Animated E. coli Bacteria Drawing

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Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding - Nature Communications

Bacteriophages are the most abundant life form on earth and can be applied to eliminate or engineer bacteria. Here, authors demonstrate RNA barcoding as a high throughput tool to measure bacteriophage...

nature.com

Plasmids weaponize conjugation to eliminate non-permissive recipients

Horizontal gene transfer via conjugative plasmids is a major driver of bacterial evolution. While antibiotic exposure selects for the resistance genes carried by some plasmids, much uncertainty remains in how plasmids persist and spread in microbial communities in the absence of such external selection. Here we show that conjugative plasmids drive their own spread, in part, by using their transfer machinery to enforce a join-or-die ultimatum that selectively eliminates non-permissive recipients through the process of lethal zygosis -- the T4SS-mediated elimination of recipients that fail to establish the plasmid. We found that this contact-dependent killing effectively clears a competitive niche for plasmid donors by turning bacterial immune systems into a fatal liability. Specifically, cells resisting plasmid establishment via CRISPR-Cas or Restriction-Modification systems are selectively killed because they fail to acquire the protective exclusion genes encoded on the plasmid, leading to lethal unregulated transfer. We leveraged this insight to resolve an obstacle in bacterial editing by developing "shielded" transposon vectors that co-deliver exclusion genes, increasing the efficiency of gene editing by orders of magnitude. Our results reveal the role of "coercive assimilation" in horizontal gene transfer, exposing a trade-off where the advantage of bacterial immunity to foreign DNA is counterbalanced by lethal zygosis. ### Competing Interest Statement The Regents of the University of California have patents pending related to this work on which J.N.V.M. and B.E.R. are inventors. Leona M. and Harry B. Helmsley Charitable Trust, https://ror.org/011x6n313, G-2302-06692 Lyda Hill Philanthropies, https://ror.org/032sf2845 Acton Family Giving Valhalla Foundation Hastings/Quillin Fund - an advised fund of the Silicon Valley Community Foundation CH Foundation, https://ror.org/05nnhd665 Laura and Gary Lauder and Family the Sea Grape Foundation Emerson Collective (United States), https://ror.org/04537p149 Mike Schroepfer and Erin Hoffman Family Fund Anne Wojcicki Foundation Shurl and Kay Curci Foundation, https://ror.org/05t9fgt79 Innovative Genomics Institute, https://ror.org/01r4tcq81

biorxiv.org

Cross-order detection of bacteriophage transduction in communities using ribosomal RNA barcoding

Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map pha...

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Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology

Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.

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Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology

Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.

nature.com