References
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., … & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature505(7484), 559-563.
Modi, S. R., Collins, J. J., & Relman, D. A. (2014). Antibiotics and the gut microbiota. The Journal of Clinical Investigation124 (10), 4212-4218.
Schluter, J., Peled, J. U., Taylor, B. P., Markey, K. A., Smith, M., Taur, Y., … & Xavier, J. B. (2020). The gut microbiota is associated with immune cell dynamics in humans. Nature588 (7837), 303-307.
Coyte, K. Z., & Rakoff-Nahoum, S. (2019). Understanding competition and cooperation within the mammalian gut microbiome. Current Biology29 (11), R538-R544.
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics123 (3), 585-595.
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., … & Segata, N. (2019). Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell176 (3), 649-662.
Harris, C. D., Torrance, E. L., Raymann, K., & Bobay, L. M. (2021). CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. Molecular Biology and Evolution38 (2), 727-734.
Galperin, M. Y., Wolf, Y. I., Makarova, K. S., Vera Alvarez, R., Landsman, D., & Koonin, E. V. (2021). COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Research49 (D1), D274-D281.
Katoh, K., Misawa, K., Kuma, K. I., & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research30 (14), 3059-3066.
Archer, F. I., Adams, P. E., & Schneiders, B. B. (2017). stratag: An r package for manipulating, summarizing and analysing population genetic data. Molecular Ecology Resources17 (1), 5-11.
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological)57 (1), 289-300.
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Molecular Biology and Evolution , 36 (6), 1925-1927.
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., Von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Bology and Evolution37 (5), 1530-1534.
Letunic, I., & Bork, P. (2021). Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research49 (W1), W293-W296.
Revell, L. J. (2012). phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution3 (2), 217-223.
Meyer, D., Dimitriadou, E., Hornik, K., Weingessel, A., Leisch, F., Chang, C. C., … & Meyer, M. D. (2019). Package ‘e1071’. The R Journal .
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., … & Zhuravleva, M. (2021). RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research49 (D1), D437-D451.
Mészáros, B., Erdős, G., & Dosztányi, Z. (2018). IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Research46 (W1), W329-W337.
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology157 (1), 105-132.
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research25 (7), 1043-1055.
Huttenhower, C.J., Human Microbiome Project Consortium. (2012). Structure, function, and diversity of the healthy human microbiome. Nature486 (7402), 207.
Banerjee, S., Lo, K., Ojkic, N., Stephens, R., Scherer, N. F., & Dinner, A. R. (2021). Mechanical feedback promotes bacterial adaptation to antibiotics. Nature Physics17 (3), 403-409.
Card, K. J., Thomas, M. D., Graves, J. L., Barrick, J. E., & Lenski, R. E. (2021). Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences USA118 (5).
Du, D., Wang-Kan, X., Neuberger, A., van Veen, H. W., Pos, K. M., Piddock, L. J., & Luisi, B. F. (2018). Multidrug efflux pumps: structure, function and regulation. Nature Reviews Microbiology16 (9), 523-539.
Okusu, H., Ma, D., & Nikaido, H. (1996). AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. Journal of Bacteriology178 (1), 306-308.
Blair, J. M., Bavro, V. N., Ricci, V., Modi, N., Cacciotto, P., Kleinekathӧfer, U., … & Piddock, L. J. (2015). AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity. Proceedings of the National Academy of Sciences USA112 (11), 3511-3516.
Blanco, P., Hernando-Amado, S., Reales-Calderon, J. A., Corona, F., Lira, F., Alcalde-Rico, M., … & Martinez, J. L. (2016). Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants. Microorganisms4 (1), 14.
Lanfear, R., Kokko, H., & Eyre-Walker, A. (2014). Population size and the rate of evolution. Trends in Ecology & Evolution29 (1), 33-41.
Sonnenburg, E. D., & Sonnenburg, J. L. (2019). The ancestral and industrialized gut microbiota and implications for human health. Nature Reviews Microbiology17 (6), 383-390.
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … & Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature486 (7402), 222-227.
Moeller, A. H., Li, Y., Ngole, E. M., Ahuka-Mundeke, S., Lonsdorf, E. V., Pusey, A. E., … & Ochman, H. (2014). Rapid changes in the gut microbiome during human evolution. Proceedings of the National Academy of Sciences USA111 (46), 16431-16435.