Publications
91. Nelson Frazão and Isabel Gordo. Ecotype formation and prophage domestication during gut bacterial evolution. Bioassays (2023). https://doi.org/10.1002/bies.202300063
90. Nelson Frazão and Isabel Gordo. Shared Evolutionary Path in Social Microbiomes. Mol Biol Evol (2023). https://doi.org/10.1093/molbev/msad153.
89. Barreto, H.C., Gordo, I. Intrahost evolution of the gut microbiota. Nat Rev Microbiol (2023). https://doi.org/10.1038/s41579-023-00890-6
88. J. M. de Sousa, M. Lourenço, I. Gordo. Horizontal gene transfer among host-associated microbes. Review. Cell Host & Microbe 31: 4 (2023). https://doi.org/10.1016/j.chom.2023.03.017
87. A.-H. Ghenu, A. Amado, I. Gordo, and C. Bank. Epistasis decreases with increasing antibiotic pressure but not temperature. Phil. Trans. R. Soc. B378:20220058. 20220058. (2023) https://doi.org/10.1098/rstb.2022.0058
86. Nelson Frazão, Anke Konrad, Massimo Amicone, Elsa Seixas, Daniela Güleresi, Michael Lässig, and Isabel Gordo. Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations. Nat Commun 13, 5604 (2022). https://doi.org/10.1038/s41467-022-33412-8. PRESS RELEASE Press
85. Borges, V., Isidro, J., Trovão, N.S. et al. SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal. Commun Med 2, 10 (2022). https://doi.org/10.1038/s43856-022-00072-0
84. Hugo C. Barreto, Beatriz Abreu, Isabel Gordo. Fluctuating selection on bacterial iron regulation in the mammalian gut. Current Biology 2022, ISSN 0960-9822. https://doi.org/10.1016/j.cub.2022.06.017
83. Mukherjee, D., Chora, Â.F., Lone, JC. et al. Host lung microbiota promotes malaria-associated acute respiratory distress syndrome. Nat Commun 13, 3747 (2022). https://doi.org/10.1038/s41467-022-31301-8
82. Dragan Stajic, Claudia Bank, Isabel Gordo, Adaptive Potential of Epigenetic Switching During Adaptation to Fluctuating Environments. Genome Biology and Evolution, Volume 14, Issue 5, May 2022, evac065, https://doi.org/10.1093/gbe/evac065
81. Massimo Amicone, Vítor Borges, Maria João Alves, Joana Isidro, Líbia Zé-Zé, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes, Isabel Gordo, Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evolution, Medicine, and Public Health, Volume 10, Issue 1, 2022, Pages 142–155, https://doi.org/10.1093/emph/eoac010
80. Gordo I. (2022) Population size matters for mutations. Nature Ecology &Evolution: https://doi.org/10.1038/s41559-022-01670-w
79. Dapa T., Ramiro RS., Pedro MF., Gordo I., Xavier KB. (2022) Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe. S1931-3128(22)00038-5. doi: 10.1016/j.chom.2022.01.002
78. Durão, P., Amicone, M., Perfeito, L., & Gordo, I. (2021) Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities. Ecology and Evolution, 11, 15085– 15097. https://doi.org/10.1002/ece3.8191
76. Amicone, M. and Gordo, I. (2021) Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation. Evolution. https://doi.org/10.1111/evo.14315
75. Pinto, C., Melo-Miranda, R., Gordo, I., & Sousa, A. (2021) The Selective Advantage of the lac Operon for Escherichia coli Is Conditional on Diet and Microbiota Composition. Frontiers in microbiology, 12, 709259. https://doi.org/10.3389/fmicb.2021.709259
74. Balbontín R, Frazão N, Gordo I (2021) DNA Breaks-Mediated Fitness Cost Reveals RNase HI as a New Target for Selectively Eliminating Antibiotic-Resistant Bacteria. Mol Biol Evol. 38(8):3220-3234. doi: 10.1093/molbev/msab093
73. Borges, V., Isidro, J., Cortes-Martins, H., Duarte, S., Vieira, L., Leite, R., Gordo, I., Caetano, C. P., Nunes, B., Sá, R., Oliveira, A., Guiomar, R., Portuguese network for SARS-CoV-2 genomics, & Gomes, J. P. (2020). Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging microbes & infections, 9(1), 2488–2496. https://doi.org/10.1080/22221751.2020.1844552
72. Cardoso LL, Durão P, Amicone M, Gordo I (2020) Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut. Nat Ecol Evol. https://doi.org/10.1038/s41559-020-1235-1
71. HC Barreto, N Frazão, A Sousa, A Konrad, I Gordo (2020) Mutation Accumulation and Horizontal Gene Transfer in Escherichia coli Colonizing the Gut of Old Mice. Communicative & Integrative Biology. https://doi.org/10.1080/19420889.2020.1783059. Mentioned on national TV RTP1 - Bom Dia Portugal
70. Durão, P., Ramiro, R. S., Pereira, C., Jurič, J., Pereira, D., & Gordo, I. (2020). Radial Expansion Facilitates the Maintenance of Double Antibiotic Resistances. Antimicrobial agents and chemotherapy, 64(9), e00668-20. https://doi.org/10.1128/AAC.00668-20
69. Ramiro RS, Durão P, Bank C, Gordo I (2020) Low Mutational Load Allows for High Mutation Rate Variation in Gut Commensal Bacteria. PLoS Biol 18(3): e3000617. https://doi.org/10.1371/journal.pbio.3000617
68. Barreto H, Sousa A and Gordo I (2020) The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice. Current Biology 30, 1102–1109. https://doi.org/10.1016/j.cub.2020.01.037
67. Batista-Barroso J, Pedro M, Dias J, Pinto C, Pereira H, Demengeot J, Gordo I, Xavier K (2019). Specific Eco-Evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Current Biology 30, 1049–1062. https://doi.org/10.1016/j.cub.2020.01.050
66. Barreto, H.C., Cordeiro, T.N., Henriques, A.O. et al. Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate. Sci Rep 10, 18886 (2020). https://doi.org/10.1038/s41598-020-76017-1
65. Gordo I (2019). Evolutionary change in the human gut microbiome: From a static to a dynamic view. PloS Biology. PLoS Biol 17(2): e3000126. https://doi.org/10.1371/journal.pbio.3000126
64. Pedro M, Batista-Barroso J, Pinto C, Dias J, Gordo I, Xavier K (2019) Understanding metabolic processes shaping adaptation of in the gut. Access Microbiology 1 (1A). https://doi.org/10.1099/acmi.ac2019.po0215
63. Frazão N, Sousa A, Lässig M, Gordo I (2019) Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc Natl Acad Sci USA. 116 (36): 17906-17915. doi: 10.1073/pnas.1906958116
62. Özkaya Ö, Balbontín R, Gordo I and Xavier KB (2018) Cheating on Cheaters Stabilizes Cooperation in Pseudomonas aeruginosa. Current Biology 28(13):2070-2080.
https://doi.org/10.1016/j.cub.2018.04.093
61. Durão P, Balbontín R and Gordo I (2018) Evolutionary mechanisms shaping the maintenance of antibiotic resistance. Trends in Microbiology 26 (8).
https://doi.org/10.1016/j.tim.2018.01.005
60. Sousa A, Ramiro RS, Barroso-Batista J, Güleresi D, Lourenço M, (2017) Recurrent Reverse Evolution Maintains Polymorphism After Strong Bottlenecks in Commensal Gut Bacteria. Molecular Biology and Evolution 34(11):2879-2892. doi: 10.1093/molbev/msx221.
59. Sousa A, Frazão N, Ramiro RS, (2017) Evolution of commensal bacteria in the intestinal tract of mice. Current Opinion in Microbiology38, 114-121. https://doi.org/10.1016/j.mib.2017.05.007
58. Proença JT, Barral DC, (2017) Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli-macrophage interaction. Scientific Reports 7 (1):4504. https://doi.org/10.1038/s41598-017-04081-1
57. Moura-de-Sousa J, Balbontin R, Durão P, (2017) Multi-drug Resistant Bacteria Compensate for the Epistasis between Resistances. PLoS Biology 15 (4), e2001741. https://doi.org/10.1371/journal.pbio.2001741
56. Lourenço M, Ramiro RS, Güleresi D, Barroso-Batista J, Xavier KB, A Sousa (2016) A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Adaptation to the Gut. PLoS Genetics 12 (11): e1006420.
doi:10.1371/journal.pgen.1006420
55. Moura de Sousa JA, Alpedrinha J, Campos PRA, (2016) Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model. PeerJ 4:e2256 https://doi.org/10.7717/peerj.2256
54. Ramiro, R. S., Costa, H. and . (2016), Macrophage adaptation leads to parallel evolution of genetically diverse i small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol Appl, 9: 994–1004. https://doi.org/10.1111/eva.12397
53. Durão P, Gülereşi D, Proença J, . (2016) Enhanced Survival of Rifampin- and Streptomycin-Resistant Inside Macrophages. Antimicrobial Agents and Chemotherapy 60 (7):4324-4332. https://doi.org/10.1128/AAC.00624-16
52. Azevedo M, A Sousa, JM de Sousa, JA Thompson, JT Proença, (2016) Trade-Offs of Adaptation to an Intracellular Lifestyle in Macrophages. PLOS One11 (1).
https://doi.org/10.1371/journal.pone.0146123
51. Barroso-Batista J, Demengeot J, Xavier KB, (2015) Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nature Communications 6:8945. https://doi.org/10.1038/ncomms9945
50. Moura-de-Sousa J, Sousa A, Bourgard C, I Gordo (2015) Potential for adaptation overrides cost of resistance. Future Microbiology 10:1415-1431. https://doi.org/10.2217/fmb.15.61
49. P Durão, S Trindade, A Sousa, I Gordo (2015) Multiple Resistance at no cost: Rifampicin and Streptomycin a dangerous liaison in the spread of antibiotic resistance. Molecular Biology and Evolution 32 (10): 2675–2680, https://doi.org/10.1093/molbev/msv143
48. I Gordo Demengeot J, Xavier KB, (2014) Escherichia coli adaptation to the gut environment, a constant fight for survival. Future Microbiology 9, 1235-1238. https://doi.org/10.2217/fmb.14.86
47. Barroso-Batista J, Sousa A, Lourenço M, Bergman M-L, Sobral D, Demengeot J, Xavier KB, I Gordo (2014) The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genetics 10(3): e1004182. https://doi.org/10.1371/journal.pgen.1004182
46. Gordo I, M Miskinyte (2014) Fitness Measurements of Evolved Esherichia coli. Bio-protocol 4 (17), e1228. DOI: 10.21769/BioProtoc.1228
45. Gordo I, M Miskinyte (2014) Evolution of Escherichia coli to macrophage cell line. Bio-protocol 4 (17), e1227. DOI: 10.21769/BioProtoc.1227
44. Perfeito L, A Sousa, T Bataillon and I Gordo (2014) Rates of fitness decline and rebound suggest pervasive epistasis. Evolution. 68 (1), 150-162. DOI: 10.1111/evo.12234
43. Miskinyte M, A Sousa, R Ramiro, JA. Moura de Sousa, J Kotlinowski, I Caramalho, S Magalhães, M Soares and I Gordo (2013) The genetic basis of Escherichia coli pathoadaptation to macrophages. PloS Pathogens. 9 (12), e1003802. https://doi.org/10.1371/journal.ppat.1003802. Recommended by F1000.
42. Sousa A, C. Bourgard, L. Wahl L, I Gordo (2013) Rates of transposition in Escherichia coli. Biology Letters. 9 (6), 20130838. http://dx.doi.org/10.1098/rsbl.2013.0838
41. Chelo IM, Nedli J, Gordo I and H Teotónio (2013) An experimental test on the probability of extinction of new genetic variants. Nature Communications 4:2417. https://doi.org/10.1038/ncomms3417
40. Avelar AT, L Perfeito, I Gordo and MG Ferreira (2013) Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy. Nature Communications 4:2235. https://doi.org/10.1038/ncomms3235. See also Highlight on this paper in Nature Reviews Genetics: Molecular evolution: Rearrangements for fitness p676 | doi:10.1038/nrg3578.
39. Gordo I and PRA Campos (2013) Evolution of clonal populations approaching a fitness peak. Biology Letters 9 (1), 20120239. https://doi.org/10.1098/rsbl.2012.0239
38. Moura de Sousa JA, PRA Campos and I. Gordo (2013) An ABC method for estimating the rate and distribution of effects of beneficial mutations. Genome Biology and Evolution 5(5):794-806. https://doi.org/10.1093/gbe/evt045
37. Brito PH, Rocha EPC, Xavier KB and I Gordo (2013) Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception. Genome Biology and Evolution 5(1):16-30. https://doi.org/10.1093/gbe/evs122
36. Miskinyte M and I. Gordo (2013) Increased survival of antibiotic resistant Escherichia coli inside macrophages. Antimicrobial Agents and Chemotherapy 57(1):189-195.
https://doi.org/10.1128/AAC.01632-12
35. Trindade S, A Sousa and I Gordo (2012) Antibiotic resistance and stress in the light of Fisher’s model. Evolution 66:3815-3824. https://doi.org/10.1111/j.1558-5646.2012.01722.x
34. Sousa A., Magalhães S and I. Gordo (2012) Cost of antibiotic resistance and the geometry of adaptation. Molecular Biology and Evolution 29(5):1417-28.
https://doi.org/10.1093/molbev/msr302
33. Silva RF, Mendonça SCM, Carvalho LM, Reis AM, Gordo I, Trindade S and F Dionisio (2011) Pervasive sign epistasis between conjugative plasmids and drug resistance chromosomal mutations. PloS Genetics 7(7), e1002181.
https://doi.org/10.1371/journal.pgen.1002181
32. Gordo I, L. Perfeito and A Sousa (2011) Fitness effects of mutations in bacteria. J Mol Microb Biotech 21:20-35. https://doi.org/10.1159/000332747
31. Brito, P, Guilherme E, H. Soares and I. Gordo (2010) Mutation accumulation in Tetrahymnena. BMC Evolutionary Biology 10:354. https://doi.org/10.1186/1471-2148-10-354
30. Marais GAB, PRA Campos and I. Gordo (2010) Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study. Genome Biology and Evolution vol 2, 347-57. https://doi.org/10.1093/gbe/evq026
29. Gordo, I. and A. Sousa (2010) Mutation, selection and genetic interactions in bacteria. Enciclopedia of Life Sciences. https://doi.org/10.1002/9780470015902.a0022175
28. Trindade S., Perfeito L and I. Gordo (2010) Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli. Phil. Trans. R. Soc. B vol. 365 1177-1186.
27. Viana D, Gordo I, Sucena E, M Moita (2010) Cognitive and Motivational Requirements for the Emergence of Cooperation in a Rat Social Game. Plos One e8483.
https://doi.org/10.1371/journal.pone.0008483
26. Charlesworth, B., A.J. Betancourt, V.B. Kaiser and I. Gordo (2009) Genetic Recombination and molecular evolution. Cold Spring Harbor Symposia on Quantitative Biology 74, 177-186
25. Trindade S, Sousa A, Xavier KB, Dionisio F, Ferreira MG and I. Gordo (2009) Positive epistasis drives the acquisition of multidrug resistance. Plos Genetics 5(7):e1000578.
https://doi.org/10.1371/journal.pgen.1000578
24. Gordo I., Gomes M.G.M., Reis, D.G. and P.R.A. Campos (2009) Genetic diversity in The SIR model of pathogen evolution. Plos One 4(3): e4876.
https://doi.org/10.1371/journal.pone.0004876
23. Gordo I. and PRA Campos (2008) Sex and deleterious mutations. Genetics 179(1): 621-6.
https://doi.org/10.1534/genetics.108.086637
22. Campos PRA, P.S.C.A. Neto, V.M. de Oliveira and I. Gordo (2008) Environmental heterogeneity enhances clonal interference. Evolution 62(6):1390.
https://doi.org/10.1111/j.1558-5646.2008.00380.x
21. Perfeito L., Pereira MI, PRA Campos and I. Gordo (2008) The effect of spatial structure on adaptation in Escherichia coli. Biology Letters 4:57-9. https://doi.org/10.1098/rsbl.2007.0481
20. Perfeito L, L. Fernandes, C. Mota and I. Gordo (2007) Adaptive mutations in bacteria: high rate and small effects. Science 317:813-15. DOI: 10.1126/science.1142284 (Highlighted in Nature)
19. Gordo, I and PRA Campos (2007) Patterns of genetic variation in populations of infectious agents. BMC Evolutionary Biology 7:116. https://doi.org/10.1186/1471-2148-7-116
18. Combadão J., P.R.A Campos, F. Dionisio and I. Gordo (2007) Small-world networks decrease the speed of Muller’s ratchet. Genetics Research 89(1):7-18.
https://doi.org/10.1017/S0016672307008658
17. Dionisio F. and I. Gordo (2007) Controlling excludability in the evolution of cooperation. Evolution Ecology Research 9 (2): 365-373.
16. Gökaydin D., J.B. Oliveira-Martins, I. Gordo, and M.G.M Gomes (2007) The reinfection threshold regulates pathogen diversity: the case of influenza. Journal of Royal Society Interface 4(12):137-42.
15. Campos, PRA and I. Gordo. (2006) Pathogen genetic variation in small-world host contact structures. Journal of Statistical Mechanics: Theory and Experiment, Issue 12, pp. L12003.
14. Campos P.R.A., Combadão J., F. Dionisio and I. Gordo (2006) Muller's ratchet in random graphs and scale free networks. Physical Review E 74 (4): 042901
13. Faro J, Combadão J and I. Gordo (2006) Did Germinal Centers evolve under differential effects of diversity vs affinity? Lecture Notes in Computer Science. 4163: 1-8.
12. Perfeito L, I. Gordo and PRA Campos (2006) The effect of spatial structure in adaptive evolution. European Physical Journal B, 51, 301-306.
11. Gordo, I. and P.R.A. Campos (2006). Adaptive evolution in a spatially structured asexual population. Genetica, 127: 217 – 229.
10. Dionisio, F. and I. Gordo (2006) The tragedy of the commons, the public goods dilemma and the significance of rivalry and excludability in Evolutionary Biology. Evolution and Ecology Research 8: 321-332.
9. Rosas, A., I. Gordo and P.R.A. Campos (2005) Scaling, genetic drift and clonal interference in the extinction pattern of asexual populations. Physical Review E 72, 012901.
8. Gordo, I. and F. Dionisio (2005) A non-equilibrium model for estimating the parameters of deleterious mutations. Physical Review E 71: 031907.
7. Dionisio, F., I. C. Conceição, A. C. R. Marques, L. Fernandes and I. Gordo (2005) The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Proc Roy. Soc London- Biology Letters 1, 250–252.
6. Bachtrog, D. and I. Gordo (2004) Adaptive evolution of asexual populations under Muller’s ratchet. Evolution 58(7):1403-13.
5. Gordo, I., A. Navarro and B. Charlesworth (2002) Muller’s ratchet and the pattern of variation at a neutral locus. Genetics 161:835-48. IF: 4.389 Cit: 74 Q: 1.
4. Gordo, I. and B. Charlesworth. (2001) The speed of Muller’s ratchet with background selection, and the degeneration of Y chromosomes. Genetics Research 78:149-61.
3. Gordo, I. and B. Charlesworth. (2001) Genetic linkage and molecular evolution. Current Biology 11:R684-6.
2. Gordo, I. and B. Charlesworth (2000) On the speed of Muller’s ratchet. Genetics 156: 2137-40.
1. Gordo, I. and B. Charlesworth (2000) The degeneration of asexual haploid populations and the speed of Muller’s ratchet. Genetics 154: 1379-87.