Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).
Granato, E. T., Meiller-Legrand, T. A. & Foster, K. R. The evolution and ecology of bacterial warfare. Curr. Biol. 29, R521–R537 (2019).
Soucy, S. M., Huang, J. & Gogarten, J. P. Horizontal gene transfer: building the web of life. Nat. Rev. Genet. 16, 472–482 (2015).
Hussain, F. A. et al. Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages. Science 374, 488–492 (2021).
Wang, T. et al. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat. Chem. Biol. 18, 1245–1252 (2022).
Kreitz, J. et al. Programmable protein delivery with a bacterial contractile injection system. Nature 616, 357–463 (2023).
Nikel, P. I., Martínez-García, E. & de Lorenzo, V. Biotechnological domestication of pseudomonads using synthetic biology. Nat. Rev. Microbiol. 12, 368–379 (2014).
Brophy, J. A. N. et al. Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nat. Microbiol. 3, 1043–1053 (2018).
Blazejewski, T., Ho, H.-I. & Wang, H. H. Synthetic sequence entanglement augments stability and containment of genetic information in cells. Science 365, 595–598 (2019).
Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721 (2005).
Heinemann, J. A. & Sprague, G. F. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340, 205–209 (1989).
Lopatkin, A. J. et al. Antibiotics as a selective driver for conjugation dynamics. Nat. Microbiol. 1, 16044 (2016).
Lu, T. K. & Collins, J. J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl Acad. Sci. USA 106, 4629–4634 (2009).
Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011).
Zhou, H., Beltrán, J. F. & Brito, I. L. Functions predict horizontal gene transfer and the emergence of antibiotic resistance. Sci. Adv. 7, eabj5056 (2021).
Nazarian, P., Tran, F. & Boedicker, J. Q. Modeling multispecies gene flow dynamics reveals the unique roles of different horizontal gene transfer mechanisms. Front. Microbiol. 9, 2978 (2018).
Cheng, H.-Y., Masiello, C. A., Bennett, G. N. & Silberg, J. J. Volatile gas production by methyl halide transferase: an in situ reporter of microbial gene expression in soil. Environ. Sci. Technol. 50, 8750–8759 (2016).
Bethke, J. H. et al. Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli. Sci. Adv. 6, eaax3173 (2020).
Davison, J. Genetic exchange between bacteria in the environment. Plasmid 42, 73–91 (1999).
Hughes, V. M. & Datta, N. Conjugative plasmids in bacteria of the ‘pre-antibiotic’ era. Nature 302, 725–726 (1983).
Schmidt, M. & de Lorenzo, V. Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett. 586, 2199–2206 (2012).
Sørensen, S. J., Bailey, M., Hansen, L. H., Kroer, N. & Wuertz, S. Studying plasmid horizontal transfer in situ: a critical review. Nat. Rev. Microbiol. 3, 700–710 (2005).
Brito, I. L. Examining horizontal gene transfer in microbial communities. Nat. Rev. Microbiol. 19, 442–453 (2021).
Ronda, C., Chen, S. P., Cabral, V., Yaung, S. J. & Wang, H. H. Metagenomic engineering of the mammalian gut microbiome in situ. Nat. Methods 16, 167–170 (2019).
Stegemann, S. & Bock, R. Exchange of genetic material between cells in plant tissue grafts. Science 324, 649–651 (2009).
Hertle, A. P., Haberl, B. & Bock, R. Horizontal genome transfer by cell-to-cell travel of whole organelles. Sci. Adv. 7, eabd8215 (2021).
Babić, A., Lindner, A. B., Vulić, M., Stewart, E. J. & Radman, M. Direct visualization of horizontal gene transfer. Science 319, 1533–1536 (2008).
Rubin, B. E. et al. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 7, 34–47 (2022).
Morris, E. R., Grey, H., McKenzie, G., Jones, A. C. & Richardson, J. M. A bend, flip and trap mechanism for transposon integration. eLife 5, e15537 (2016).
Spencer, S. J. et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J 10, 427–436 (2016).
Yaffe, E. & Relman, D. A. Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat. Microbiol. 5, 343–353 (2019).
Cech, T. R. The chemistry of self-splicing RNA and RNA enzymes. Science 236, 1532–1539 (1987).
Gambill, L., Staubus, A., Mo, K. W., Ameruoso, A. & Chappell, J. A split ribozyme that links detection of a native RNA to orthogonal protein outputs. Nat. Commun. 14, 543 (2023).
Waring, R. B., Towner, P., Minter, S. J. & Davies, R. W. Splice-site selection by a self-splicing RNA of Tetrahymena. Nature 321, 133–139 (1986).
Sullenger, B. A. & Cech, T. R. Ribozyme-mediated repair of defective mRNA by targeted trans-splicing. Nature 371, 619–622 (1994).
Been, M. D. & Cech, T. R. One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell 47, 207–216 (1986).
Bremer, H. & Dennis, P. P.Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus 3, 5.2.3 (2008).
Bernstein, J. A., Khodursky, A. B., Lin, P.-H., Lin-Chao, S. & Cohen, S. N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA 99, 9697–9702 (2002).
Bhattarai-Kline, S. et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature 608, 217–225 (2022).
Loveless, T. B. et al. Open-ended molecular recording of sequential cellular events into DNA. Nat. Chem. Biol. https://doi.org/10.1038/s41589-024-01764-5 (2024).
Neil, K., Allard, N., Grenier, F., Burrus, V. & Rodrigue, S. Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114. Commun. Biol. 3, 523 (2020).
Alderliesten, J. B. et al. Effect of donor–recipient relatedness on the plasmid conjugation frequency: a meta-analysis. BMC Microbiol. 20, 135 (2020).
Li, L. et al. Estimating the transfer range of plasmids encoding antimicrobial resistance in a wastewater treatment plant microbial community. Environ. Sci. Technol. Lett. 5, 260–265 (2018).
Jahn, M., Vorpahl, C., Hübschmann, T., Harms, H. & Müller, S. Copy number variability of expression plasmids determined by cell sorting and droplet digital PCR. Microb. Cell Fact. 15, 211 (2016).
Ares-Arroyo, M., Rocha, E. P. C. & Gonzalez-Zorn, B. Evolution of ColE1-like plasmids across γ-Proteobacteria: from bacteriocin production to antimicrobial resistance. PLoS Genet. 17, e1009919 (2021).
Sheth, R. U. & Wang, H. H. DNA-based memory devices for recording cellular events. Nat. Rev. Genet. 19, 718–732 (2018).
Munck, C., Sheth, R. U., Freedberg, D. E. & Wang, H. H. Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR–Cas spacer acquisition platform. Nat. Commun. 11, 95 (2020).
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
Yang, L. et al. Permanent genetic memory with >1-byte capacity. Nat. Methods 11, 1261–1266 (2014).
Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358, 1457–1461 (2017).
Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. Molecular recordings by directed CRISPR spacer acquisition. Science 353, aaf1175 (2016).
Kempton, H. R., Love, K. S., Guo, L. Y. & Qi, L. S. Scalable biological signal recording in mammalian cells using Cas12a base editors. Nat. Chem. Biol. 18, 742–750 (2022).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
Johns, N. I. et al. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nat. Methods 15, 323–329 (2018).
Ceroni, F., Algar, R., Stan, G.-B. & Ellis, T. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat. Methods 12, 415–418 (2015).
Loveless, T. B. et al. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nat. Chem. Biol. 17, 739–747 (2021).
Jeltsch, A. & Pingoud, A. Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction–modification systems. J. Mol. Evol. 42, 91–96 (1996).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
Weinstock, M. T., Hesek, E. D., Wilson, C. M. & Gibson, D. G. Vibrio natriegens as a fast-growing host for molecular biology. Nat. Methods 13, 849–851 (2016).
Ferrières, L. et al. Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J. Bacteriol. 192, 6418–6427 (2010).
Hoeflinger, J. L., Hoeflinger, D. E. & Miller, M. J. A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python. J. Microbiol. Methods 132, 83–85 (2017).
Untergasser, A. et al. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35, W71–W74 (2007).
Untergasser, A., Ruijter, J. M., Benes, V. & van den Hoff, M. J. B. Web-based LinRegPCR: application for the visualization and analysis of (RT)–qPCR amplification and melting data. BMC Bioinformatics 22, 398 (2021).
Madeira, F. et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 50, W276–W279 (2022).
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).
Chakravorty, S., Helb, D., Burday, M., Connell, N. & Alland, D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 69, 330–339 (2007).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Janssen, S. et al. Phylogenetic placement of exact amplicon sequences improves associations with clinical information. mSystems 3, e00021–18 (2018).
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).
Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
Robeson, M. S. et al. RESCRIPt: reproducible sequence taxonomy reference database management. PLoS Comput. Biol. 17, e1009581 (2021).
Fernandes, A. D. et al. Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome 2, 15 (2014).
Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).
Klümper, U. et al. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community. ISME J. 9, 934–945 (2015).
