Publications
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Highlights
This work dissects how quantitative patterns of convergence and variation observed in microbial community assembly depend on quantitative metabolic traits and the inherent stochasticity of population dynamics.
Estrela, S.*#; J.C.C. Vila, N. Lu, D. Bajić, M. Rebolleda-Gomez, C-Y. Chang, A. Sánchez #,
Cell Systems. 13(1):29-42. 2022
A state-of-the-art platform for genome-scale metabolic modeling of multi-species communities.
Dukovski*, I; D. Bajić*,J.M. Chacon*, M. Quintin*, J.C.C. Vila, S. Sulheim, A.R. Pacheco, D.B.Bernstein, W.J. Riehl, K.S. Korolev, A. Sánchez, W.R. Harcombe, D. Segrè
Nature Protocols. 16:5030–5082. 2021
Here we discuss ideas about the evolution and diversity microbial metabolic strategies, their prediction from genomic data and their consequences for microbial communities.
Bajić, D. and A. Sánchez
Current Opinion in Biotechnology. 62:123-128. 2020
We extended the theory of fitness landscapes to characterize an ecological structure-function landscape, the map between the composition and function of microbial consortia. This allowed us to separate the effect of behavioral and population dynamics interactions, and show that higher-order interactions critically affect our ability to predict and engineer complex ecosystem function.
Sánchez-Gorostiaga*, A; D. Bajić*, M.L. Osborne, J.F. Poyatos, and A. Sánchez
PLoS Biology. 17(12): e3000550. 2019
In this work, we formally defined a new kind of ecologically mediated genetic interaction, that we called “non-commutative epistasis”. We used it to quantitatively chart eco-evolutionary interactions on an empirical genotype-phenotype map, showing how they can deform fitness landscapes profoundly altering long-term evolution.
D. Bajić*#, J.C.C. Vila*, Z. Blount, A. Sánchez #
PNAS. 115 (44): 11286–11291. 2018
We demonstrated in a novel experimental system that function and coarse-grained taxonomy of microbial communities are predictable and governed by resource availability, despite species-level variability. We also showed that these features are emergent properties of the assembly of large microbial communities due to the presence of cross-feeding.
Goldford*, J.E.; N. Lu*, D. Bajić, S. Estrela, M. Tikhonov, A. Sánchez-Gorostiaga, D. Segrè, P. Mehta #, A. Sánchez #,
Science. 361(6401):469-474. 2018
Full List
[20] Chang, C-Y.; D. Bajić#, J.C.C. Vila, S. Estrela, A. Sanchez#
Emergent coexistence in multispecies microbial communities
bioRxiv, 492860. 2022
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[19] Diaz-Colunga, J*; A. Skwara*, K., J.C.C. Vila, D. Bajić#, A. Sanchez#
Emergent ecosystem functions follow simple quantitative rules
bioRxiv, 496987. 2022
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[18] Sanchez, A.; D. Bajić, J. Diaz-Colunga, A. Skwara, J.C.C. Vila, S. Kuehn
The community-function landscape of microbial consortia
ecoevoRxiv, 2022/6/28. 2022
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[17] Diaz-Colunga, J; A. Skwara, K. Gowda, R. Diaz-Uriarte, M. Tikhonov, D. Bajić, A. Sanchez
Global epistasis on fitness landscapes
arXiv, arXiv:2210.03677. 2022
bioRxiv - -
[16] Estrela, S.*#; J.C.C. Vila, N. Lu, D. Bajić, M. Rebolleda-Gomez, C-Y. Chang, A. Sánchez #,
Functional attractors in microbial community assembly
Cell Systems, 13(1):29-42. 2022
bioRxiv - -
[15] Dukovski*, I; D. Bajić*,J.M. Chacon*, M. Quintin*, J.C.C. Vila, S. Sulheim, A.R. Pacheco, D.B.Bernstein, W.J. Riehl, K.S. Korolev, A. Sánchez, W.R. Harcombe, D. Segrè
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Nature Protocols, 16:5030–5082. 2021
arXiv - -
[14] de Oliveira Lino, F.S.; D. Bajić, J.C.C. Vila, A. Sánchez, M.O.A. Sommer
Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation
Nature communications, 12(1):1-12. 2021
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[13] Bajić D #; M. Rebolleda-Gomez, M.M. Muñoz, A. Sánchez #
The macroevolutionary consequences of niche construction in microbial metabolism
Frontiers in Microbiology, . 2021
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[12] Peralta-Marzal L.N.#; N. Prince, D. Bajić, L. Roussin, L. Naudon, S. Rabot, J. Garssen, A.D. Kraneveld, P. Pérez-Pardo #
The Impact of Gut Microbiota-Derived Metabolites in Autism Spectrum Disorders
International Journal of Molecular Sciences, 22(18):10052. 2021
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[11] Alonso-Lavin A.J; D. Bajić, J.F. Poyatos
Tolerance to NADH/NAD+ imbalance anticipates aging and anti-aging interventions
iScience, 102697. 2021
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[10] Kovács*, K.; Z. Farkas*, D. Bajić*, D. Kalapis, A. Daraba, K. Almási, B. Kintses, Z. Bódi, R. Notebaart, J.F. Poyatos, P. Kemmeren, F.C.P. Holstege, C. Pál, B. Papp,
Suboptimal global transcriptional response increases the harmful effects of loss-of-function mutations
Molecular Biology and Evolution, 38(3):1137–1150. 2020
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[9] Bajić, D. and A. Sánchez
The ecology and evolution of microbial metabolic strategies
Current Opinion in Biotechnology, 62:123-128. 2020
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[8] Chang, C-Y* and M.L. Osborne*, D. Bajić, A. Sánchez
Artificially selecting bacterial communities using propagule strategies},
Evolution, 74(10):2392-2403. 2020
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[7] Sánchez-Gorostiaga*, A; D. Bajić*, M.L. Osborne, J.F. Poyatos, and A. Sánchez
High-order interactions distort the functional landscape of microbial consortia,
PLoS Biology, 17(12): e3000550. 2019
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[6] D. Bajić*#, J.C.C. Vila*, Z. Blount, A. Sánchez #
On the deformability of an empirical fitness landscape by microbial evolution
Proceedings of the National Academy of Sciences, 115 (44): 11286–11291. 2018
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[5] Goldford*, J.E.; N. Lu*, D. Bajić, S. Estrela, M. Tikhonov, A. Sánchez-Gorostiaga, D. Segrè, P. Mehta #, A. Sánchez #,
Emergent simplicity in microbial community assembly,
Science, 361(6401):469-474. 2018
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[4] G. Rodrigo, D. Bajić, I. Elola, J.F. Poyatos
Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function
NPJ systems biology and applications, 3(1):1–9. 2017
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[3] G. Rodrigo, D. Bajić, I. Elola, J.F. Poyatos
Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli
Scientific Reports, 6 (1): 1–10. 2016
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[2] Bajić, D; C. Moreno-Fenoll, J.F. Poyatos
Rewiring of genetic networks in response to modification of genetic background},
Genome Biology and Evolution, 6(12):3267–3280. 2014
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[1] D. Bajić, J. Poyatos
Balancing noise and plasticity in eukaryotic gene expression
Proceedings of the National Academy of Sciences, 13 (1): 1–12. 2012
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