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For: Gowda K, Ping D, Mani M, Kuehn S. Genomic structure predicts metabolite dynamics in microbial communities. Cell 2022;185:530-546.e25. [PMID: 35085485 DOI: 10.1016/j.cell.2021.12.036] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/16/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Narla AV, Hwa T, Murugan A. Dynamic coexistence driven by physiological transitions in microbial communities. Proc Natl Acad Sci U S A 2025;122:e2405527122. [PMID: 40244660 PMCID: PMC12037064 DOI: 10.1073/pnas.2405527122] [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: 03/19/2024] [Accepted: 03/17/2025] [Indexed: 04/18/2025]  Open
2
He Y, Zhuo S, Li M, Pan J, Jiang Y, Hu Y, Sanford RA, Lin Q, Sun W, Wei N, Peng S, Jiang Z, Li S, Li Y, Dong Y, Shi L. Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications. MICROBIOME 2025;13:94. [PMID: 40189564 PMCID: PMC11974145 DOI: 10.1186/s40168-025-02077-y] [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] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 03/04/2025] [Indexed: 04/09/2025]
3
Belda I, Izquierdo-Gea S, Benitez-Dominguez B, Ruiz J, Vila JCC. Wine Fermentation as a Model System for Microbial Ecology and Evolution. Environ Microbiol 2025;27:e70092. [PMID: 40222749 DOI: 10.1111/1462-2920.70092] [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: 10/08/2024] [Revised: 03/11/2025] [Accepted: 03/24/2025] [Indexed: 04/15/2025]
4
Malik D, Kumar S, Sindhu SS. Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture. 3 Biotech 2025;15:82. [PMID: 40071128 PMCID: PMC11891127 DOI: 10.1007/s13205-025-04243-3] [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: 10/12/2024] [Accepted: 02/14/2025] [Indexed: 03/14/2025]  Open
5
Wang M, Gao X, Zhang L. Advances in the study of the correlation between balanoposthitis and skin microecology. Front Microbiol 2025;16:1564675. [PMID: 40207153 PMCID: PMC11978672 DOI: 10.3389/fmicb.2025.1564675] [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: 01/22/2025] [Accepted: 03/11/2025] [Indexed: 04/11/2025]  Open
6
Goldman DA, Xue KS, Parrott AB, Lopez JA, Vila JCC, Jeeda RR, Franzese LR, Porter RL, Gray IJ, DeFelice BC, Petrov DA, Good BH, Relman DA, Huang KC. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. Proc Natl Acad Sci U S A 2025;122:e2322440122. [PMID: 40063808 PMCID: PMC11929384 DOI: 10.1073/pnas.2322440122] [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: 01/04/2024] [Accepted: 12/30/2024] [Indexed: 03/19/2025]  Open
7
Crocker K, Skwara A, Kannan R, Murugan A, Kuehn S. Microbial functional guilds respond cohesively to rapidly fluctuating environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.30.635766. [PMID: 39974892 PMCID: PMC11838272 DOI: 10.1101/2025.01.30.635766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
8
Kaur R, Gupta S, Tripathi V, Bharadwaj A. Unravelling the secrets of soil microbiome and climate change for sustainable agroecosystems. Folia Microbiol (Praha) 2025;70:19-40. [PMID: 39249146 DOI: 10.1007/s12223-024-01194-9] [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: 03/15/2024] [Accepted: 08/20/2024] [Indexed: 09/10/2024]
9
Arya S, George AB, O'Dwyer J. The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes. Curr Opin Microbiol 2025;83:102580. [PMID: 39848217 DOI: 10.1016/j.mib.2025.102580] [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: 07/16/2024] [Revised: 12/27/2024] [Accepted: 01/13/2025] [Indexed: 01/25/2025]
10
Chen X, Crocker K, Kuehn S, Walczak AM, Mora T. Inferring resource competition in microbial communities from time series. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.631910. [PMID: 39829848 PMCID: PMC11741390 DOI: 10.1101/2025.01.08.631910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
11
Song C. Assembly Graph as the Rosetta Stone of Ecological Assembly. Environ Microbiol 2025;27:e70030. [PMID: 39806523 DOI: 10.1111/1462-2920.70030] [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: 08/01/2024] [Revised: 12/02/2024] [Accepted: 12/18/2024] [Indexed: 01/16/2025]
12
Sun X, Buchanan PJ, Zhang IH, San Roman M, Babbin AR, Zakem EJ. Ecological dynamics explain modular denitrification in the ocean. Proc Natl Acad Sci U S A 2024;121:e2417421121. [PMID: 39693347 PMCID: PMC11670096 DOI: 10.1073/pnas.2417421121] [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: 08/26/2024] [Accepted: 11/20/2024] [Indexed: 12/20/2024]  Open
13
Du L, Zhong H, Guo X, Li H, Xia J, Chen Q. Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;951:175561. [PMID: 39153640 DOI: 10.1016/j.scitotenv.2024.175561] [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: 05/05/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
14
Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol 2024;9:2022-2037. [PMID: 38977908 PMCID: PMC11386527 DOI: 10.1038/s41564-024-01752-4] [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: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024]
15
Meroz N, Livny T, Friedman J. Quantifying microbial interactions: concepts, caveats, and applications. Curr Opin Microbiol 2024;80:102511. [PMID: 39002491 DOI: 10.1016/j.mib.2024.102511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
16
Tong K, He Y, Wei Y, Yun Y, Sang N. Diel variations of airborne microbes and antibiotic resistance genes in Response to urban PM2.5 chemical properties during the heating season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024;352:124120. [PMID: 38729506 DOI: 10.1016/j.envpol.2024.124120] [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: 02/16/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
17
Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024;53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
18
Diaz-Colunga J, Skwara A, Vila JCC, Bajic D, Sanchez A. Global epistasis and the emergence of function in microbial consortia. Cell 2024;187:3108-3119.e30. [PMID: 38776921 DOI: 10.1016/j.cell.2024.04.016] [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: 06/09/2023] [Revised: 12/06/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
19
Hiis EG, Vick SHW, Molstad L, Røsdal K, Jonassen KR, Winiwarter W, Bakken LR. Unlocking bacterial potential to reduce farmland N2O emissions. Nature 2024;630:421-428. [PMID: 38811724 PMCID: PMC11168931 DOI: 10.1038/s41586-024-07464-3] [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: 11/27/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
20
Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define the response of the soil microbiome to environmental change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.584851. [PMID: 38559185 PMCID: PMC10980070 DOI: 10.1101/2024.03.15.584851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
21
Yang X, Shi Y, Ying G, Li M, He Z, Shu L. Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;923:171395. [PMID: 38447730 DOI: 10.1016/j.scitotenv.2024.171395] [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: 12/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
22
Ho PY, Nguyen TH, Sanchez JM, DeFelice BC, Huang KC. Resource competition predicts assembly of gut bacterial communities in vitro. Nat Microbiol 2024;9:1036-1048. [PMID: 38486074 DOI: 10.1038/s41564-024-01625-w] [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: 04/30/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024]
23
Ho PY, Huang KC. Challenges in quantifying functional redundancy and selection in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586891. [PMID: 38586050 PMCID: PMC10996602 DOI: 10.1101/2024.03.26.586891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
24
Goyal A, Rocks JW, Mehta P. A universal niche geometry governs the response of ecosystems to environmental perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583107. [PMID: 38496409 PMCID: PMC10942395 DOI: 10.1101/2024.03.02.583107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
25
Ban S, Cheng W, Wang X, Niu J, Wu Q, Xu Y. Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making. mSystems 2024;9:e0058623. [PMID: 38206013 PMCID: PMC10878095 DOI: 10.1128/msystems.00586-23] [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: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]  Open
26
LaSarre B, Morlen R, Neumann GC, Harwood CS, McKinlay JB. Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired. Appl Environ Microbiol 2024;90:e0174123. [PMID: 38078768 PMCID: PMC10807417 DOI: 10.1128/aem.01741-23] [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: 10/04/2023] [Accepted: 11/04/2023] [Indexed: 01/25/2024]  Open
27
Schmitt MS, Colen J, Sala S, Devany J, Seetharaman S, Caillier A, Gardel ML, Oakes PW, Vitelli V. Machine learning interpretable models of cell mechanics from protein images. Cell 2024;187:481-494.e24. [PMID: 38194965 PMCID: PMC11225795 DOI: 10.1016/j.cell.2023.11.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/20/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
28
Narla AV, Hwa T, Murugan A. Dynamic coexistence driven by physiological transitions in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575059. [PMID: 38260536 PMCID: PMC10802591 DOI: 10.1101/2024.01.10.575059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
29
Bell E, Chen J, Richardson WDL, Fustic M, Hubert CRJ. Denitrification genotypes of endospore-forming Bacillota. ISME COMMUNICATIONS 2024;4:ycae107. [PMID: 39263550 PMCID: PMC11388526 DOI: 10.1093/ismeco/ycae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024]
30
Gralka M. Searching for Principles of Microbial Ecology Across Levels of Biological Organization. Integr Comp Biol 2023;63:1520-1531. [PMID: 37280177 PMCID: PMC10755194 DOI: 10.1093/icb/icad060] [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: 02/27/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]  Open
31
Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023;24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
32
Li Z, Selim A, Kuehn S. Statistical prediction of microbial metabolic traits from genomes. PLoS Comput Biol 2023;19:e1011705. [PMID: 38113208 PMCID: PMC10729968 DOI: 10.1371/journal.pcbi.1011705] [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: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]  Open
33
Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Global patterns in gene content of soil microbiomes emerge from microbial interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542950. [PMID: 38014336 PMCID: PMC10680560 DOI: 10.1101/2023.05.31.542950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
34
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: 22] [Impact Index Per Article: 11.0] [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]
35
Martínez-Calvo A, Trenado-Yuste C, Lee H, Gore J, Wingreen NS, Datta SS. Interfacial morphodynamics of proliferating microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563665. [PMID: 37961366 PMCID: PMC10634769 DOI: 10.1101/2023.10.23.563665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
36
Gralka M, Pollak S, Cordero OX. Genome content predicts the carbon catabolic preferences of heterotrophic bacteria. Nat Microbiol 2023;8:1799-1808. [PMID: 37653010 DOI: 10.1038/s41564-023-01458-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
37
Blumenthal E, Mehta P. Geometry of ecological coexistence and niche differentiation. Phys Rev E 2023;108:044409. [PMID: 37978666 DOI: 10.1103/physreve.108.044409] [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: 06/08/2023] [Accepted: 09/29/2023] [Indexed: 11/19/2023]
38
Zhao Y, Chen L, Yao S, Chen L, Huang J, Chen S, Yu Z. Genome-centric investigation of the potential succession pattern in gut microbiota and altered functions under high-protein diet. Curr Res Food Sci 2023;7:100600. [PMID: 37840698 PMCID: PMC10569982 DOI: 10.1016/j.crfs.2023.100600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]  Open
39
McKinlay JB. Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding. Annu Rev Microbiol 2023;77:277-297. [PMID: 37285553 DOI: 10.1146/annurev-micro-032521-023815] [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] [Indexed: 06/09/2023]
40
Ruiz J, de Celis M, Diaz‐Colunga J, Vila JCC, Benitez‐Dominguez B, Vicente J, Santos A, Sanchez A, Belda I. Predictability of the community-function landscape in wine yeast ecosystems. Mol Syst Biol 2023;19:e11613. [PMID: 37548146 PMCID: PMC10495813 DOI: 10.15252/msb.202311613] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]  Open
41
Chan DTC, Baldwin GS, Bernstein HC. Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology. BIODESIGN RESEARCH 2023;5:0016. [PMID: 37849456 PMCID: PMC10432152 DOI: 10.34133/bdr.0016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/17/2023] [Indexed: 10/19/2023]  Open
42
Peduzzi C, Sagia A, Burokienė D, Nagy IK, Fischer-Le Saux M, Portier P, Dereeper A, Cunnac S, Roman-Reyna V, Jacobs JM, Bragard C, Koebnik R. Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas. PHYTOPATHOLOGY 2023;113:1185-1191. [PMID: 36611232 DOI: 10.1094/phyto-10-22-0373-sc] [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: 06/17/2023]
43
Sun CC, Zhao WJ, Yue WZ, Cheng H, Sun FL, Wang YT, Wu ML, Engel A, Wang YS. Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China. Front Microbiol 2023;14:1180321. [PMID: 37425997 PMCID: PMC10322874 DOI: 10.3389/fmicb.2023.1180321] [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: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]  Open
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Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023;14:3165. [PMID: 37258505 PMCID: PMC10232422 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023]  Open
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Venkataram S, Kryazhimskiy S. Evolutionary repeatability of emergent properties of ecological communities. Philos Trans R Soc Lond B Biol Sci 2023;378:20220047. [PMID: 37004728 PMCID: PMC10067272 DOI: 10.1098/rstb.2022.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 04/04/2023]  Open
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Xu S, Li X, Zhang S, Qi C, Zhang Z, Ma R, Xiang L, Chen L, Zhu Y, Tang C, Bourgonje AR, Li M, He Y, Zeng Z, Hu S, Feng R, Chen M. Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study. BMC Med 2023;21:179. [PMID: 37170220 PMCID: PMC10173549 DOI: 10.1186/s12916-023-02878-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023]  Open
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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: 11] [Impact Index Per Article: 5.5] [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
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Blumenthal E, Mehta P. Geometry of ecological coexistence and niche differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537832. [PMID: 37131730 PMCID: PMC10153274 DOI: 10.1101/2023.04.21.537832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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Naranjo HD, Lebbe L, Cnockaert M, Lassalle F, Chin Too C, Willems A. Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov. Syst Appl Microbiol 2023;46:126420. [PMID: 37031612 DOI: 10.1016/j.syapm.2023.126420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
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Silverstein MR, Segrè D, Bhatnagar JM. Environmental microbiome engineering for the mitigation of climate change. GLOBAL CHANGE BIOLOGY 2023;29:2050-2066. [PMID: 36661406 DOI: 10.1111/gcb.16609] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 05/28/2023]
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