Reprogramming Bacteria for Symbiont Conversion: A Review
Bacteria are prokaryotic cells some of which have positive effects upon the human organism and some of which have negative effects. I coined the term “symbiont conversion” for methods that convert, or reprogram, bacteria (and other cells, such as tumor cells) that have a negative effect to cells that have a positive effect. With such methods the urgent problem of antibiotic resistance could be solved. [Volko2025]
This short paper is about such methods, but in a more broad context – I want to review different approaches towards the reprogramming of bacteria and not necessarily in the context of symbiont conversion, although symbiont conversion is the motivation for doing this literature survey.
Basically a literature survey shows that there are two different approaches towards the reprogramming of bacteria: On the one hand, bacteria can be reprogrammed by altering their genes, for example by using bacteriophages (viruses that target bacteria) or methods like CRISPR/Cas9. These approaches are usually conducted ex vivo. On the other hand, there is metabolic reprogramming: by adding certain substances to the bacteria, the behavior of the bacteria is modified. This can even be done in vivo.
For true symbiont conversion, it seems an in vivo approach would be more desirable, as the objective is to “cure” living patients. However, this might perhaps be only possible by extracting bacteria from the human organism, modifying them ex vivo and then inserting them into the human organism again.
Many papers also state that their approach is related to “synthetic biology”. Indeed, synthetic biology is a method of creating artificial organisms with custom properties. Synthetic biology is also an ex vivo method, and it is very powerful. However, the objective of symbiont conversion is not to engineer novel bacterial species but to modify existing species and “tame” them.
Moreover, some papers deal with the modification of bacteria for the sake of cancer therapy. This is actually compatible with symbiont conversion theory. If a formerly harmful bacterium is modified and now helps the host organism to prevent cancer, that may be called successful symbiont conversion.
Metabolic approaches found in the literature include dietary interventions using prebiotics and probiotics, fecal microbiota transplantation, biguanides, mTOR inhibitors, glutaminase inhibition, and ion channels as drug targets. These approaches are quite rich in variety and have to be studied in detail. Their common advantage is that they can be done in vivo.
In [Xia2020] CRISPR/Cas9 was used to modify single nucleotides in the genes of a bacterium, partly to insert stop codons in order to prevent acetate and ethanol production. Primarily this should serve industry-related purposes. In [Cheng2023] a bacterium was engineered using synthetic biology with the purpose of detecting particular DNA sequences. [Liu2018] is also related to synthetic biology, a bacterium with a light-sensing circuit was engineered. In [Bendriss2023] the gut microbiota were reprogrammed using dietary interventions (prebiotics and probiotics) and fecal microbiota transplantation. In [Gardlik2014] bacteria were reprogrammed in vivo by application of modified bacteria with a plasmid that contained beneficial genes. [Cooper2023] used a synthetic biology approach to engineer bacteria that detect DNA sequences in cancer cells. [Fu2023] dealt with bacteria-mediated cancer therapy (BMCT) and “developed a genetic circuit for dynamically programming bacterial lifestyles (planktonic, biofilm or lysis), to precisely manipulate the process of bacterial adhesion, colonization and drug release in the BMCT process, via hierarchical modulation of the lighting power density of near-infrared (NIR) light”. [Navarro2002] provides a review of metabolic programming to treat cancer using “biguanides, mTOR inhibitors, glutaminase inhibition, and ion channels as drug targets”. [Sieow2021] is a review of methods of reprogramming bacteria to fight cancer, mostly using synthetic biology. [Hsu2020] reprogrammed the gut bacteria in vivo by administration of a bacteriophage. In [Meier2024] sensor histidine kinases were targeted by various types of light. [Gallivan2007] deals with the expression of modified genes by means of riboswitches, which are synthetic RNA sequences. In [Perera2024] plasmids were inserted into bacteria. In [Chowdhury2019] a non-pathogenic strain of E. coli was engineered using methods of synthetic biology. [Ngo2024] dealt with the application of plasmids for switching genes on and off. [Fredens2019] re-engineered an entire E. coli bacterium using synthetic biology. [Apura2019] triggered genes by insertion of RNA switches.
The central question the scientific community has to answer is: Is it possible to reprogram bacteria in vivo so that their pathogenic properties are neutralized and, perhaps, even properties beneficial for the host organism are added? For instance, is it possible to extract some bacteria, modify them using CRISPR/Cas9 and re-insert them, hoping that the modified genes will be passed to the other bacteria as well? Or might bacteriophages be a viable solution?
Symbiont conversion means that cells with parasitic behavior that harm the host organism are transformed in vivo to cells that exhibit beneficial behavior. So ex vivo methods are not useful for this purpose, except if they comprise taking cells from living tissue and re-inserting them afterwards. One in vivo method that was used in several of the cited publications is the insertion of plasmids. This, as well as the use of bacteriophages, i.e. viruses that modify the DNA of a bacterium, seems to be one of the most promising methods to achieve symbiont conversion. However, I would also like to encourage the readers to think about other ways of achieving symbiont conversion; perhaps some of them will have good ideas.
Some basic experiments that should be considered:
Gene modification using CRISPR/Cas9 and bacteriophage therapy seem to be the two most viable ways of achieving symbiont conversion, therefore related experiments have the highest priority and should be conducted as soon as possible in spite of the costs.
References
[Apura2019] Apura P et al: Reprogramming Bacteria with RNA Regulators, Biochemical Society Transactions 2019) 47 1279-1289, https://doi.org/10.1042/BST20190173
[Bendriss2023] Bendriss, G.; MacDonald, R.; McVeigh, C. Microbial Reprogramming in Obsessive– Compulsive Disorders: A Review of Gut–Brain Communication and Emerging Evidence. Int. J. Mol. Sci. 2023, 24, 11978. https://doi.org/ 10.3390/ijms241511978
[Cheng2023] Cheng, YY., Chen, Z., Cao, X. et al. Programming bacteria for multiplexed DNA detection. Nat Commun 14, 2001 (2023). https://doi.org/10.1038/s41467-023-37582-x
[Chowdhury2019] Chowdhury S et al: Programmable bacteria induce durable tumor regression and systemic antitumor immunity, Nature Medicine Vol 24 July 2019 1047-1063, https://doi.org/10.1038/s41591-019-0498-z
[Cooper2023] Cooper R. et al, Engineered Bacteria detect tumor DNA, Science. 2023 August 11; 381(6658): 682–686. doi:10.1126/science.adf3974.
[Fredens2019] Fredens J et al: Total Synthesis of Escherichia coli with a recoded Genome, Nature Vol 569 23 May 2019, https://doi.org/10.1038/s41586-019-1192-5
[Fu2023] Fu S. et al, Programming the lifestyles of engineered bacteria for cancer therapy, National Science Review 10: nwad031, 2023 https://doi.org/10.1093/nsr/nwad031
[Gallivan2007] Gallivan JP: Toward reprogramming bacteria with small molecules and RNA, Current Opinion in Chemical Biology 2007, 11:612-619, DOI 10.1016/j.cbpa.2007.10.004
[Gardlik2014] Gardlik, R. et al, Effects of bacteria-mediated reprogramming and antibiotic pretreatment on the course of colitis in mice, MOLECULAR MEDICINE REPORTS 10: 983-988, 2014, DOI: 10.3892/mmr.2014.2244
[Hsu2020] Hsu B. et al: In situ reprogramming of gut bacteria by oral delivery, NATURE COMMUNICATIONS | (2020) 11:5030 | https://doi.org/10.1038/s41467-020-18614-2
[Liu2018] Liu Z, Zhang J, Jin J, Geng Z, Qi Q and Liang Q (2018) Programming Bacteria With Light—Sensors and Applications in Synthetic Biology. Front. Microbiol. 9:2692. doi: 10.3389/fmicb.2018.02692
[Meier2024] Meier S. S. M. et al: Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling, Nature Communications volume 15, Article number: 4876 (2024)
[Navarro2022] Navarro, C.; Ortega, Á.; Santeliz, R.; Garrido, B.; Chacín, M.; Galban, N.; Vera, I.; De Sanctis, J.B.; Bermúdez, V. Metabolic Reprogramming in Cancer Cells: Emerging Molecular Mechanisms and Novel Therapeutic Approaches. Pharmaceutics 2022, 14, 1303. https://doi.org/10.3390/ pharmaceutics14061303
[Ngo2024] Ngo HTT et al: Reprogramming a Doxycycline-Inducible Gene Switch System for Bacteria-Mediated Cancer Therapy, Molecular Imaging and Biology (2024) 26:148-161, https://doi.org/10.1007/s11307-023-01879-6
[Perera2024] Perera PGT et al: Genetic Transformation of Plasmid DNA into Escherichia coli Using High Frquency Electromagnetic Energy, Nano Lett 2024 24 1145-1152
[Sieow2021] Sieow B. et al, Tweak to Treat: Reprograming Bacteria for Cancer Treatment, Trends in Cancer, May 2021, Vol. 7, No. 5 https://doi.org/10.1016/j.trecan.2020.11.004
[Volko2025] Volko, CD: Symbiont Conversion Theory. Biomedical Science and Clinical Research, DOI: 10.33140/BSCR
[Xia2020] Xia, PF et al: Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination, ACS Synth. Biol. 2020, 9, 8, 2162–2171
Claus D. Volko
This short paper is about such methods, but in a more broad context – I want to review different approaches towards the reprogramming of bacteria and not necessarily in the context of symbiont conversion, although symbiont conversion is the motivation for doing this literature survey.
Basically a literature survey shows that there are two different approaches towards the reprogramming of bacteria: On the one hand, bacteria can be reprogrammed by altering their genes, for example by using bacteriophages (viruses that target bacteria) or methods like CRISPR/Cas9. These approaches are usually conducted ex vivo. On the other hand, there is metabolic reprogramming: by adding certain substances to the bacteria, the behavior of the bacteria is modified. This can even be done in vivo.
For true symbiont conversion, it seems an in vivo approach would be more desirable, as the objective is to “cure” living patients. However, this might perhaps be only possible by extracting bacteria from the human organism, modifying them ex vivo and then inserting them into the human organism again.
Many papers also state that their approach is related to “synthetic biology”. Indeed, synthetic biology is a method of creating artificial organisms with custom properties. Synthetic biology is also an ex vivo method, and it is very powerful. However, the objective of symbiont conversion is not to engineer novel bacterial species but to modify existing species and “tame” them.
Moreover, some papers deal with the modification of bacteria for the sake of cancer therapy. This is actually compatible with symbiont conversion theory. If a formerly harmful bacterium is modified and now helps the host organism to prevent cancer, that may be called successful symbiont conversion.
Metabolic approaches found in the literature include dietary interventions using prebiotics and probiotics, fecal microbiota transplantation, biguanides, mTOR inhibitors, glutaminase inhibition, and ion channels as drug targets. These approaches are quite rich in variety and have to be studied in detail. Their common advantage is that they can be done in vivo.
In [Xia2020] CRISPR/Cas9 was used to modify single nucleotides in the genes of a bacterium, partly to insert stop codons in order to prevent acetate and ethanol production. Primarily this should serve industry-related purposes. In [Cheng2023] a bacterium was engineered using synthetic biology with the purpose of detecting particular DNA sequences. [Liu2018] is also related to synthetic biology, a bacterium with a light-sensing circuit was engineered. In [Bendriss2023] the gut microbiota were reprogrammed using dietary interventions (prebiotics and probiotics) and fecal microbiota transplantation. In [Gardlik2014] bacteria were reprogrammed in vivo by application of modified bacteria with a plasmid that contained beneficial genes. [Cooper2023] used a synthetic biology approach to engineer bacteria that detect DNA sequences in cancer cells. [Fu2023] dealt with bacteria-mediated cancer therapy (BMCT) and “developed a genetic circuit for dynamically programming bacterial lifestyles (planktonic, biofilm or lysis), to precisely manipulate the process of bacterial adhesion, colonization and drug release in the BMCT process, via hierarchical modulation of the lighting power density of near-infrared (NIR) light”. [Navarro2002] provides a review of metabolic programming to treat cancer using “biguanides, mTOR inhibitors, glutaminase inhibition, and ion channels as drug targets”. [Sieow2021] is a review of methods of reprogramming bacteria to fight cancer, mostly using synthetic biology. [Hsu2020] reprogrammed the gut bacteria in vivo by administration of a bacteriophage. In [Meier2024] sensor histidine kinases were targeted by various types of light. [Gallivan2007] deals with the expression of modified genes by means of riboswitches, which are synthetic RNA sequences. In [Perera2024] plasmids were inserted into bacteria. In [Chowdhury2019] a non-pathogenic strain of E. coli was engineered using methods of synthetic biology. [Ngo2024] dealt with the application of plasmids for switching genes on and off. [Fredens2019] re-engineered an entire E. coli bacterium using synthetic biology. [Apura2019] triggered genes by insertion of RNA switches.
The central question the scientific community has to answer is: Is it possible to reprogram bacteria in vivo so that their pathogenic properties are neutralized and, perhaps, even properties beneficial for the host organism are added? For instance, is it possible to extract some bacteria, modify them using CRISPR/Cas9 and re-insert them, hoping that the modified genes will be passed to the other bacteria as well? Or might bacteriophages be a viable solution?
Symbiont conversion means that cells with parasitic behavior that harm the host organism are transformed in vivo to cells that exhibit beneficial behavior. So ex vivo methods are not useful for this purpose, except if they comprise taking cells from living tissue and re-inserting them afterwards. One in vivo method that was used in several of the cited publications is the insertion of plasmids. This, as well as the use of bacteriophages, i.e. viruses that modify the DNA of a bacterium, seems to be one of the most promising methods to achieve symbiont conversion. However, I would also like to encourage the readers to think about other ways of achieving symbiont conversion; perhaps some of them will have good ideas.
Some basic experiments that should be considered:
- A culture of pathogenic bacterial cells should be created. Some of the bacteria should be taken out of it and modified using e.g. CRISPR/Cas9. Then these bacteria should be inserted into the cell culture again and it should be measured if their modified genes spread. That could be done by inserting genes that produce a protein the concentration of which could be measured.
Materials required for this experiment: everything that is needed for performing CRISPR/Cas9 (enzymes, equipment to make cell cultures, amino acids, equipment to synthesize double-sided DNA strands, etc.) and equipment to measure the concentration of the product (this could be done with an ELISA assay, for example). Estimated costs: at least 1 – 2 mio. USD. If the experiment succeeds, costs for applying the method in clinical practice will be lower, because it will be enough to grow a culture of modified bacteria, which can then be given to patients.
- A culture of pathogenic bacterial cells should be created. Engineered bacteriophages should be added. Then it should be measured if the cells are infected by the bacteriophages by measuring the concentration of the produced protein.
Materials required for this experiment: bacteriophages, amino acids, equipment to synthesize double-sided DNA strands, and equipment to measure the concentration of the product (e.g. ELISA). Bacteriophage production is rather cheap, it should cost less than 100 USD.
Gene modification using CRISPR/Cas9 and bacteriophage therapy seem to be the two most viable ways of achieving symbiont conversion, therefore related experiments have the highest priority and should be conducted as soon as possible in spite of the costs.
References
[Apura2019] Apura P et al: Reprogramming Bacteria with RNA Regulators, Biochemical Society Transactions 2019) 47 1279-1289, https://doi.org/10.1042/BST20190173
[Bendriss2023] Bendriss, G.; MacDonald, R.; McVeigh, C. Microbial Reprogramming in Obsessive– Compulsive Disorders: A Review of Gut–Brain Communication and Emerging Evidence. Int. J. Mol. Sci. 2023, 24, 11978. https://doi.org/ 10.3390/ijms241511978
[Cheng2023] Cheng, YY., Chen, Z., Cao, X. et al. Programming bacteria for multiplexed DNA detection. Nat Commun 14, 2001 (2023). https://doi.org/10.1038/s41467-023-37582-x
[Chowdhury2019] Chowdhury S et al: Programmable bacteria induce durable tumor regression and systemic antitumor immunity, Nature Medicine Vol 24 July 2019 1047-1063, https://doi.org/10.1038/s41591-019-0498-z
[Cooper2023] Cooper R. et al, Engineered Bacteria detect tumor DNA, Science. 2023 August 11; 381(6658): 682–686. doi:10.1126/science.adf3974.
[Fredens2019] Fredens J et al: Total Synthesis of Escherichia coli with a recoded Genome, Nature Vol 569 23 May 2019, https://doi.org/10.1038/s41586-019-1192-5
[Fu2023] Fu S. et al, Programming the lifestyles of engineered bacteria for cancer therapy, National Science Review 10: nwad031, 2023 https://doi.org/10.1093/nsr/nwad031
[Gallivan2007] Gallivan JP: Toward reprogramming bacteria with small molecules and RNA, Current Opinion in Chemical Biology 2007, 11:612-619, DOI 10.1016/j.cbpa.2007.10.004
[Gardlik2014] Gardlik, R. et al, Effects of bacteria-mediated reprogramming and antibiotic pretreatment on the course of colitis in mice, MOLECULAR MEDICINE REPORTS 10: 983-988, 2014, DOI: 10.3892/mmr.2014.2244
[Hsu2020] Hsu B. et al: In situ reprogramming of gut bacteria by oral delivery, NATURE COMMUNICATIONS | (2020) 11:5030 | https://doi.org/10.1038/s41467-020-18614-2
[Liu2018] Liu Z, Zhang J, Jin J, Geng Z, Qi Q and Liang Q (2018) Programming Bacteria With Light—Sensors and Applications in Synthetic Biology. Front. Microbiol. 9:2692. doi: 10.3389/fmicb.2018.02692
[Meier2024] Meier S. S. M. et al: Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling, Nature Communications volume 15, Article number: 4876 (2024)
[Navarro2022] Navarro, C.; Ortega, Á.; Santeliz, R.; Garrido, B.; Chacín, M.; Galban, N.; Vera, I.; De Sanctis, J.B.; Bermúdez, V. Metabolic Reprogramming in Cancer Cells: Emerging Molecular Mechanisms and Novel Therapeutic Approaches. Pharmaceutics 2022, 14, 1303. https://doi.org/10.3390/ pharmaceutics14061303
[Ngo2024] Ngo HTT et al: Reprogramming a Doxycycline-Inducible Gene Switch System for Bacteria-Mediated Cancer Therapy, Molecular Imaging and Biology (2024) 26:148-161, https://doi.org/10.1007/s11307-023-01879-6
[Perera2024] Perera PGT et al: Genetic Transformation of Plasmid DNA into Escherichia coli Using High Frquency Electromagnetic Energy, Nano Lett 2024 24 1145-1152
[Sieow2021] Sieow B. et al, Tweak to Treat: Reprograming Bacteria for Cancer Treatment, Trends in Cancer, May 2021, Vol. 7, No. 5 https://doi.org/10.1016/j.trecan.2020.11.004
[Volko2025] Volko, CD: Symbiont Conversion Theory. Biomedical Science and Clinical Research, DOI: 10.33140/BSCR
[Xia2020] Xia, PF et al: Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination, ACS Synth. Biol. 2020, 9, 8, 2162–2171
Claus D. Volko
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