The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
Open accessAbstract
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metabolic models for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice and applied it to engineered communities. First, we predicted and experimentally confirmed the species ratio to which a two-species mutualistic consortium converges and the equilibrium composition of a newly engineered three-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the "eclipse dilemma": does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding that the net outcome is beneficial highlights the complex nature of metabolic interactions in microbial communities while at the same time demonstrating their predictability.
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Cites
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533
What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903
The Microbial Engines That Drive Earth's Biogeochemical Cycles
Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008) · Science · doi:10.1126/science.1153213 · Cited by 3,379
An ecological and evolutionary perspective on human–microbe mutualism and disease
Dethlefsen, L., McFall-Ngai, M., & Relman, D. A. (2007) · Nature · doi:10.1038/nature06245 · Cited by 1,660
High-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, C. S., DeJongh, M., Best, A. A., Frybarger, P. M., Linsay, B., & Stevens, R. L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1672 · Cited by 1,090
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., & Palsson, B. Ø. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.65 · Cited by 1,006
Dynamic flux balance analysis of diauxic growth in Escherichia coli
Mahadevan, R., Edwards, J. S., & Doyle, F. J. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)73903-9 · Cited by 945
Multidimensional Optimality of Microbial Metabolism
Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., & Sauer, U. (2012) · Science · doi:10.1126/science.1216882 · Cited by 420 · cited 3×
“However, even the assumption that evolution has acted on a population to optimize a simple objective has been challenged by new data and analyses (Harcombe et al., 2013; Schuetz et al., 2012).”
Imaging mass spectrometry in microbiology
Watrous, J. D., & Dorrestein, P. C. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2634 · Cited by 338
Cited by
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Identification of bioactive metabolites using activity metabolomics
Rinschen, M. M., Ivanisevic, J., Giera, M., & Siuzdak, G. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0108-4 · Cited by 1,008
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie, S., Ghaffari, P., Kovatcheva-Datchary, P., Mardinoglu, A., Sen, P., Pujos-Guillot, E., de Wouters, T., Juste, C., Rizkalla, S., Chilloux, J., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.001 · Cited by 420
Fermented Foods as Experimentally Tractable Microbial Ecosystems
Wolfe, B. E., & Dutton, R. J. (2015) · Cell · doi:10.1016/j.cell.2015.02.034 · Cited by 386
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
Pacheco, A. R., Moel, M., & Segrè, D. (2019) · Nature Communications · doi:10.1038/s41467-018-07946-9 · Cited by 328
Self-citation
Metadata
- Authors
- Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Leiby, N., Mehta, P., Marx, C. J., & Segrè, D.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2014-05
- Volume
- 7
- Issue
- 4
- Pages
- 1104-1115
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2122093325
- Cited by
- 515
- References
- 11
- FWCI
- 15.21
- Type
- journal article
- Language
- en
- Open access
- gold
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- Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Leiby, N., Mehta, P., Marx, C. J., & Segrè, D. (2014). Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics. Cell Reports. https://doi.org/10.1016/j.celrep.2014.03.070
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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