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).
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).
CAS PubMed PubMed Central Google Scholar
Segers, A. & Depoortere, I. Circadian clocks in the digestive system. Nat. Rev. Gastroenterol. Hepatol. 18, 239–251 (2021).
Yang, Y. & Zhang, J. Bile acid metabolism and circadian rhythms. Am. J. Physiol. Gastrointest. Liver Physiol. 319, G549–G563 (2020).
Frazier, K. & Chang, E. B. Intersection of the gut microbiome and circadian rhythms in metabolism. Trends Endocrinol. Metab. 31, 25–36 (2020).
Wang, Y. et al. The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science 357, 912–916 (2017).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Diard, M. et al. Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium. Curr. Biol. 24, 2000–2005 (2014).
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).
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).
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).
CAS PubMed PubMed Central Google Scholar
Zhu, W. et al. Precision editing of the gut microbiota ameliorates colitis. Nature 553, 208–211 (2018).
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).
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 causes long-term alteration to the gut microbiota. Cell 173, 1742–1754.e17 (2018).
CAS PubMed PubMed Central Google Scholar
Weiss, A. S. et al. In vitro interaction network of a synthetic gut bacterial community. ISME J. 16, 1095–1109 (2022).
Gibbs, K. A. & Greenberg, E. P. Territoriality in Proteus: advertisement and aggression. Chem. Rev. 111, 188–194 (2011).
Chatzidaki-Livanis, M., Geva-Zatorsky, N., Comstock, L. E. & Hooper, L. V. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. Proc. Natl Acad. Sci. USA 113, 3627–3632 (2016).
CAS PubMed PubMed Central Google Scholar
Yao, L. et al. A selective gut bacterial bile salt hydrolase alters host metabolism. Elife 7, e37182 (2018).
Wahlström, A., Sayin, S. I., Marschall, H.-U. & Bäckhed, F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 24, 41–50 (2016).
Baquero, F., Lanza, V. F., Baquero, M. R., del Campo, R. & Bravo-Vázquez, D. A. Microcins in enterobacteriaceae: peptide antimicrobials in the eco-active intestinal chemosphere. Front. Microbiol. 10, 2261 (2019).
Jost, T., Lacroix, C., Braegger, C. & Chassard, C. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health. Nutr. Rev. 73, 426–437 (2015).
Bode, L. Human milk oligosaccharides in the prevention of necrotizing enterocolitis: a journey from in vitro and in vivo models to mother-infant cohort studies. Front. Pediatr. 6, 385 (2018).
PubMed PubMed Central Google Scholar
Tailford, L. E., Crost, E. H., Kavanaugh, D. & Juge, N. Mucin glycan foraging in the human gut microbiome. Front. Genet. 6, 81 (2015).
PubMed PubMed Central Google Scholar
Cani, P. D. & de Vos, W. M. Next-generation beneficial microbes: the case of akkermansia muciniphila. Front. Microbiol. 8, 1765 (2017).
PubMed PubMed Central Google Scholar
Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005).
Chen, L. et al. The long-term genetic stability and individual specificity of the human gut microbiome. Cell 184, 2302–2315.e12 (2021).
Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9, e1003388 (2013).
PubMed PubMed Central Google Scholar
Palmer, J. D. & Foster, K. R. Bacterial species rarely work together. Science 376, 581–582 (2022).
留言 (0)