Graphene Oxide: A New Weapon Against Bacteria Without Harming Human Cells

 

The search for new ways to combat harmful microorganisms has taken on greater urgency as antibiotic resistance continues to rise worldwide. Scientists are therefore exploring innovative materials that can prevent bacterial growth without relying on conventional antibiotics. One promising candidate is graphene oxide (GO), a modified form of graphene that possesses remarkable antibacterial properties while remaining compatible with human tissues.

By Tim Sandle  

Researchers at the Korea Advanced Institute of Science and Technology (KAIST) have now uncovered the molecular mechanism behind graphene oxide's antibacterial activity. Their findings provide important evidence explaining how the material can selectively eliminate bacteria while leaving human cells unharmed.

Understanding Graphene Oxide

Graphene oxide is derived from graphene, a material consisting of a single layer of carbon atoms arranged in a honeycomb lattice. Unlike pure graphene, graphene oxide contains oxygen-containing chemical groups attached to its surface. These groups improve its ability to disperse in water and allow it to interact with biological systems in unique ways.

Although graphene oxide has long been known to exhibit antibacterial effects, the precise reason for this activity remained poorly understood. The KAIST study has now provided a detailed explanation at the molecular level.

How Graphene Targets Bacteria

The research team discovered that graphene oxide displays what they describe as selective antibacterial action. Rather than damaging all cells indiscriminately, graphene oxide specifically targets bacterial cell membranes.

The key lies in a bacterial membrane component known as phosphatidylglycerol (POPG). This phospholipid is abundant in bacterial membranes but largely absent from human cell membranes. Oxygen-containing groups on the surface of graphene oxide recognize and bind to POPG, enabling the material to attach directly to bacterial cells.

Once attached, graphene oxide disrupts membrane integrity, leading to bacterial cell death. Human cells, lacking significant amounts of POPG, are largely unaffected by this mechanism. In effect, graphene oxide acts like a highly selective antimicrobial agent that can distinguish bacterial cells from human tissues.

This discovery is particularly significant because many conventional disinfectants and antimicrobial compounds can damage both microbial and human cells, resulting in toxicity or irritation.

Activity Against Antibiotic-Resistant Organisms

One of the most important findings from the study was graphene oxide's effectiveness against a broad range of bacterial species, including antibiotic-resistant organisms often referred to as "superbugs."

The emergence of antimicrobial resistance is among the most serious challenges facing public health. As bacteria evolve resistance mechanisms against existing antibiotics, there is increasing interest in non-antibiotic approaches to infection control.

Graphene oxide could represent one such strategy. Rather than interfering with bacterial metabolism or protein synthesis, the material physically damages bacterial membranes. This mode of action may reduce the likelihood of resistance development and provide an additional tool for controlling microbial contamination.

 

Supporting Wound Healing

The researchers also investigated the material in animal wound-healing models. In addition to suppressing bacterial growth, graphene oxide-containing nanofibers promoted faster wound healing without triggering significant inflammatory responses.

From a microbiological perspective, this is particularly interesting since wound management frequently requires a balance between antimicrobial activity and tissue compatibility. Materials capable of both preventing infection and supporting tissue regeneration are highly desirable for advanced wound care applications.

Durable and Washable Antimicrobial Textiles

Another notable advantage relates to durability. The investigators found that graphene oxide nanofibers retained their antibacterial effectiveness even after repeated washing cycles.

This characteristic creates opportunities for practical applications in areas where hygiene is critical, including:

• Healthcare uniforms
• Wound dressings
• Face coverings
• Sportswear
• Military clothing
• Hospital textiles
• Consumer hygiene products

Unlike many conventional antimicrobial coatings, which gradually lose effectiveness through use and laundering, graphene oxide appears capable of providing sustained antimicrobial performance.

Moving From Research to Commercial Products

Importantly, graphene-based antimicrobial technologies are already moving beyond the laboratory.

A graphene antibacterial toothbrush developed through patents associated with the startup company Materials Creation Co., Ltd. has reportedly sold more than 10 million units. This demonstrates that there is already substantial commercial interest in graphene-enabled hygiene products.

The technology has also been incorporated into GrapheneTex, an antimicrobial textile platform. The material was used in uniforms worn by the Taekwondo demonstration team during the 2024 Paris Olympics and is expected to appear in sportswear at future international events, including the 2026 Asian Games.

These examples illustrate how nanomaterials research can successfully transition into real-world products with everyday consumer applications.

Future Medical Applications

The implications extend beyond clothing and personal care products. Graphene oxide could potentially be incorporated into:

• Medical textiles
• Implant coatings
• Catheter materials
• Wearable health technologies
• Smart wound dressings
• Biosensors
• Healthcare devices

Because the material combines antimicrobial activity with biocompatibility, it may offer an attractive platform for designing next-generation infection-control technologies.

As Professor Sang Ouk Kim noted, understanding why graphene oxide selectively kills bacteria while remaining safe for human cells provides a scientific foundation for developing a much broader range of applications.

A Sustainable Alternative?

Perhaps the most exciting aspect of the research is its potential contribution to a more sustainable approach to infection control. Rather than relying exclusively on antibiotics or chemical disinfectants, materials engineered with selective antibacterial properties could become part of a broader strategy for reducing microbial contamination.

As antimicrobial resistance continues to threaten healthcare systems globally, innovative materials such as graphene oxide may help reduce dependence on traditional antibiotics while improving hygiene, patient safety, and public health outcomes.

Reference

Cha S, Chung JY, Yang S, Lee SC, Lee CW, Cheng CWL, Kim JB, Kim NJ, Park A, Choi H, Sinn J, Weissleder R, Kotov NA, Seo M, Chung HJ, Kim SO. Biocompatible but Antibacterial Mechanism of Graphene Oxide for Sustainable Antibiotics. Advanced Functional Materials. 2026. DOI: 10.1002/adfm.74695.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Genomes reveal five E. coli 'armor' types behind most multidrug-resistant bloodstream infections

                                                            Image designed by Tim Sandle

The first large-scale genetic study of E. coli's protective armour has identified the five capsule types that are responsible for 70% of all multidrug-resistant bloodstream infections in Europe. Researchers, including those at the Wellcome Sanger Institute, the University of Oslo, and their collaborators, analysed over 18,000 bacterial genomes from samples across all continents to investigate E. coli's armour and find new ways to penetrate it. 

Provided by Wellcome Trust Sanger Institute 

The study, published in Nature Microbiology, uncovered 90 different types of protective capsules, of which only 34% had been previously documented. The team also identified the capsule types that enable the bacterium to have the highest invasive potential, meaning it can transition from a harmless gut resident to a dangerous bloodstream invader.

By providing a blueprint of the armor that each E. coli strain has, this research can help in designing targeted vaccines and new treatments that can combat the most dangerous strains of E. coli while minimizing harm to beneficial strains of E. coli gut bacteria.

Science and microbiology gifts via Babbling Bacteria 

Escherichia coli (E. coli) is the leading cause of bloodstream infections worldwide. Most strains of E. coli are harmless and commonly found in the gut, however, if the bacterium gets into the bloodstream or the urinary tract, it can cause infections that range from mild to severe, particularly in people with a weakened immune system.

As an added challenge for health care providers, antibiotic resistance has become a frequent feature of such infections. Rates of antibiotic resistance in E. coli vary globally and, in the UK, over 40% of E. coli bloodstream infections are resistant to a key antibiotic.

Some bacteria, such as E. coli, have protective capsules that help shield the bacteria from the immune system and certain treatments, influencing the bacteria's ability to cause infections. Each bacterial strain has a different capsule makeup, and the capsules have markers, called antigens.

These antigens are often used as targets for new vaccines and treatments. However, for effective therapies to be developed, researchers need to know which capsule commonly causes the infection.

Traditional methods of mapping E. coli capsules are labor-intensive and uncommon. To address this, the team at the Sanger Institute and their collaborators genetically analyzed 18,000 E. coli samples. This allowed them to create the first digital database mapping capsule type and E. coli strain. They were then able to determine how common each type is using samples from nearly 8,000 people, ranging from newborns to those over 80 years old.

They found that capsule types are much more diverse than previously thought, mapping 90 different types, including 69 that had not been previously documented. The team also noted that different capsules were common in high-resource settings, such as the UK, compared to less industrialized regions such as Malawi and Pakistan.

For example, the researchers found that five specific capsule types (K1, K5, K52, K2, and K14) account for over 50% of all E. coli bloodstream infections and urinary tract infections across the UK, Norway, and France. Furthermore, a slightly different set (K1, K5, K52, K2, and K100) is responsible for 70% of multidrug-resistant E. coli infections in Europe.

While two of these (K1 and K5) do cause infections globally, there is more diversity in the strains that cause serious infections in low and middle-income countries than in Europe.

Due to these differences, the researchers highlight the importance of global data in future research, especially around drug and vaccine development, as the bacterial capsule types being targeted would vary depending on where the individual lived.

The team also found that E. coli has the ability to swap the genes that encode the capsule, sharing the information to build different types of armor between them.

Dr. Rebecca Gladstone, first and corresponding author at the University of Oslo, said, "By creating a digital library from over 18,000 bacterial genomes, we can see the true complexity of how E. coli protects itself, and how this armor is encoded in the genes. This research has expanded our scientific map from just a handful of known bacterial shields to a comprehensive database of 90 unique types, including nearly two-thirds that were previously unknown.

"Ultimately, this database provides the missing blueprint to identify strains most likely to cause serious infections, and design targeted vaccines and treatments to stop these."

Professor Jukka Corander, senior author at the Wellcome Sanger Institute and the University of Oslo, said, "This new research enables us to identify the strains of E. coli that are the biggest threats to human health. With this database, we can now see the bacterial capsule types that are prevalent in different countries, whether they cause serious infections, or if they are resistant to treatments.

"What our research also shows is the stark differences between capsule groups found in different regions, highlighting the need for systematic and standardized global data collection. Especially as we have found that E. coli can trade the genes for their protective shields between different genetic lineages.

"Understanding how these bacteria, especially the most drug-resistant ones, swap their coats, and having the global data to track this, is crucial for staying one step ahead of them in the fight against serious bloodstream infections."

Dr. Trevor Lawley, co-author at the Wellcome Sanger Institute, said, "Our microbiomes are made up of thousands of bacteria, and while the majority of these are beneficial, some strains can cause infections if they get into the bloodstream, such as E. coli.

"Large-scale population studies, such as the Baby Biome study, that provide a high-resolution view into the microbiome are essential for understanding the risk associated with certain bacterial strains, the genetic tools they use to cause infections, and how often they are found in the population.

"Understanding and tracking the E. coli strains that are most able to use their protective shield to move into the bloodstream and cause infection allows for the development of future targeted treatments while minimizing the harmful effects on the microbiome."

Publication details

Identification of transporter-dependent capsular K loci associated with invasive potential of Escherichia coli, Nature Microbiology (2026). DOI: 10.1038/s41564-026-02283-w

Journal information: Nature Microbiology 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

5,000 year old ice cave bacterium resists modern antibiotics

 Cave. Image by Tim Sandle

Bacteria are remarkably adaptable, thriving in some of the harshest places on Earth, from boiling hot springs to deep freezes far below zero. Ice caves are one such extreme habitat, home to diverse microorganisms that scientists are only beginning to understand. These frozen environments may contain vast stores of genetic material that have gone largely unexplored. 

Deep inside a Romanian ice cave, locked away in a 5,000-year-old layer of ice, scientists have uncovered a bacterium with a startling secret: it’s resistant to many modern antibiotics. Despite predating the antibiotic era, this cold-loving microbe carries more than 100 resistance-related genes and can survive drugs used today to treat serious infections like tuberculosis and UTIs.

Psychrobacter 

The Psychrobacter SC65A.3 bacterial strain isolated from Scarisoara Ice Cave, despite its ancient origin, shows resistance to multiple modern antibiotics and carries over 100 resistance-related genes.

The bacterium can also inhibit the growth of several major antibiotic-resistant 'superbugs' and shows important enzymatic activities with important biotechnological potential.

Psychrobacter SC65A.3 belongs to a group of cold-adapted bacteria known as Psychrobacter. While some members of this genus can cause infections in people or animals, they are also considered promising for biotechnology applications. Until now, however, little was known about how these bacteria respond to antibiotics. 

Studying microbes such as Psychrobacter SC65A.3 retrieved from millennia-old cave ice deposits reveals how antibiotic resistance evolved naturally in the environment, long before modern antibiotics were ever used.

How the organism was isolated 

To retrieve the organism, the team drilled a 25-meter ice core from a section of the cave called the Great Hall, capturing a frozen record spanning 13,000 years. To prevent contamination, ice samples were sealed in sterile bags and transported in frozen conditions back to the laboratory. There, scientists isolated bacterial strains and sequenced their genomes to identify genes responsible for surviving extreme cold, as well as genes linked to antimicrobial resistance and activity.

The researchers then tested SC65A.3 against 28 antibiotics across 10 different classes. These drugs are commonly prescribed or reserved for serious bacterial infections. Some had already been associated with known resistance genes or mutations, allowing the team to compare predicted resistance mechanisms with actual laboratory results. "The 10 antibiotics we found resistance to are widely used in oral and injectable therapies used to treat a range of serious bacterial infections in clinical practice," Purcarea noted. Among them were rifampicin, vancomycin, and ciprofloxacin, medications used to treat conditions such as tuberculosis, colitis, and UTIs.

SC65A.3 is the first Psychrobacter strain found to resist certain antibiotics, including trimethoprim, clindamycin, and metronidazole. These drugs are typically used to treat UTIs and infections affecting the lungs, skin, bloodstream, and reproductive system. The strain's resistance profile suggests that bacteria adapted to cold environments could serve as reservoirs of resistance genes, which are segments of DNA that enable survival when exposed to antibiotics.

Significance of the discovery 

Genetic analysis of Psychrobacter SC65A.3 revealed nearly 600 genes with unknown functions, pointing to a largely untapped resource for uncovering new biological processes. The team also identified 11 genes that may have the ability to kill or inhibit bacteria, fungi, and even viruses.

As antibiotic resistance continues to rise worldwide, insights from ancient microbes are becoming increasingly valuable. Studying genomes preserved in ice helps scientists trace how resistance emerged and spread long before modern medicine existed.

Research paper

Victoria Ioana Paun, Corina Itcus, Paris Lavin, Mariana Carmen Chifiriuc, Cristina Purcarea. First genome sequence and functional profiling of Psychrobacter SC65A.3 preserved in 5,000-year-old cave ice: insights into ancient resistome, antimicrobial potential, and enzymatic activities. Frontiers in Microbiology, 2026; 16 DOI: 10.3389/fmicb.2025.1713017 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Engineering Clostridium sporogenes to fight cancer

Image: Clostridium sporogenes. Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #15884 (public domain).
 

Researchers are engineering bacteria to invade tumors and consume them from the inside. Because tumor cores lack oxygen, they’re the perfect breeding ground for these microbes. The team added a genetic tweak that helps the bacteria survive longer near oxygen-exposed edges — but only once enough of them are present to trigger the change. It’s a carefully programmed biological attack that could one day offer a new way to destroy cancer.

The engineering of living cells and microbes is ushering in a new era of cancer therapy.

Scientists at the University of Waterloo (Canada) are working on a new cancer treatment that uses specially engineered bacteria to consume tumors from the inside. The strategy relies on microbes that naturally thrive in oxygen-free environments, which makes the interior of many solid tumors an ideal target.

Clostridium sporogenes is a species of Gram-positive bacteria that belongs to the genus Clostridium. Like other strains of Clostridium, it is an anaerobic, rod-shaped bacterium that produces oval, subterminal endospores and is commonly found in soil. The organism is being investigated for its cancer cell killing properties. 

Bacteria spores enter the tumor, finding an environment where there are lots of nutrients and no oxygen, which this organism prefers, and so it starts eating those nutrients and growing in size.

At the centre of this approach is Clostridium sporogenes, a bacterium commonly found in soil. It can survive only in places that contain absolutely no oxygen. The inner core of solid tumors is made up of dead cells and lacks oxygen, creating the perfect conditions for this microbe to multiply and spread.

Difficult challenge

There is a challenge, however. As the bacteria expand outward and reach areas of the tumor exposed to small amounts of oxygen, they begin to die off before fully eliminating the cancer.

To address this limitation, the team inserted a gene from a related bacterium that is more tolerant of oxygen. This modification allows the engineered microbes to survive longer near the tumor's outer regions.

The researchers also needed a way to control when that oxygen-tolerance feature turns on. Activating it too early could allow the bacteria to grow in oxygen-rich areas such as the bloodstream, which would be unsafe. To prevent that, they used a natural bacterial communication process called quorum sensing.

Quorum sensing relies on chemical signals released by bacteria. As their numbers increase, the signal grows stronger. Only after enough bacteria have accumulated inside a tumor does the signal reach a level that switches on the oxygen-resistant gene. This timing ensures the bacteria activate their survival mechanism only when it is needed.

Synthetic Biology and DNA Circuits

In an earlier study, the team showed that Clostridium sporogenes could be genetically altered to better withstand oxygen. In a follow-up experiment, they tested their quorum sensing design by programming bacteria to produce a green fluorescent protein, allowing them to confirm that the system activated at the intended moment.

The next step is to combine both the oxygen-tolerance gene and the quorum-sensing control system into a single bacterium and evaluate it against tumors in pre-clinical trials.

Research paper 

The research appears in the journal ACS Synthetic Biology, titled " Construction and Functional Characterization of a Heterologous Quorum Sensing Circuit in Clostridium sporogenes."

 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Plastic-eating bacteria discovered in the ocean

 Image created by Tim Sandle

Beneath the ocean’s surface, bacteria have evolved specialized enzymes that can digest PET plastic, the material used in bottles and clothes. Researchers at KAUST discovered that a unique molecular signature distinguishes enzymes capable of efficiently breaking down plastic. Found in nearly 80% of ocean samples, these PETase variants show nature’s growing adaptation to human pollution.

A large-scale global study by scientists at KAUST (King Abdullah University of Science and Technology) revealed that these marine microbes are widespread and genetically prepared to consume polyethylene terephthalate (PET) -- the tough plastic used in everyday items like drink bottles and fabrics. Their remarkable ability stems from a distinct structural feature on a plastic-degrading enzyme called PETase. This feature, known as the M5 motif, acts as a molecular signature that signals when an enzyme can truly break down PET. 

For decades, scientists believed PET was almost impossible to degrade naturally. That belief began to shift in 2016, when a bacterium discovered in a Japanese recycling plant was found to survive by consuming plastic waste. It had developed a PETase enzyme capable of dismantling plastic polymers into their building blocks.

Yet it remained unclear whether oceanic microbes had developed similar enzymes independently.

Using a combination of artificial intelligence modeling, genetic screening, and laboratory testing, Duarte and his team confirmed that the M5 motif distinguishes true PET-degrading enzymes from inactive look-alikes. In experiments, marine bacteria carrying the complete M5 motif efficiently broke down PET samples. Genetic activity maps showed that M5-PETase genes are highly active throughout the oceans, especially in areas heavily polluted with plastic.

Global Spread of Plastic-Eating Microbes

To understand how widespread these enzymes are, the researchers examined more than 400 ocean samples collected from across the globe. Functional PETases containing the M5 motif appeared in nearly 80 percent of the tested waters, ranging from surface gyres filled with floating debris to nutrient-poor depths nearly two kilometers below.

In the deep sea, this ability may give microbes an important edge. The ability to snack on synthetic carbon may confer a crucial survival advantage, noted Intikhab Alam, a senior bioinformatics researcher and co-leader of the study.

The discovery highlights a growing evolutionary response: microorganisms are adapting to human pollution on a planetary scale.

Although this adaptation reveals nature's resilience, Duarte cautions against optimism. "By the time plastics reach the deep sea, the risks to marine life and human consumers have already been inflicted," he warns. The microbial breakdown process is far too slow to offset the massive flow of plastic waste entering the oceans each year.

Turning Discovery Into Real-World Solutions

On land, however, the findings could accelerate progress toward sustainable recycling.

The identification of the M5 motif offers a roadmap for engineering faster, more effective enzymes. It reveals the structural traits that work under real environmental conditions rather than just in test tubes. If scientists can replicate and enhance these natural mechanisms, humanity's battle against plastic pollution may find powerful new allies in one of the planet's most unexpected places: the deep ocean.

Research paper 

See: Intikhab Alam, Ramona Marasco, Afaque A Momin et al. Widespread distribution of bacteria containing PETases with a functional motif across global oceans. The ISME Journal, 2025; 19 (1) DOI: 10.1093/ismejo/wraf121

 Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Treating anthrax beyond the 'point of no return'

Source: CDC - This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #2226

Anthrax, an infectious disease caused by the bacterium Bacillus anthracis, is often treatable in its early stages. But once the disease has progressed beyond the "point of no return" after just a few days, patients are most likely to die.

In a new study, University of Pittsburgh researchers show that a cocktail of growth factors reversed would-be lethal cell damage in mice with anthrax, suggesting that this approach could be adapted for use in patients beyond the brink.

When B. anthracis enters the body through inhalation, ingestion, injection or contact with skin, it produces two proteins that combine to form lethal toxin.

Early on, anthrax can be treated with antibiotics that eliminate the bacterium or antibodies that neutralize lethal toxin before it enters cells. But once inside cells, the toxin inactivates members of a group of enzymes known as MEKs by cleaving off one of their ends, disrupting the important pathways they control and rapidly causing widespread cellular, tissue and organ damage -- and death.

To learn more about the roles of MEK-controlled pathways in anthrax toxicity,the researchers generated mice with modified MEKs that were resistant to being cleaved by lethal toxin. These included MEK1 and MEK2, which control a pathway called ERK involved in cellular division and survival, and MEK3 and MEK6, which regulate the p38 pathway that's involved in stress-induced defense.

When exposed to lethal toxin or B. anthracis, mice with either modified MEK1/2 or MEK3/6 had much greater survival than normal animals, indicating that anthrax must inactivate both the ERK and p38 pathways to kill its host.

In mice and human cells exposed to lethal toxin or B. anthracis, a combination of three growth factors -- all individually approved as treatments for other conditions -- reactivated the ERK pathway and brought them back from the point of no return.

Because different types of cells in the body may require different growth factors to activate ERK, the researchers are now working to optimize a treatment for anthrax in humans.

See: 

Liu, J., Zuo, Z., Ewing, M. et al. ERK pathway reactivation prevents anthrax toxin lethality in mice. Nat Microbiol, 2025 DOI: 10.1038/s41564-025-01977-x

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Why here? Why now? Protein-triggering bacteria spore formation characterized

A protein that enables bacteria to shut down into dormant spores under extreme conditions has been discovered. Sporulation is an effective survival mechanism, a state of dormancy, that some types of bacteria can enter into.

While many bacteria can tolerate harsh environments (like endolithic microorganisms, obtaining their energy and nutrients from rocks), the most extreme environments require sporulation to maintain survival. The process of sporulation enables bacteria to become very resistant to heat and radiation, creating life capsules for bacteria to survive in uninhabitable places including the most extreme places on the planet, such as under the permafrost, in the depths of the ocean or outer space (as some space missions have shown).

Discovering a new protein involved in sporulation in a group of bacteria could further our understanding of bacteria's ability to survive and potentially open up new avenues for antimicrobial therapies.

In this week’s article, the new research into the sporulating trigger protein is highlighted as well as an overview of some general aspects of bacterial sporulation. 

See: LinkedIn article

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Ch-ch-ch-ch-changes: Bacteria, mutations & lab testing

 

Determining the presence of bacteria – either to know some cells are present or to target a specific number – requires growth and growth using a culture-based method is expressed by an increase in cells and/or biomass. The basis of many techniques is taking extremely low levels of various microbial types in a sample, and with the provision of suitable nutrients, atmosphere and temperature, enabling these cells to multiply up to levels that are high enough to count or identify.

To sustain microorganisms in the laboratory setting, subculturing is required. Uncontrolled subculturing can lead to temporary variations or to mutations occurring. This can affect the phenotypic properties or genetic nature of the cell.

How do these variations and mutations occur and why do they matter? Turn and face the strange...This week’s article considers culturing, culture media, subculturing, variations and mutations and what the implications are.

To read see: Mutations

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Ref: https://www.linkedin.com/pulse/ch-ch-ch-ch-changes-bacteria-mutations-lab-testing-tim-z9bze/?published=t 

Diet matters less than evolutionary relationships in shaping gut microbiome

 

Gut microbes provide many services for their hosts, including digesting their food. Researchers have long known that mammals with specialized diets, such as carnivores and anteaters, have special types of gut microbes that allow them to eat that diet.

Is the same true in primates? In the largest published comparative dataset of non-human primate gut microbiomes to date, a new Northwestern University study set out to find whether leaf-eating primates have similar gut microbes that help them break down their leafy diet, which is full of fiber and toxins.

A common theme in the microbiome field is that host diet has large effects on the gut microbiome — both across lifespans (week-to-week changes in host diet change the gut microbiome) and across evolution (mammals with similar diets have similar gut microbes regardless of their evolutionary histories), said Katherine Amato, lead author of the study and assistant professor of anthropology in the Weinberg College of Arts and Sciences at Northwestern.

Therefore, they expected to see many similarities between leaf-eating primates, regardless of how closely related they were to each other. Rather, the researchers discovered that diet mattered much less than host evolutionary relationships in shaping the gut microbiome.

“Our data suggest that, across evolution, the effect of primate diet on the primate gut microbiome is not large,” Amato said. “Evolutionary relationships between primates are much more important for predicting microbiome composition and function.” 

The study is the first cross-species comparison of the gut microbiota that exclusively uses samples from wild animals.

“We conclude that although gut microbes play a critical role in supporting host dietary specializations, their impact is regulated through host physiology,” Amato said.

“Leaf-eating primates shared very few gut microbial characteristics. Instead, New World monkeys shared the most gut microbial characteristics with each other, regardless of diet. The same was true for Old World monkeys, lemurs and apes. These patterns appear to be the result of host physiological traits such as how the gastrointestinal tract is built.”

Cross-mammal examinations of the gut microbiome have been performed, Amato said, but they all had weaknesses in that species with similar diets also had similar evolutionary histories or physiology. Many studies also mixed captive and wild animals, and captivity is known to change the gut microbiome.

“This study was able to eliminate these issues due to the fact that leaf-eating evolved independently multiple times in the order Primates and is associated with a different physiology in each part of the primate tree,” Amato said. “We also only used wild primates, which compared to captive primates, are more likely to have gut microbiomes like those they evolved with.”

Further research could involve looking at more primate species with more varied diets and understanding how the human gut microbiome fits into this bigger evolutionary picture and what it can tell us about our physiology and health, Amato said.

“Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes” published online earlier this month in the ISME Journal: Multidisciplinary Journal of Microbial Ecology.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Bacillus spizizenii

 

The American Type Culture Collection (ATCC) #6633 bacterium Bacillus subtilis subsp. spizizenii (commonly Bacillus subtilis) has been reclassified as Bacillus spizizenii.

The change was the result of whole genome sequencing and the paper triggering the change was issued in 2020. However, several culture collections (and providers of cultures) were slow to adopt the taxonomic change.

Bacillus subtilis encompassed four subspecies: Bacillus subtilis subsp. subtilis, Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris.

As a result of the research, each has become a separate species. Bacillus spizizenii is retained as the strain commonly used by the world’s culture collections for activities including growth promotion testing.

Reference:

Christopher A. Dunlap . Michael J. Bowman . Daniel R. Zeigler. Promotion of Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris to species status. Antonie van Leeuwenhoek (2020) 113:1–12
 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Microbiology and Infectious Disease

Reviewed title: 'Dimer-monomer transition defines a novel hyper-thermostable peptidoglycan hydrolase mined from bacterial proteome'

DOI link: https://doi.org/10.7554/eLife.98266.1

Summary: This study details a method to identify new antimicrobial drugs with therapeutic promise from bacterial datasets, providing clues for discovering alternatives to traditional antibiotics. eLife's editors describe it as a valuable new strategy for identifying novel lysins (a type of enzyme) with antimicrobial activity, and say that it provides solid evidence for the therapeutic potential of two such lysins discovered during the work.

Full eLife press release for further details: 'Harnessing big data helps scientists hone in on new antimicrobials' – https://elifesciences.org/for-the-press/a444a8f0/harnessing-big-data-helps-scientists-hone-in-on-new-antimicrobials

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Endospores and mechanisms of resistance

 Image created by Tim Sandle

Endospores present a concern in controlled environments due to their resistance and indefinite survivability. The production of a spore is part of a sophisticated stress response. Here, the bacterial genome is copied and transferred into the safety of a spore (sporulation).

The spore remains dormant until environmental conditions improve. When conditions are favorable, the spore will germinate (generally rapidly) and become a functioning, vegetative cell.

This week’s article looks at what endospores are, how they are formed, and their relative resistance as part of improving our understanding of contamination control.

See:  https://www.linkedin.com/pulse/resistance-so-futile-endospores-mechanisms-tim-sfaxe/  

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Evolution of Pseudomonas aeruginosa

 

Two hundred years ago, give or take the odd decade, Pseudomonas aeruginosa was an environmental bacterium (1), apparently not one, as far as medical records in the pre-microbiology days can be discerned, associated as a human pathogen (2).

Today, P. aeruginosa is associated with a high number of multidrug-resistant infections (3), many of which are nosocomial. Those especially vulnerable to the bacterium are people with underlying lung conditions.

It is estimated that P. aeruginosa is responsible for communicable diseases leading to over 500,000 deaths per year around the world, of which over 300,000 are associated with antimicrobial resistance (AMR). People who are immunocompromised as a result of conditions such as COPD (smoking-related lung damage), cystic fibrosis (CF), and non-CF bronchiectasis, are particularly susceptible.

This week’s article looks at the bacterium and also highlights some new research that charts how the organism evolved rapidly and then proceeded to spread globally over the last 200 years. At the heart of this are changes in human behavior. 

See: https://www.linkedin.com/pulse/200-year-old-problem-evolution-multi-drug-resistant-tim-lqn4e/  

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Why hydrogen peroxide decontamination cycles can fail

Image designed by Tim Sandle.

When it works well, hydrogen peroxide in vapor or areolized form can be an effective means of ‘no-touch’ biodecontamination. However, operational limitations can create technical challenges for industrial‐scale adoption and inconsistency in the method of delivery can sometimes lead to fragility affecting the reproducibility of cycles.

This week’s article looks at hydrogen peroxide in the vapor or autolyzed form and considers what can result in cycle failures

See: Sandle on hydrogen peroxide decontamination

 Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Introducing the Burkholderia cepacia complex

Image: CDC/Janice CarrContent Providers: Public Health Image Library (PHIL). Public Domain, https://commons.wikimedia.org/w/index.php?curid=2208169

Members of the Burkholderia cepacia complex (BCC), of which there are 18 different species, which are grouped into nine genomovars. These are aerobic organisms, widely distributed, and found in soil and water[i]. Importantly they can additionally survive for long periods in low-nutrient moist environments[ii], which make these organisms probable survivors within pharmaceutical grade water systems.

By Tim Sandle

B. cepacia is a human opportunistic pathogen and can cause pneumonia in immunocompromised individuals (when introduced into the air passages of a susceptible population); other risks to patients include endocarditis, wound infections, intravenous bacteremia, foot infection, respiratory infections. Some patient groups are at a greater risk than others, including elderly people, young children, cancer patients, pregnant women, and people with chronic illness[iii].

 

Bcc is of concern in relation to many pharmaceutical and healthcare facilities because many of the organisms within the group are resistant to organic solvents and antiseptics, and, to a degree, certain disinfectants[iv], with the resistance arising from several factors, including efflux pump mechanisms and resistance conferred through the organisms having a tendency to form biofilms under optimal conditions. Bcc organisms are also persistent, and they can readily survive in low nutrient conditions (such purified or distilled water).

 

It is important to understand the potential points or origin in pharmaceutical facilities (which is primarily low-nutrient environs like water, with the organisms adept at surviving under low nutrient conditions[v] [vi]; and which are reflective of the organisms often being able to adapt to different environmental conditions[vii]).

 

Organism characteristics

 

Burkholderia is a genus composed of over 60 organisms, many of which were formerly classed as Pseudomonas species. Within this are the Burkholderia cepacia complex, a group of some 17 organisms which are so closely related that they can, for the most part, only be differentiated by using a combination of multiple molecular diagnostic procedures.

 

Members of the Burkholderia cepacia complex are Gram-negative bacteria of the β-proteobacteria subdivision. This group is composed of plant, animal, and human pathogens. The organisms are widespread in both natural and ‘as built’ habitats[viii]. The organism after which the group is named was known as Pseudomonas cepacia prior to 1992. The bacterium was discovered by Walter H. Burkholder at Cornell Universityin1947.  Burkholder identified the bacterium as the source of onion skin rot (cepacia is Latin for “like onion”).

 

Burkholderia cepacia, along with other members, is an aerobic bacterium, elliptically shaped with a length of 5–15 μm. In term of biohazard, the organism has a biosafety level of 2.

 

Origins in pharmaceutical and healthcare

 

Bcc organisms are common to the environment and to water[ix].  With the manufacturing of drug products, the most common point of origin is with pharmaceutical water systems; a review by Sandle (2015) indicated that organisms fall into the top five category of recovered water-borne contaminants, as assessed over a fifteen year period[x]. This related to recoveries of water microbiota from purified water and Water-for-Injections systems. Issues arise foremost due to deficiencies in the design, operation and monitoring of water systems. A key risk relates to maintenance work like valve changes or where the system requires ‘cutting into’, such as to alter pipework[xi].

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[i] Lipuma J.J.. Update on the Burkholderia cepacia complex, Curr Opin Pulm Med. 2005; 11(6): 528-33

[ii] Lipuma, J.J, Currie B.J, Lum G.D, and Vandamme P. Burkholderia, Stenotrophomonas, Ralstonia, Cupriavidus, Pandoraea, Brevundimonas, Comamonas, Delftia, and Acidovorax In: Murray P.R, Baron E J, Jorgensen J.H, Landry ML, and Pfaller MA, editors. Manual of Clinical Microbiology. 9th Ed. Washington DC: ASM Press; 2007. p. 749-769.

[iii] Torbeck L, D. Raccasi, D.E. Guilfoyle, R.L. Friedman, D. Hussong. 2011. Burkholderia cepacia: This Decision is Overdue. PDA J. Pharm. Sci. Tech., 65(5): 535-43.

[iv] Hugo, WB et al. 1986. Factors Contributing to the Survival of a Strain of Pseudomonas cepacia In Chlorhexidine Solutions. Lett Appl Microbiol. 2:37-42

[v] W. Beckman and T.G. Lessie. Response of Pseudomonas cepacia to p-lactam antibiotics: utilization of penicillin G as the carbon source. J. Bacteriol. 1979; 140: 1126-1128

[vi] Martin, M et al 2011. Hospital-wide outbreak of Burkholderia contaminans caused by prefabricated moist washcloths. J Hosp Infect 77:267-270

[vii] Vial, L., et al 2011. The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation. Envir Microb 13(1):1-12

[viii] E. Mahenthiralingam, T.A. Urban, and J.B. Goldberg. The multifarious, multireplicon Burkholderia cepacia complex. Nature Reviews Microbiol. 2005; 3(2): 144–156

[ix] Springman, A.; Jacobs, J. L.; Somvanshi, V. S.; Sundin, G. W.; Mulks, M. H.; Whittam, T. S.; Viswanathan, P.; Gray, R. L.; Lipuma, J. J.; Ciche, T. A. Genetic diversity and multihost pathogenicity of clinical and environmental strains of Burkholderia cenocepacia. Appl. Environ. Microbiol. 2009, 75 (16), 5250–5260

[x] Sandle T (2015) Characterizing the Microbiota of a Pharmaceutical Water System-A Metadata Study. SOJ Microbiol Infect Page 5 of 8 Dis 3(2): 1-8

[xi] Ali, M. (2016) Burkholderia Cepacia in Pharmaceutical Industries, Int J Vaccines Vaccin 3(2): 00064. DOI: 10.15406/ijvv.2016.03.00064

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)