Cryptic Prophage (phage 🧬🪤 in 🦠)

TAs 🛑 phages ('96), phages ➡️ persisters, E. c. CRISPR 🛑 cryptic prophages, indole=interkingdom signal, AI2 incr biofilm & TqsA exports (Prof. Thomas K. Wood)

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/DP3yC6rlen
We clone ANME-1 Mcr to reverse methanogenesis and convert the greenhouse gases CH4 & CO2 into ethanol. We also provide additional evidence that native, methanogenic Mcr is capable of operating in reverse to capture CH4 & CO2 as we found in 2016.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

Along with Fe+3 & acetate, Ferry and Yan also use our ANME-1 methane-activated promoter from 2016, but unlike our current 2026 study, they clone two E's (Adh & Fnr) to get ethanol whereas we used the native E's of the host to go from acetate to ethanol.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

Add'l proof methanogenesis is reversed for growth by M. acetivorans using our 2016 discovery (DOI 10.1186/s12934-015-0397-z) the terminal e-acceptor Fe+3 must be used & that CH4 is converted to acetate. We also made ethanol by cloning ANME-1 Mcr (doi 10.1038/s43247-026-03601-0).

[Evgenii Protasov @protasov_evgeni]

Reversing methanogenic archaea to mitigate anthropogenic methane emissions and generate value-added products
#microbiololgy #methanogens #archaea #biotechnology
@TrendsinBiotech
https://t.co/MhGhVkbd6o

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

Ser reported here to increase chemotaxis during resuscitation but we also previously reported that Ala increases chemotaxis during persister resuscitation (2020, doi 10.1016/j.isci.2019.100792).

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/c7aXVcypb6
Additional evidence different amino acids influence persister resuscitation; here Ser important. We previously tested all 20 aa's and found Ala most important in 2020 (not cited, doi 10.1016/j.isci.2019.100792) and deduced mechanism.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

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).

[Demo lab @Demolab6]

We poked E. coli while it was “taking a nap” and… turns out it’s REALLY good at hitting snooze and bouncing back 😴➡️⚡ #CeitecMasarykUniversity #Ribosome #RNA #CryoEM
Our new paper in Nat. Commun. dives into how bacteria recover from growth arrest.
https://t.co/gyFLbQwUAN

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/MMIYEHGsvt
Cells with low ribosome content form persisters 80-fold more than those with normal ribosomes levels (ampicillin) & 50-fold more (ciprofloxacin). Therefore, low ribosome levels result in persistence and ribosome levels must increase for resuscitation.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/HurShznkaJ
Of 8 ribosomal proteins id'ed in the phage, 1 is an acetyltransferase (assoc. with bacterial stress response doi 10.1016/j.bbrc.2011.06.076) & 1 is related to trans-translation (ribosome rescue) so intriguing that phage may control the stress response.

[Cameron Thrash @jcamthrash]

Persister Cells Form Based on Low Ribosome Content in Escherichia coli https://t.co/pwmXf6e9rM

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/P6CktlTVpR
Extraordinarily informative review.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

"...the ability of biofilms to thwart highly corrosive anaerobic microbes is untested" is patently false. Biocorrosion from same SRB accomplished by the 1st engr'd biofilm for any application, which secreted anti-SRB peptides in 1999.

[Derek Lovley @microbeelectric]

"Preemptive biofilm colonization blocks microbial metal corrosion"
https://t.co/jbJvn3esxj
“Rust never sleeps”- but engineered E. coli biofilms stop even the most aggressive microbial corrosion of steel.

Towards effective, sustainable corrosion mitigation

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

@EgillRichard Authors here define Abi by citing ref 21 (Sorek, Ann Rev Virol, 2020, "Abortive infection: bacterial SUICIDE...") which defines Abi solely as death. So authors define Abi as death and provide no evidence of it. We should stop using the term Abi & stop redefining it to suit needs.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

@EgillRichard Authors here define Abi by citing ref 21 (Sorek, Ann Rev Virol, 2020, "Abortive infection: bacterial SUICIDE...") which defines Abi solely as death. So authors define Abi as death and provide no evidence of it. We should stop using the term Abi & stop redefining it to suit needs.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

Drinking the Kool-Aid: You indicate that ToxIN works by "an abortive infection mechanism" yet Fineran et al. themselves originally published in 2009 that there is no Abi as there was no cell lysis, even with pBAD overexpression (https://t.co/M3HkpkfFNf).

[Kotaro Kiga @KotaroKiga]

Very excited to share our new paper! Homing endonuclease SegB drives segmental amplification of anti-defense loci, enabling phages to escape multiple bacterial defense systems.
https://t.co/fxHCmBmYoL
Big thanks to Kotaro Chihara and to the Vasili lab.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/kcoapWB4dP
More excellent proof that cells are dormant via ribosome dimerization/inactivation in E. coli and EHEC persister cells during various stresses and that resuscitation activates ribosomes.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/aIF893A7KD
Let's put an end to this trend in phage micro: Calling these bacteria dormant is absurd. Replace with better term, "non-dividing". Takes E. coli 2 wks after starving to become dormant (doi:10.1111/1462-2920.14075). So RNA phages not removed by persisters.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

@microbeelectric
https://t.co/s0UlvBot0A
"...the ability of biofilms to thwart highly corrosive anaerobic microbes is untested"; 1st report my ass! Biocorrosion from same SRB accomplished by the 1st engr'd biofilm for any application, which secreted anti-SRB peptides in 1999.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

@microbeelectric
https://t.co/s0UlvBot0A
"...the ability of biofilms to thwart highly corrosive anaerobic microbes is untested"; 1st report my ass! Biocorrosion from same SRB accomplished by the 1st engr'd biofilm for any application, which secreted anti-SRB peptides in 1999.

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

And we have shown TA system promoters and toxic genes mutate within hours if one is not careful:
https://t.co/Ze9QguUAAp

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

https://t.co/aICTTi3yKs
🧐I note that (i) hundreds of reports have verified our original discovery that TAs act as phage defense in 1996 and (ii) the Laub lab corroborated our results 25 years later since they were sent our strains (doi 10.1016/j.molcel.2021.03.027).

[Cryptic Prophage (phage 🧬🪤 in 🦠) @crypticprophage]

Authors fail to show to show activity of Hok/Sok in any way.