Genome content predicts the carbon catabolic preferences of heterotrophic bacteria. M Gralka, S Pollak, OX Cordero. Nature Microbiology, 1-10

Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. K Amarnath, AV Narla, S Pontrelli, J Dong, J Reddan, BR Taylor, T Caglar, J Schwartzman, U Sauer, OX Cordero, T Hwa. Nature Communications 14 (1), 3165

Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle. G Capovilla, R Braakman, GP Fournier, T Hackl, J Schwartzman, X Lu, A Yelton, K Longnecker, MC Kido Soule, E Thomas, G Swarr, A Mongera, JG Payette, KG Castro, JR Waldbauer, EB Kujawinski, OX Cordero, Sallie W Chisholm. Proceedings of the National Academy of Sciences 120 (20), e2213271120

Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria. G D’Souza, A Ebrahimi, A Stubbusch, M Daniels, J Keegstra, R Stocker, OX Cordero and M Ackermann. The ISME Journal 17 (5), 703-711

Annotation-free discovery of functional groups in microbial communities. X Shan, A Goyal, R Gregor, OX Cordero. Nature Ecology & Evolution 7 (5), 716-724

A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01. A Iffland-Stettner, H Okano, M Gralka, G Guessous, K Amarnath, K Amarnath, OX Cordero, T Hwa, S Bonhoeffer. Msystems 8 (2), e00377-22

Mutation-induced infections of phage-plasmids. X Shan, RE Szabo, OX Cordero. Nature Communications 14 (1), 2049

Identifying microbial guilds on the basis of ecological patterns. X Shan, OX Cordero. Nature Ecology & Evolution

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. F Vincent, M Gralka, G Schleyer, D Schatz, M Cabrera-Brufau, C Kuhlisch, A Sichert, S Vidal-Melgosa, K Mayers, N Barak-Gavish, JM Flores, M Masdeu-Navarro, JK Egge, A Larsen, J Hehemann, C Marrasé, R Simó, OX Cordero, Assaf Vardi. Nature communications 14 (1), 510

Mapping gut bacteria into functional niches reveals the ecological structure of human gut microbiomes. L Anthamatten, P Rogalla von Bieberstein, C Thabuis, C Menzi, M Reichlin, M Meola, B Rodriguez, OX Cordero, C Lacroix, T de Wouters, GE Leventhal. bioRxiv, 2023.07. 04.547750

Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities.. G D’souza, J Schwartzman, J Keegstra, JE Schreier, M Daniels, OX Cordero, R Stocker, M Ackermann. bioRxiv, 2023.03. 22.533748

Historical contingencies and phage induction diversify bacterioplankton communities at the microscale. RE Szabo, S Pontrelli, J Grilli, JA Schwartzman, S Pollak, U Sauer and OX Cordero. Proceedings of the National Academy of Sciences 119 (30), e2117748119

Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. JA Schwartzman, A Ebrahimi, G Chadwick, Y Sato, BRK Roller, VJ Orphan and OX Cordero. Current Biology 32 (14), 3059-3069. e7

Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. TTH Nguyen, EJ Zakem, A Ebrahimi, J Schwartzman, T Caglar, … Nature Communications 13 (1), 1-9

Particle foraging strategies promote microbial diversity in marine environments. A Ebrahimi, A Goyal, OX Cordero. eLife 11, e73948

Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. S Pontrelli, R Szabo, S Pollak, J Schwartzman, D Ledezma-Tejeida, … Science Advances 8 (8), eabk3076

Interactions between strains govern the eco-evolutionary dynamics of microbial communities. A Goyal, LS Bittleston, GE Leventhal, L Lu, OX Cordero. (2022) eLife 2022;11:e74987.

Evolutionary Ecology of Natural Comammox Nitrospira Populations. A Palomo, A Dechesne, OX Cordero, BF Smets. Msystems 7 (1), e01139-21

Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. J Liao, X Guo, DL Weller, S Pollak, DH Buckley, M Wiedmann, … Nature Microbiology 6 (8), 1021-1030

Public good exploitation in natural bacterioplankton communities. S Pollak, M Gralka, Y Sato, J Schwartzman, L Lu, OX Cordero. (2021). Science Advances. Vol 7Issue 31

Trophic Interactions and the Drivers of Microbial Community Assembly. M Gralka, R Szabo, R Stocker, OX Cordero (2020). Current Biology 30 (19), R1176-R1188

Context-dependent dynamics lead to the assembly of functionally distinct pitcher-plant microbiomes. LS Bittleston,  M Gralka,  GE Leventhal,  I Mizrahi,  OX Cordero. Nature Communications volume 11, Article number: 1440 (2020)

Deconstructing the association between abiotic factors and species assemblages in the global ocean microbiome. X Shan, OX Cordero (2020). doi:

Polysaccharide-bacteria interactions from the lens of evolutionary ecology. A Sichert, OX Cordero. Frontiers in Microbiology 12

The genetic law of the minimum. MF Polz, OX Cordero. Science 370 (6517), 655-656

Rhizobiome shields plants from infection. S Pollak, OX Cordero. Nature Microbiology 5 (8), 978-979

Illuminating microbial species-specific effects on organic matter remineralization in marine sediments. N Mahmoudi, TN Enke, SR Beaupre, A Testke, OX Cordero and Ann Pearson (2019). Environmental Microbiology, doi:10.1111/1462-2920.14871.

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics. O Furman, L Shenhav, G Sasson, F Kokou, H Honig, S Jacoby, T Hertz, … Nature Communications 11 (1), 1-13

Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria. Ali Ebrahimi, Julia Schwartzman and Otto X. Cordero (2019). Proceedings of the National Academy of Science, November 12, 2019 116 (46) 23309-23316

Modular assembly of polysaccharide-degrading marine microbial communities. TN Enke, MS Datta, J Schwartzman, N Cermak, D Schmitz, J Barrere, A Pascual-Garcia and OX Cordero. (2019) Current Biology. Vol 29, issue 9, P1528-1535.E6 2019

Physics-based prediction of biopolymer degradation. R Abi-Akl, E Ledieu, T Enke, OX Cordero, T Cohen. (2019) Soft Matter, Issue 20.

Multicellular behavior enables cooperation in microbial cell aggregates. Ali Ebrahimi, Julia Schwartzman, Otto X Cordero (2019) Proceedings of the Royal Society B.

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities. Tim N. Enke, Gabriel E. Leventhal, Matthew Metzger, José T. Saavedra & Otto X. Cordero. Nature Communications. Volume 9, Article number: 2743 (2018) . 10.1038/s41467-018-05159-8

Within-species diversity drives alternative community types in millimeter scale granular biofilms (2018). GE Leventhal, C Boix, U Kuechler, T Enke, E Sliwerska, C Holliger and OX Cordero. Nature Microbiology (2018). 10.1038/s41564-018-0242-3

Solving the structure–function puzzle. Lei Ma & Otto X. Cordero. Nature Microbiology. Volume 3, pages 750–751 (2018)

OX Cordero (2017). Endemic Cyanophages and the Puzzle of Phage-Bacteria Coevolution. Environ Microbiol 19 (2), 420-422.

OX Cordero and R Stocker (2017). A particularly useful system to study the ecology of microbes. Environ Microbiol Rep. 2016 Oct 19

MF Polz and OX Cordero (2016). Bacterial evolution: Genomics of metabolic trade-offs. Nature Microbiol. 2016 Oct 26;1(11):16181

Datta, E Sliwerska, J Gore, MF Polz, and OX Cordero (2016). Microbial interactions lead to rapid micro-scale successions on model marine particles. Nature Communications, 7: 11965.

OX Cordero and MS Datta (2016). Microbial interactions and community assembly at microscales. Current Opinion in Microbiology. Volume 31, Pages 227–234

Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG. (2016) A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. ISME J. Apr 29

S Widder, R J Allen, T Pfeiffer, T P Curtis, C Wiuf, W T Sloan, OX Cordero, S P Brown, B Momeni, W Shou, H Kettle, H J Flint, A F Haas, B Laroche, JU Kreft, P B Rainey, S Freilich, S Schuster, K Milferstedt, J R van der Meer, T Groβkopf, J Huisman, A Free, C Picioreanu, C Quince, I Klapper, S Labarthe, B F Smets, H Wang, I Newton Institute Fellows and Orkun S Soyer. (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal.

OX Cordero (2015). Viewpoint: Microbial Ecosystem Follows Deterministic Dynamic. APS Physics 8, 101

​N Takeuchi, OX Cordero, EV Koonin, K Kaneko (2015). Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection. BMC Biology. DOI: 10.1186/s12915-015-0131-7

H Xue, OX Cordero, FM Camas, W Trimble, F Meyerd, J Guglielminie, E Rocha, MF Polz (2015). Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations. mBio. 6(3):e00552-15

Y Yawata, OX Cordero, F Menolascina, JH Hehemann, MF Polz, R Stocker (2014). A competition-dispersal trade-off ecologically differentiates recently speciated marine bacterioplankton population. Proceedings of the National Academy of Sciences. 2014 April, 111 (15) 5622-5627.

OX Cordero and MF Polz. Explaining microbial genomic diversity in light of evolutionary ecology (2014). Nature Reviews In Microbiology, 12, pages 263–273

Sharma AK, Becker JW, Ottesen EA, Bryant JA, Duhamel S, Karl DM, Cordero OX, Repeta DJ, Delong EF. (2013) Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environmental Microbiology

OX Cordero, L Ventouras, EF DeLong and MF Polz. (2012) Public Good Dynamics Drive Evolution of Iron Acquisition Strategies in Natural Bacterioplankton Populations. Proceedings of the National Academy of Sciences. 2012 Dec 4;109(49):20059-64

OX Cordero, H Windschutte, BC Kirkup, S Proehl, FA Hussain, F Le Roux, T Mincer and MF Polz. (2012) Ecological populations of bacteria act as units of antibiotic production and resistance. Science. Vol. 337, Issue 6099, pp. 1228-1231

BJ Shapiro, J Friedman, OX Cordero, S Preheim, D Hunt, S Timberlake, MF Polz, and EJ Alm. (2012) Population genomics of early events in the ecological differentiation of bacteria. Science 336(6077):48-51

CS Smillie, MB Smith, J Friedman, OX Cordero, LA David and EJ Alm. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, pages241–244

Y Boucher, OX Cordero, A Takemura, DE. Hunt, K Schliep, E Bapteste, P Lopez, CL Tarrd, and MF Polz. (2011) Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations. Mbio 2(2):e00335-10

L Wang, S Chen, KL Vergin, SJ Giovannoni, SW Chan, MS DeMott, K Taghizadeh, OX Cordero, M Cutler, S Timberlake, EJ Alm, MF Polz, J Pinhassi, Z Deng, PC Dedon. (2011) DNA phosphorothioation is widespread and quantized in bacterial genomes. Proceedings of the National Academy of Sciences 108 (7) 2963-2968.

OX Cordero and P Hogeweg. (2009) The impact of long-distance horizontal gene transfer on prokaryotic genome size. Proceedings of the National Academy of Sciences 106(51): 21748–21753.

OX Cordero and P Hogeweg (2009) The consequences of base pair composition biases for regulatory network organization in prokaryotes.Molecular Biology and Evolution

OX Cordero and P Hogeweg (2009) Regulome size in prokaryotes: universality and lineage specific variations. Trends in Genetics

OX Cordero, B Snel and P Hogeweg (2008) Coevolution of gene families in prokaryotes. Genome Research.

OX Cordero and P Hogeweg (2007) Large changes in regulome size herald the main prokaryotic lineages. Trends in Genetics

OX Cordero and P Hogeweg (2006) Feed forward loop circuits as a side effect of genome mutational dynamics. Cordero and Hogeweg. Molecular Biology and Evolution.