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. Nature , 505(7484), 559-563.
Modi, S. R., Collins, J. J., & Relman, D. A. (2014). Antibiotics and
the gut microbiota. The Journal of Clinical
Investigation , 124 (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. Nature , 588 (7837),
303-307.
Coyte, K. Z., & Rakoff-Nahoum, S. (2019). Understanding competition and
cooperation within the mammalian gut microbiome. Current
Biology , 29 (11), R538-R544.
Tajima, F. (1989). Statistical method for testing the neutral mutation
hypothesis by DNA polymorphism. Genetics , 123 (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. Cell , 176 (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
Evolution , 38 (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 Research , 49 (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 Research , 30 (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 Resources , 17 (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 Evolution , 37 (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 Research , 49 (W1), W293-W296.
Revell, L. J. (2012). phytools: an R package for phylogenetic
comparative biology (and other things). Methods in Ecology and
Evolution , 3 (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 Research , 49 (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 Research , 46 (W1),
W329-W337.
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the
hydropathic character of a protein. Journal of Molecular
Biology , 157 (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
Research , 25 (7), 1043-1055.
Huttenhower, C.J., Human Microbiome Project Consortium. (2012).
Structure, function, and diversity of the healthy human
microbiome. Nature , 486 (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 Physics , 17 (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
USA , 118 (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
Microbiology , 16 (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
Bacteriology , 178 (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 USA , 112 (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. Microorganisms , 4 (1), 14.
Lanfear, R., Kokko, H., & Eyre-Walker, A. (2014). Population size and
the rate of evolution. Trends in Ecology &
Evolution , 29 (1), 33-41.
Sonnenburg, E. D., & Sonnenburg, J. L. (2019). The ancestral and
industrialized gut microbiota and implications for human
health. Nature Reviews Microbiology , 17 (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. Nature , 486 (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 USA , 111 (46), 16431-16435.