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The Microscopic Revolution Reshaping Earth and Human Health

Wednesday, 12 November 2025 01:15

Summary

A new wave of scientific breakthroughs is redefining the capabilities of microbial life and cellular engineering, moving fundamental biology from the laboratory bench to industrial and clinical application. Researchers have uncovered a novel bacterial metabolism, dubbed MISO, where microbes 'breathe' iron minerals to detoxify marine environments, offering a natural mechanism to combat oceanic dead zones. Simultaneously, advances in enzyme engineering, powered by artificial intelligence, have yielded a 'plastic-eating' enzyme capable of breaking down polyethylene terephthalate (PET) waste in under 24 hours, accelerating the prospect of a circular plastics economy. In medicine, a two-part bacterial consortium has demonstrated the ability to eradicate tumours in preclinical models without relying on the patient's immune system, addressing a critical limitation of current immunotherapies. Furthermore, the integration of AI with cellular biology is decoding the complex chemical language of the human gut microbiome and inspiring a new generation of ion-based computing systems that mimic the learning processes of the brain's synapses.

The Deep Ecology of Rust-Breathing Microbes

The planet’s most fundamental biogeochemical cycles are being re-evaluated following the discovery of a previously unknown microbial metabolism in marine sediments and wetland soils11,12. An international team of researchers, led by microbiologists at the University of Vienna, identified a group of microorganisms, now known as MISO bacteria, that possess the unique ability to ‘breathe’ iron minerals11,12,24. This process, termed MISO metabolism, involves the microbes using solid iron(III) oxide minerals—essentially rust—as an electron acceptor to oxidise toxic hydrogen sulfide12,24. Hydrogen sulfide is a poisonous gas often found in oxygen-poor environments, and its accumulation is a primary driver in the formation of oceanic ‘dead zones’ where most marine life cannot survive12,24. Until this discovery, the reaction between sulfide and iron minerals was believed to be a purely abiotic, or chemical, process12,24. The new research demonstrates that microorganisms are, in fact, the main force behind this transformation in natural environments, performing the reaction at a much faster rate than its purely chemical counterpart11,12. The MISO metabolism links the cycling of sulfur, iron, and carbon in oxygen-free settings, directly producing sulfate and bypassing intermediate steps in the sulfur cycle11,24. Scientists estimate that MISO activity in marine sediments could be responsible for as much as seven per cent of all global sulfide oxidation to sulfate11,12. This natural detoxification mechanism is continuously fuelled by the steady flow of reactive iron entering the oceans from rivers and melting glaciers11. The finding not only highlights the metabolic ingenuity of microorganisms but also suggests a powerful, natural ally in mitigating the expansion of oxygen-depleted aquatic environments11,24.

Engineering the Circular Plastics Economy

The global crisis of plastic pollution, with hundreds of millions of tonnes of waste disposed of annually, has spurred a race to develop biological recycling solutions18,30. A significant breakthrough in this area involves the engineering of a highly efficient, plastic-degrading enzyme18. Researchers at the University of Texas at Austin utilised artificial intelligence and machine learning to engineer a variant of the polyethylene terephthalate (PET) hydrolase enzyme18,30. This new enzyme, named Functional, Active, Stable, and Tolerate PETase, or FAST-PETase, is capable of breaking down PET plastic into its original molecular components in under 24 hours18,30. PET is a widely used polymer, accounting for approximately 12 per cent of all global solid waste, and is the material used in most plastic bottles and polyester clothing fibres18,28,30. The development builds upon earlier discoveries, such as the *Ideonella sakaiensis* bacterium found in Japan in 2016, which naturally evolved the ability to degrade plastic18,25. Previous attempts to use enzymes for PET breakdown were often hampered by the enzymes’ vulnerability to temperature and pH fluctuations, as well as their slow reaction rates30. The FAST-PETase, however, functions effectively at 'normal' temperatures, making it robust enough for non-laboratory, industrial applications18,30. The process demonstrated a complete circular recycling loop, where plastic samples were broken down and the resulting materials were used to generate entirely new pieces of PET30. This technology holds immense promise for cleaning up landfills and enabling a truly circular economy for plastics, offering a sustainable alternative to traditional recycling methods that struggle with coloured, opaque, and multilayered PET products28,30.

A New Paradigm for Cancer Treatment

Oncology research has seen a major advancement with the development of a bacteria-based cancer therapy that operates independently of the patient’s immune system4,5. This innovation, known as AUN therapy, directly addresses a critical limitation of modern immunotherapies, such as checkpoint inhibitors and CAR-T cells, which are often ineffective for patients whose immune systems are compromised by chemotherapy or radiotherapy4,7. The AUN therapy, developed by a joint research team from the Japan Advanced Institute of Science and Technology (JAIST), Daiichi Sankyo, and the University of Tsukuba, uses a consortium of two naturally occurring bacterial species4,7,9. The first bacterium, *Proteus mirabilis* (A-gyo), is a tumour-resident microbe, while the second, *Rhodopseudomonas palustris* (UN-gyo), is a photosynthetic bacterium5,7. The two species work synergistically to achieve significant tumour eradication in both murine and human cancer models, even in environments lacking immune cell involvement5,8. The mechanism of action is multifaceted, involving the selective destruction of tumour blood vessels and cancer cells5,9. A key element is a structural transformation in A-gyo, where tumour-derived metabolites trigger a process called filamentation, which enhances its anti-tumour potency5,9. Furthermore, the ratio of the bacteria within the tumour shifts dramatically during the treatment, moving from an initial 3 per cent A-gyo to 97 per cent UN-gyo to a final balance of approximately 99 per cent A-gyo to 1 per cent UN-gyo, which optimises the cancer-killing effect8,9. The therapy has also shown high biocompatibility and minimal side effects, notably suppressing the risk of cytokine release syndrome (CRS), a serious immune reaction associated with some immunotherapies7,8. The research team plans to establish a startup to accelerate the technology toward clinical trials within six years, marking a potential new era for patients previously excluded from effective immunotherapy8,9.

The Hidden Speed of Bacterial Spread

A surprising finding in public health microbiology has revealed that certain strains of common gut bacteria can spread through human populations at rates comparable to highly transmissible viruses1,10. Researchers from the Wellcome Sanger Institute, the University of Oslo, and other collaborators in the UK and Norway, estimated the transmission rates of *Escherichia coli* (*E. coli*) for the first time in a community setting1,16. The study focused on three closely related genotypes of the main *E. coli* type ST131, which is a frequent cause of urinary tract and bloodstream infections and is often resistant to multiple antibiotics1,13,16. The analysis, which used genomic data to model bacterial transmission, found that one strain, ST131-A, spreads between individuals at a velocity similar to that of the swine flu (H1N1)1,10,13. This finding was unexpected because, unlike influenza viruses, *E. coli* is not transmitted through airborne droplets but via the fecal-oral route, involving hands, surfaces, and contaminated food or drink13,16. The ability of a gut-colonising bacterium to spread so efficiently demands a re-evaluation of public health monitoring and hygiene strategies13. The other two variants investigated, ST131-C1 and ST131-C2, which are multi-drug resistant, did not spread as quickly among healthy individuals10,16. However, these resistant strains pose a major threat in healthcare settings, such as hospitals and care homes, where they can propagate more swiftly among vulnerable and immunocompromised patients10,16.

Artificial Intelligence and the Microbial Language

The complexity of the human gut microbiome, which contains an estimated 100 trillion bacterial cells, has long presented a formidable challenge to researchers seeking to understand its influence on health2,6,21. Scientists at the University of Tokyo have now deployed a specialised form of artificial intelligence to decode the intricate chemical communication within this ecosystem2,6. The system, a Bayesian neural network called VBayesMM, was designed to identify genuine biological links between specific bacterial groups and the thousands of chemical compounds, or metabolites, they produce2,6. These metabolites act as chemical messengers, circulating throughout the body and influencing metabolism, immunity, and even brain function2,6. Traditional data analysis methods often struggle to distinguish meaningful biological relationships from random correlations within the vast, high-dimensional datasets of the microbiome2,3. VBayesMM addresses this by using a Bayesian approach that measures the uncertainty in its predictions, thereby helping to prevent overconfident or incorrect conclusions2,21. When tested on real-world data from studies on obesity, sleep disorders, and cancer, the AI system consistently outperformed existing methods2,6,21. The ability to accurately map these bacteria-metabolite relationships moves research closer to the ultimate goal of personalised medicine, where specific bacterial targets could be identified for dietary or therapeutic interventions2,21.

Bio-Inspired Computing and Synaptic Mimicry

The field of bio-inspired technology is advancing rapidly, with researchers looking to cellular mechanisms to develop new forms of computing15,27. Scientists at the École Polytechnique Fédérale de Lausanne (EPFL) have made a significant step by unravelling the complex behaviour of biological nanopores, tiny molecular holes found in cell membranes15,17. These pore-forming proteins, such as the bacterial pore aerolysin, are essential for molecular transport in nature and are widely used in biotechnology for applications like DNA sequencing15,27. The EPFL team investigated two puzzling behaviours of these pores: rectification, where ion flow changes based on the applied voltage’s sign, and gating, where ion flow suddenly decreases or stops15,23,31. Through experiments with 26 engineered variants of aerolysin, the researchers discovered that these effects are governed by the pore’s internal electrical charges and their interaction with passing ions15,17,27. Crucially, the team demonstrated that this understanding allows for the fine-tuning of nanopore properties17. They successfully engineered a nanopore that mimics synaptic plasticity, the brain’s ability to modulate the strength of neural connections in response to stimuli17,23,27. This molecular ‘learning’ from voltage pulses suggests a new bio-inspired computing paradigm15,23. By harnessing the dynamics of ion flow, these systems could one day form the basis of ion-based processors, offering a fundamentally different approach to information processing than current electronic systems17,27,31.

Conclusion

The confluence of microbiology, cellular engineering, and artificial intelligence is ushering in a transformative era of scientific capability. From the deep ocean to the human gut, microscopic life is proving to be a powerful, adaptable engine for both planetary and human health solutions11,2,5. The discovery of MISO bacteria fundamentally alters the understanding of global element cycles, providing a biological mechanism for environmental detoxification12,24. Simultaneously, the engineering of enzymes like FAST-PETase, guided by machine learning, demonstrates a clear path toward industrial-scale biological solutions for the plastic waste crisis18,30. In medicine, the development of immune-independent bacterial therapies, such as AUN, offers a lifeline to immunocompromised patients, moving beyond the limitations of current immune-dependent treatments4,7. These advancements, coupled with the use of AI to decode the complex language of the microbiome and to inspire new forms of ion-based computing, illustrate a profound shift in how scientists interact with and harness the natural world2,15,31. The smallest organisms are increasingly providing the largest solutions to the most complex global challenges, signalling a future where biotechnology plays a central role in ecological and medical remediation1,9,25.

References

  1. Scientists shocked to find E. coli spreads as fast as the swine flu | ScienceDaily

    Supports the finding that one E. coli strain spreads as fast as swine flu and the use of genomic data to model transmission rates in the UK and Norway.

  2. AI unravels the hidden communication of gut microbes | ScienceDaily

    Supports the use of the VBayesMM Bayesian neural network by University of Tokyo researchers to decode gut bacteria chemical signals (metabolites) and its application in studies of obesity, sleep disorders, and cancer.

  3. AI-empowered human microbiome research - Gut

    Supports the general context of AI models being used to extract microbial features, decode complex interactions, and link microbiome signatures to clinical outcomes.

  4. Bacterial Therapy Developed for Immune-Independent Cancer Treatment

    Supports the development of the AUN bacteria-based cancer therapy by JAIST and collaborators that does not rely on the immune system, addressing limitations of conventional immunotherapy.

  5. Bacteria-based cancer therapy achieves tumor eradication without immune cells

    Supports the composition of AUN therapy (Proteus mirabilis/A-gyo and Rhodopseudomonas palustris/UN-gyo), its efficacy in immunocompromised models, and the mechanism of selective destruction of tumor blood vessels and cancer cells.

  6. AI Decodes the Secret Language of Your Gut Bacteria - SciTechDaily

    Supports the staggering complexity of the microbiome, the role of metabolites as chemical messengers, and the VBayesMM system's ability to distinguish key players from less relevant microbes.

  7. Immune-Independent Bacterial Cancer Therapy | - The Indian Practitioner

    Supports the historical context of bacterial cancer therapy, the limitation of modern immunotherapies for immunocompromised patients, and the AUN consortium's ability to avoid cytokine release syndrome (CRS).

  8. Bacteria duo kills cancer without immune system help - Modern Sciences

    Supports the dramatic shift in the bacterial ratio within the tumour (3:97 to 99:1) and the plan to launch a startup for clinical trials within six years.

  9. Breakthrough Cancer Treatment Developed Using Immune-Independent Bacterial Therapy - SSBCrack News

    Supports the structural change (filamentation) in A-gyo triggered by tumour-specific metabolites and the overall significance of the AUN therapy as a new chapter in bacterial cancer treatment.

  10. E. coli Spreads Through Populations at Rates Comparable to Swine Flu, New Study Finds - SSBCrack News

    Supports the comparison of the ST131-A strain's spread velocity to swine flu and the finding that multi-drug resistant strains (ST131-C1 and ST131-C2) propagate more swiftly in healthcare settings.

  11. Microbes that breathe rust could help save Earth's oceans | ScienceDaily

    Supports the discovery of MISO bacteria by the University of Vienna team, their ability to 'breathe' iron minerals by oxidising toxic sulfide, and the estimate of their contribution to global sulfide oxidation (7%).

  12. New Study: Bacteria That Breathe Iron Could Help Reduce Ocean Pollution - Asianet Newsable

    Supports the MISO bacteria using rust similarly to how humans use oxygen, the role of hydrogen sulfide in dead zones, and the previous belief that the reaction was purely chemical.

  13. Understanding E. coli and Its Risks | Food Poisoning News

    Supports the estimation of the basic reproduction number (R₀) for ST131-A and the distinction that E. coli spreads via the fecal-oral route, not airborne droplets.

  14. Brain-like learning found in bacterial nanopores - ScienceDaily

    Supports the EPFL research on bacterial nanopores (aerolysin), the puzzling behaviours of rectification and gating, and the creation of a nanopore that mimics synaptic plasticity for bio-inspired computing.

  15. New research sheds light on E. coli spread in human communities - News-Medical

    Supports the focus on the ST131 main type of E. coli, the use of patient samples from Norway and the UK, and the finding that multi-drug resistant types are more likely transmitted in hospitals and care homes.

  16. Nanopores act like electrical gates - News - EPFL

    Supports the finding that rectification and gating are governed by the pore's internal electrical charges, the use of 26 nanopore variants, and the potential for ion-based processors.

  17. Plastic-Eating Bacteria: Saving the World in 2025? - Play It Green

    Supports the development of the FAST-PETase enzyme by the University of Texas, its ability to complete a 'circular process' in as little as 24 hours, and the use of machine learning to engineer it.

  18. AI decodes gut bacteria to provide clues about health - The Statesman

    Supports the comparison of human cells to gut bacteria (30-40 trillion vs 100 trillion) and the goal of developing personalised treatments by accurately mapping bacteria-chemical relationships.

  19. Nanopores act like electrical gates - myScience.ch

    Supports the use of the bacterial pore aerolysin in sensing and the successful engineering of a nanopore to mimic synaptic plasticity.

  20. Scientists Discover Microbes That “Breathe” Iron to Detoxify the Planet - SciTechDaily

    Supports the MISO bacteria being a new form of microbial metabolism, the role of iron(III) oxide (rust) in the process, and the potential to limit the spread of 'dead zones'.

  21. Plastic-Eating Bacteria 2025: Nature's Ultimate Weapon Against Pollution - sciencepulses

    Supports the historical context of the discovery of Ideonella sakaiensis in Japan in 2016 and the general context of plastic-eating bacteria as a biological eco-solution.

  22. Nanopores Function as Electrical Gates in Breakthrough Discovery - Bioengineer.org

    Supports the role of pore-forming proteins in immune defense and as bacterial toxins, and the potential for the findings to catalyse new frontiers in bio-inspired computing.

  23. Scientists hail plastic-eating enzyme as 'breakthrough' for recycling | BusinessGreen News

    Supports PET being the most commonly used plastic and the challenge of recycling coloured, opaque, and multilayered PET products via traditional methods.

  24. This AI-Designed Enzyme Can Devour Plastic Trash In Hours: Video - Forbes

    Supports the use of AI to engineer the enzyme, the goal of a true circular plastics economy, and the enzyme's robustness to temperature variations in non-laboratory conditions.

  25. Researchers Unveil Mechanisms Behind Ion Behavior in Biological Nanopores - SSBCrack News

    Supports the role of nanopores in DNA sequencing and molecular sensing, and the potential for ion-based processing systems to exploit molecular 'learning'.