Petkov, S. The fitness landscape metaphor: dead but not gone. http://journals.openedition.org/philosophiascientiae19, 159–174 (2015).

Mustonen, V. & Lässig, M. From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet. 25, 111–119 (2009).

Article  CAS  PubMed  Google Scholar 

Lenski, R. E. & Travisano, M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl Acad. Sci. U.S.A. 91, 6808–6814 (1994).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Segers, A. & Depoortere, I. Circadian clocks in the digestive system. Nat. Rev. Gastroenterol. Hepatol. 18, 239–251 (2021).

Article  PubMed  Google Scholar 

Yang, Y. & Zhang, J. Bile acid metabolism and circadian rhythms. Am. J. Physiol. Gastrointest. Liver Physiol. 319, G549–G563 (2020).

Article  CAS  PubMed  Google Scholar 

Frazier, K. & Chang, E. B. Intersection of the gut microbiome and circadian rhythms in metabolism. Trends Endocrinol. Metab. 31, 25–36 (2020).

Article  CAS  PubMed  Google Scholar 

Wang, Y. et al. The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science 357, 912–916 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

He, C. et al. Circadian rhythm disruption influenced hepatic lipid metabolism, gut microbiota and promoted cholesterol gallstone formation in mice. Front. Endocrinol. 12, 723918 (2021).

Stearns, J. C. et al. Bacterial biogeography of the human digestive tract. Sci. Rep. 1, 170 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Cheng, H. M., Mah, K. K. & Seluakumaran, K. Intestinal Fluid Handling: Absorption. Defin. Physiol. Princ. Themes Concepts 2, 47–49 (2020).

Google Scholar 

Hoces, D. et al. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota. bioRxiv https://doi.org/10.1101/2022.06.19.496708 (2022).

Cremer, J., Arnoldini, M. & Hwa, T. Effect of water flow and chemical environment on microbiota growth and composition in the human colon. Proc. Natl Acad. Sci. U.S.A. 114, 6438–6443 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arnoldini, M., Cremer, J. & Hwa, T. Bacterial growth, flow, and mixing shape human gut microbiota density and composition. Gut Microbes 1–8 https://doi.org/10.1080/19490976.2018.1448741 (2018).

Nguyen, J., Lara-Gutiérrez, J. & Stocker, R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol. Rev. 45, fuaa068 (2021).

Bell, G. Fluctuating selection: the perpetual renewal of adaptation in variable environments. Philos. Trans. R. Soc. B Biol. Sci. 365, 87–97 (2010).

Article  Google Scholar 

Roemhild, R., Barbosa, C., Beardmore, R. E., Jansen, G. & Schulenburg, H. Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa. Evol. Appl 8, 945–955 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barreto, H. C., Abreu, B. & Gordo, I. Fluctuating selection on bacterial iron regulation in the mammalian gut. Curr. Biol. 32, 3261–3275.e4 (2022).

Article  CAS  PubMed  Google Scholar 

Dapa, T., Ramiro, R. S., Pedro, M. F., Gordo, I. & Xavier, K. B. Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe 30, 183–199.e10 (2022).

Article  CAS  PubMed  Google Scholar 

Hartl, D. L. & Clark, A. G. Principles of Population Genetics. (Sinauer, 2007).

Groisman, E. A. & Ochman, H. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87, 791–794 (1996).

Article  CAS  PubMed  Google Scholar 

McInnes, R. S., McCallum, G. E., Lamberte, L. E. & van Schaik, W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr. Opin. Microbiol. 53, 35–43 (2020).

Article  CAS  PubMed  Google Scholar 

Frazão, N., Sousa, A., Lässig, M. & Gordo, I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc. Natl Acad. Sci. U.S.A. 116, 17906–17915 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Barreto, H. C., Abreu, B. & Gordo, I. Fluctuating selection on bacterial iron regulation in the mammalian gut. Curr. Biol. https://doi.org/10.1016/J.CUB.2022.06.017 (2022).

Barroso-Batista, J. et al. The first steps of adaptation of escherichia coli to the gut are dominated by soft sweeps. PLoS Genet. 10, e1004182 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Diard, M. et al. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat. Microbiol. 6, 830–841 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Diard, M. et al. Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494, 353–356 (2013).

Article  CAS  PubMed  Google Scholar 

Ghalayini, M. et al. Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon. Mol. Ecol. 28, 4470–4485 (2019).

Article  CAS  PubMed  Google Scholar 

Lescat, M. et al. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol. Ecol. 26, 1802–1817 (2017).

Article  CAS  PubMed  Google Scholar 

Yilmaz, B. et al. Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell Host Microbe 29, 650–663.e9 (2021).

Article  CAS  PubMed  Google Scholar 

Diard, M. et al. Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium. Curr. Biol. 24, 2000–2005 (2014).

Article  CAS  PubMed  Google Scholar 

Patrick, S. et al. Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis. Microbiology 156, 3255–3269 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Porter, N. T., Canales, P., Peterson, D. A. & Martens, E. C. A subset of polysaccharide capsules in the human symbiont bacteroides thetaiotaomicron promote increased competitive fitness in the mouse gut. Cell Host Microbe 22, 494–506.e8 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu, W. et al. Precision editing of the gut microbiota ameliorates colitis. Nature 553, 208–211 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kashyap, P. C. et al. Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota. Proc. Natl Acad. Sci. USA 110, 17059–17064 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tropini, C. How the physical environment shapes the microbiota. mSystems 6, e0067521 (2021).

Tropini, C. et al. Transient osmotic perturbation c