von Wintersdorff, C. J. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).
Suay-García, B. & Pérez-Gracia, M. T. Present and future of carbapenem-resistant Enterobacteriaceae (CRE) infections. Antibiotics 8, 122 (2019).
Google Scholar
Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O. & Piddock, L. J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 13, 42–51 (2015).
Google Scholar
Codjoe, F. S. & Donkor, E. S. Carbapenem resistance: a review. Med Sci. 6, 1 (2017).
Schechner, V. et al. Asymptomatic rectal carriage of blaKPC producing carbapenem-resistant Enterobacteriaceae: who is prone to become clinically infected? Clin. Microbiol. Infect. 19, 451–456 (2013).
Google Scholar
Penders, J., Stobberingh, E. E., Savelkoul, P. H. & Wolffs, P. F. The human microbiome as a reservoir of antimicrobial resistance. Front Microbiol. 4, 87 (2013).
Google Scholar
Nordmann, P., Naas, T. & Poirel, L. Global spread of Carbapenemase-producing Enterobacteriaceae. Emerg. Infect. Dis. 17, 1791–1798 (2011).
Google Scholar
Tooke, C. L. et al. β-Lactamases and β-lactamase inhibitors in the 21st century. J. Mol. Biol. 431, 3472–3500 (2019).
Google Scholar
Sun, X. et al. Microbiota-derived metabolic factors reduce campylobacteriosis in mice. Gastroenterology 154, 1751–1763.e2 (2018).
Google Scholar
Ichinohe, T. et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 (2011).
Google Scholar
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
Google Scholar
Lieberman, T. D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat. Genet. 43, 1275–1280 (2011).
Google Scholar
Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).
Google Scholar
Chu, N. D., Smith, M. B., Perrotta, A. R., Kassam, Z. & Alm, E. J. Profiling living bacteria informs preparation of fecal microbiota transplantations. PLoS ONE 12, e0170922 (2017).
Google Scholar
Ferreiro, A., Crook, N., Gasparrini, A. J. & Dantas, G. Multiscale evolutionary dynamics of host-associated microbiomes. Cell 172, 1216–1227 (2018).
Google Scholar
Mo, Y. et al. Duration of carbapenemase-producing Enterobacteriaceae carriage in hospital patients. Emerg. Infect. Dis. 26, 2182–2185 (2020).
Google Scholar
Haverkate, M. R. et al. Duration of colonization with Klebsiella pneumoniae carbapenemase-producing bacteria at long-term acute care hospitals in Chicago, Illinois. Open Forum Infect. Dis. 3, ofw178 (2016).
Google Scholar
Korach-Rechtman, H. et al. Intestinal dysbiosis in carriers of carbapenem-resistant Enterobacteriaceae. mSphere 5, e00173–20 (2020).
Google Scholar
Yoshida, N. et al. Bacteroides vulgatus and Bacteroides dorei reduce gut microbial lipopolysaccharide production and inhibit atherosclerosis. Circulation 138, 2486–2498 (2018).
Google Scholar
Lenoir, M. et al. Butyrate mediates anti-inflammatory effects of. Gut Microbes 12, 1–16 (2020).
Google Scholar
Riedel, C. U. et al. Anti-inflammatory effects of bifidobacteria by inhibition of LPS-induced NF-κB activation. World J. Gastroenterol. 12, 3729–3735 (2006).
Google Scholar
Zeng, M. Y., Inohara, N. & Nuñez, G. Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol. 10, 18–26 (2017).
Google Scholar
Winter, S. E. & Bäumler, A. J. A breathtaking feat: to compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor. Gut Microbes 2, 58–60 (2011).
Google Scholar
Rivera-Chávez, F., Lopez, C. A. & Bäumler, A. J. Oxygen as a driver of gut dysbiosis. Free Radic. Biol. Med. 105, 93–101 (2017).
Google Scholar
Chng, K. R. et al. Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Nat. Ecol. Evol. 4, 1256–1267 (2020).
Google Scholar
Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).
Google Scholar
Stacy, A. et al. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell 184, 615–627.e17 (2021).
Google Scholar
Barreto, H. C., Sousa, A. & Gordo, I. The landscape of adaptive evolution of a gut commensal bacteria in aging mice. Curr. Biol. 30, 1102–1109.e5 (2020).
Google Scholar
Ernst, C. M. et al. Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat. Med. 26, 705–711 (2020).
Google Scholar
Zhao, S. et al. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25, 656–667.e8 (2019).
Google Scholar
Warsi, O. M., Andersson, D. I. & Dykhuizen, D. E. Different adaptive strategies in E. coli populations evolving under macronutrient limitation and metal ion limitation. BMC Evol. Biol. 18, 72 (2018).
Google Scholar
Hickman, R. A., Munck, C. & Sommer, M. O. A. Time-resolved tracking of mutations reveals diverse allele dynamics during Escherichia coli antimicrobial adaptive evolution to single drugs and drug pairs. Front. Microbiol. 8, 893 (2017).
Google Scholar
Auriol, C., Bestel-Corre, G., Claude, J. B., Soucaille, P. & Meynial-Salles, I. Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity. Proc. Natl Acad. Sci. USA 108, 1278–1283 (2011).
Google Scholar
Juers, D. H., Matthews, B. W. & Huber, R. E. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci. 21, 1792–1807 (2012).
Google Scholar
Rogers, A. W. L., Tsolis, R. M. & Bäumler, A. J. Salmonella versus the microbiome. Microbiol. Mol. Biol. Rev. 85, e00027–19 (2021).
Google Scholar
Hughes, E. R. et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis. Cell Host Microbe 21, 208–219 (2017).
Google Scholar
Gupta, S., Allen-Vercoe, E. & Petrof, E. O. Fecal microbiota transplantation: in perspective. Ther. Adv. Gastroenterol. 9, 229–239 (2016).
Google Scholar
Wortelboer, K., Nieuwdorp, M. & Herrema, H. Fecal microbiota transplantation beyond Clostridioides difficile infections. EBioMedicine 44, 716–729 (2019).
Google Scholar
Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–429 (2013).
Google Scholar
Martinson, J. N. V. et al. Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults. ISME J. 13, 2306–2318 (2019).
Google Scholar
Woyke, T., Doud, D. F. R. & Schulz, F. The trajectory of microbial single-cell sequencing. Nat. Methods 14, 1045–1054 (2017).
Google Scholar
Domingo, E. & Perales, C. Viral quasispecies. PLoS Genet. 15, e1008271 (2019).
Google Scholar
Yamada, C. et al. Molecular insight into evolution of symbiosis between breast-fed infants and a member of the human gut microbiome Bifidobacterium longum. Cell Chem. Biol. 24, 515–524.e5 (2017).
Google Scholar
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).
Google Scholar
Gao, S., Bertrand, D., Chia, B. K. & Nagarajan, N. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biol. 17, 102 (2016).
Google Scholar
Gao, S., Bertrand, D. & Nagarajan, N. FinIS: improved in silico finishing using an exact quadratic programming formulation. Lect. Notes Comput. Sci. 7534, 314–325 (2012).
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2 (2013).
Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).
Google Scholar
Franzosa, E. A. et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962–968 (2018).
Google Scholar
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
Google Scholar
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).
Google Scholar
Hawinkel, S., Mattiello, F., Bijnens, L. & Thas, O. A broken promise: microbiome differential abundance methods do not control the false discovery rate. Brief. Bioinformatics 20, 210–221 (2019).
Google Scholar
Morton, J. T. et al. Establishing microbial composition measurement standards with reference frames. Nat. Commun. 10, 2719 (2019).
Google Scholar
Inouye, M. et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 90 (2014).
Google Scholar
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517–D525 (2020).
Google Scholar
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
Google Scholar
Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189–11201 (2012).
Google Scholar
Hinrichs, A. S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).
Google Scholar
Pracana, R., Priyam, A., Levantis, I., Nichols, R. A. & Wurm, Y. The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB. Mol. Ecol. 26, 2864–2879 (2017).
Google Scholar
Quinlan, A. R. BEDTools: the Swiss-Army tool for genome feature analysis. Curr. Protoc. Bioinformatics 47, 11.12.1–34 (2014).
Google Scholar
Spedicato, G. Discrete time Markov chains with R. R J. 9.2, 84 (2017).
Google Scholar
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).
Google Scholar
Hahsler, M., Piekenbrock, M. & Doran, D. dbscan: fast density-based clustering with R. J. Stat. Softw. 91, 1–30 (2019).
Google Scholar
Galata, V., Fehlmann, T., Backes, C. & Keller, A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res. 47, D195–D202 (2019).
Google Scholar
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
Google Scholar
Quan, S. et al. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet. 8, e1002444 (2012).
Google Scholar
Tsuchido, T., VanBogelen, R. A. & Neidhardt, F. C. Heat shock response in Escherichia coli influences cell division. Proc. Natl Acad. Sci. USA 83, 6959–6963 (1986).
Google Scholar
Trubetskoy, D., Proux, F., Allemand, F., Dreyfus, M. & Iost, I. SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo. Nucleic Acids Res. 37, 6540–6549 (2009).
Google Scholar
Garoff, L., Huseby, D. L., Praski Alzrigat, L. & Hughes, D. Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli. J. Antimicrob. Chemother. 73, 3285–3292 (2018).
Google Scholar
Aponte, R. A., Zimmermann, S. & Reinstein, J. Directed evolution of the DnaK chaperone: mutations in the lid domain result in enhanced chaperone activity. J. Mol. Biol. 399, 154–167 (2010).
Google Scholar
Mundhada, H. et al. Increased production of l-serine in Escherichia coli through adaptive laboratory evolution. Metab. Eng. 39, 141–150 (2017).
Google Scholar
Conrad, T. M. et al. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc. Natl Acad. Sci. USA 107, 20500–20505 (2010).
Google Scholar
Li, Y. et al. LPS remodeling is an evolved survival strategy for bacteria. Proc. Natl Acad. Sci. USA 109, 8716–8721 (2012).
Google Scholar
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