biol 2020;16:e1008156. [PMID: 32857772 PMCID: PMC7482850 DOI: 10.1371/journal.pcbi.1008156] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 09/10/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]  Open
33
Khazaei T, Williams RL, Bogatyrev SR, Doyle JC, Henry CS, Ismagilov RF. Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community. SCIENCE ADVANCES 2020;6:eaba0353. [PMID: 32851161 PMCID: PMC7423363 DOI: 10.1126/sciadv.aba0353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
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