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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 29/09/2026

biorxiv.org/content/10.64898/2026.09.26.754597v1 Agrees with prior work discovering less fit cells (here, that lack RM), form more persisters (see doi:10.1111/j.1751-7915.2011.00327.x from 2012). Previously, using most-prevalent defense, TAs, more toxic toxin reduces fitness & increases persisters.

biorxiv.org

Loss of restriction-modification methyltransferases drives persistence to fluoroquinolones in Pseudomonas aeruginosa

The resurgence of phage therapy has renewed interest in the interplay between phage resistance and antibiotic susceptibility and has stimulated research in the emergent field of non-canonical cellular...

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 11/09/2026

What you claim, again is in error. Your figure is about "The bacterial defense literature is rapidly expanding. Hits per 100 000 citations (proportion for each search by year)". It is not about TAs in general. You should correct your error. TAs are the most prevalent phage defense, beginning 1996.

esperr.github.io

PubMed by Year

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 11/09/2026

Hello. In your Fig. 1, you indicate TAs are from the 1980s. That is incorrect and I see no reference. I discovered TAs as anti-phage systems in 1996, which you fail to cite. Why?

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 10/07/2026

Congratulations on discovering yet another toxin/antitoxin system, the most-prevalent anti-phage system, known since 1996 (doi: 10.1128/jb.178.7.2044-2050.1996). Here, another type IX TAs (see doi.org/10.1016/j.ti... for a review).

doi.org

Redirecting

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 10/07/2026

science.org/doi/10.1126/science.aed6782 Interesting new type IX, anti-phage toxin/antitoxin system 'Metis' (although it is conveniently not called that) in which toxin MisA degrades NAD+ & antitoxin MisB degrades toxin-activating signal methylateddAMP nucleotides made by phage.

science.org

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 08/07/2026

biorxiv.org/content/10.64898/2026.07.07.736952v1 For 40 years it has been thought that the methanogen Methanosarcina acetivorans converts acetate only to methane. Instead, we demonstrate here 40% of the acetate is converted into ethanol.

biorxiv.org

Methanogenic Ethanol Production from Acetate

Biological ethanol production is important for the circular carbon economy and makes up 73% of the U.S. biological fuels market. Previously, we produced ethanol by reversing methanogenesis and capturi...

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 07/07/2026

Perhaps first example of HepT/MntA and phage inhibition and another example of type VII TAs and phage inhibition.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 07/07/2026

Perhaps first example of HepT/MntA and phage inhibition and another example of type VII TAs and phage inhibition.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 29/06/2026

(2/2) We identified 2 beneficial substitutions (S60P and I154V) that increase growth 8X. Congratulations primarily to @hjhwang0822, and thanks to @mitra_ruchira and @Larvberg and the team at the U of AZ including including Ingmar Riedel-Kruse.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 15/06/2026

Excellent idea Victor! Should be standard practice to fight rising conceptual plagiarism.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 14/06/2026

Compare doi:10.1111/1462-2920.14093 and doi.org/10.1016/j.is..., etc.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 14/06/2026

nature.com/articles/s41467-026-74199-2 More evidence of importance of ribosomes in dormancy (here, for spores). Compare 5 previous publications for relevance of ribosomes in persistence (dormancy). Unfortunately, 🧐, follows usual practice in Nat. Comm. of not citing the relevant literature.

nature.com

Ribosomal allostery as a potential regulator of bacterial dormancy - Nature Communications

Ribosomes are crucial for protein synthesis and managing cellular stress. Here, authors show that ribosomal protein L11 acts as a global regulator, coordinating complex internal signaling to ensure pr...

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 11/06/2026

Perhaps cells survive between plaques since persistence triggered or some signal from lysed cells activates phage defenses.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 05/06/2026

biorxiv.org/content/10.64898/2026.06.03.729817v1 We use RNAi silencing to inhibit the activity of the host methyl-coenzyme M reductase (Mcr) that primarily produces methane such that the cloned ANME-1 Mcr enzyme can capture 14-fold more CH4 and produce 14-fold more ethanol, during growth on CH4.

biorxiv.org

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 12/05/2026

www.nature.com/articles/s41... Add'l evidence that cells in growth arrest (here stationary phase, 12 hr) recover by reviving ribosomes, as shown in 2018 for persister cells using single-cell studies (not cited) and further elaborated in 2020 (doi 10.1016/j.isci.2019.100792, not cited).

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 28/03/2026

Excellent 2nd report of CRISPR controlling prophages. First report (2022, not cited by authors) is E. coli CRISPR-Cas prevents expression of cryptic prophage lysis protein YdfD (Qin) and lysis protein RzoD (DLP-12) thru RNA-RNA interactions (www.mdpi.com/1422-0067/23...).

mdpi.com

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 27/03/2026

www.cell.com/trends/micro... Suggests a type IX class for organizing toxin–antitoxin systems, in which the toxin or antitoxin utilizes nucleotide cell signals (second class where both are enzymes). Includes discussion of toxin activation, TAs and phage defense, and TAs and persistence.

cell.com

Type IX class utilizing cell signals for organizing toxin–antitoxin systems

The toxin–antitoxin (TA) field continues to advance rapidly, especially given the recognition of TA systems as one of the most prevalent phage defenses. These systems are omnipresent in both bacteria ...

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 29/01/2026

nature.com/articles/s41586-025-10070-6 Brilliant work from former lab undergrad Sargen showing Salmonella prophage single HEPN protein HepS is activated by Gifsy-1 J tip protein then cleaves tRNAs. But Abi data not compelling and probably just shuts down host metabolism to form persisters.

nature.com

A prophage-encoded abortive infection protein preserves host and prophage spread - Nature

A Gifsy-1 prophage–encoded higher eukaryotes and prokaryotes nucleotide-binding protein, HepS, senses Siphoviridae infection, activates abortive defence by cleaving host transfer RNAs, blocks rival ph...

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 27/01/2026

How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...

journals.asm.org

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio

Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

Vivek Mutalik @vivekmutalik.bsky.social · 18/01/2026

#microsky

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 30/12/2025

nature.com/articles/s41564-025-02207-0 We found one of these pseudo-lysogenic phages, also for E. coli, named SW1, that is T1-related, provides a benefit to kin that carry it, and depends on cryptic prophage protein YfdM: doi 10.1016/j.celrep.2019.03.070 (Cell Reports 2019).

nature.com

Persistent virulent phages exist across bacterial isolates - Nature Microbiology

The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 19/12/2025

biorxiv.org/content/10.64898/2025.12.18.695105v1 Previously, we discovered ribosomes dictate persister resuscitation (Environ Micro 2018, doi:10.1111/1462-2920.14093); now we show low ribosome levels in single cells increase persister formation 80-fold, cementing the ribosome-persister mechanism.

biorxiv.org

Persister Cells Form Based on Low Ribosome Content

Persister cells survive any severe stress including antibiotics, starvation, heat, oxidative conditions, and phage attack, by entering a dormant physiological state. They arise without genetic change ...

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 16/12/2025

I am curious why this work overlooks the most-prevalent anti-phage system, toxin/antitoxins, whose transcription response to stress has been well-studied and which are induced hundreds of fold by similar stresses (see www.sciencedirect.com/science/arti...), including mqsRA (known to inhibit T2).

sciencedirect.com

Stress Can Induce Transcription of Toxin-Antitoxin Systems without Activating Toxin

Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacterial genomes, but their functions are controversial. Although they are frequently…

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 16/10/2025

Congratulations to Joy for all of her hard work and to all the visitors to my lab including Daniel, Rodolfo, and Michael, who had an incredible impact and thanks to Maria! Thanks also to the three reviewers that provided excellent insights to improve the paper.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 16/10/2025

academic.oup.com/nar/article/... We discovered a new, wide-spread phage defense system based on serine recombinase PinQ in E. coli cryptic prophage Qin that inverts 1,797 bp in another cryptic prophage, e14, to encode two chimeric proteins that block adsorption of T2 phage. @NAR_Open

academic.oup.com

Adsorption of phage T2 is inhibited due to inversion of cryptic prophage DNA by the serine recombinase PinQ

Abstract. Recombinases catalyze site-specific integration, excision, and inversion of DNA and are often found adjacent to anti-phage system genes clustered

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 12/10/2025

nature.com/articles/s41564-025-02124-2 BPOET: 1st high-throughput search (10,000 cmpds), resuscitates persisters (2020) with mechanism of activating hibernating ribosomes via 23S rRNA pseudouridine synthase RluD (E. coli, doi:10.1111/1462-2920.14828), cited, but not in context vs. new search:

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 29/09/2025

Uracil first shown 2009 to be a QS signal in P. a. & UMP path important for QS & virulence. Moreover, 5-fluorouracil is a potent QS quencher & is the first QQ compound used commercially (for catheters). Uracil also is a signal in the Drosophila GI tract.

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

Asaf Levy @asaflevylab.bsky.social · 23/09/2025

Quite insane if true

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 23/09/2025

Using DefenseFinder misses nearly all of the toxin/antitoxin systems; i.e., the most prevalent phage defense system is missing to a large degree from this database. I recommend running TAFinder or TADB. etc., too, to search for TAs, which likely are anti-phage systems.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 23/09/2025

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Reposted by Cryptic Prophage (phage 🧬🪤 in 🦠)

IKGbiofilms @ikgbiofilmlab.bsky.social · 25/08/2025

I am excited to announce a fantastic collaboration! We thank the U.S.-Israel #BSF and the National Science Foundation #NSF for funding our project with Prof. Hadar Ben-Yoav and @crypticprophage.bsky.social. We will be studying #mucin- associated #biofilms using innovative mucin-on-chip systems.

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Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage.bsky.social · 24/03/2025

Cryptic Prophage (phage 🧬🪤 in 🦠) (2/2) Not cited: doi:10.1111/1462-2920.14075 where it was shown the few live VBNCs = persisters. Also, there is no proof of differences in dormancy, i.e., no differences in persister cells (enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...).

enviromicro-journals.onlinelibrary.wiley.com

Viable but non‐culturable and persistence describe the same bacterial stress state

Bacteria are often thought of as having two dormant phenotypes: the viable but non-culturable (VBNC) state and the persister state. Here we investigate the relatedness of the two stress-induced pheno...

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