Scientists in Arkansas have developed a machine-learning approach that can identify potentially disease-causing strains of a poultry bacterium by analyzing not only which genes are present, but also how those genes are arranged across the genome. The method focuses on the “genetic neighborhoods” surrounding genes, offering a new way to distinguish harmful strains of Enterococcus cecorum from closely related strains that do not cause disease.

E. cecorum is commonly found in poultry environments, and many of its strains are harmless. However, pathogenic strains can cause arthritis, bone infections and lameness, creating serious animal-welfare problems and economic losses for poultry producers. Because pathogenic and nonpathogenic strains can share many of the same genes, identifying the genetic features associated with disease has been challenging.

The research team, led by Aranyak Goswami of the Arkansas Agricultural Experiment Station’s Center for Agricultural Data Analytics, examined the organization of genes within genomic islands. These are segments of DNA that bacteria often acquire from other microorganisms through horizontal gene transfer. Genomic islands can carry genes involved in antibiotic resistance, bacterial survival, movement of DNA and virulence, making them important regions for understanding how pathogens emerge.

Rather than treating the bacterial genome as a simple list of genetic components, the researchers analyzed it as a structured map. They investigated which genes occurred near one another, the order in which they appeared and the way groups of neighboring genes formed recurring units known as genomic-island cassettes. This architecture provided information that could be missed when genes are examined individually.

“The machine-learning model recognizes patterns in gene order much like it recognizes patterns in language,” Goswami said. In the same way that a language model can learn that certain words frequently appear together, the computational system learned that particular combinations and arrangements of bacterial genes were associated with pathogenic strains. The approach therefore captures relationships among genes rather than relying only on the presence or absence of individual DNA sequences.

For the proof-of-concept study, the researchers analyzed the genomes of 145 E. cecorum strains isolated from poultry. The dataset included 95 nonpathogenic strains and 50 pathogenic strains capable of causing illness. The analysis found that disease-associated strains were more likely to contain genomic islands enriched in genes linked to antimicrobial resistance and the transfer of genetic material between bacteria.

Those findings do not mean that every bacterium carrying such genes will necessarily cause disease. Instead, the researchers describe the system as an exploratory classification and research tool. It identifies patterns that may help scientists investigate why some bacterial lineages become harmful, while also providing clues about how resistance and virulence traits move through bacterial populations.

Current monitoring methods for E. cecorum often depend on culturing the bacterium or screening for specific genes. Such techniques remain valuable, but they may overlook broader genomic relationships. The new pipeline could complement these approaches by evaluating the wider context in which genes occur. Additional testing with larger and more geographically diverse datasets will be necessary before the method can be used for routine flock surveillance or diagnostic decision-making.

The researchers believe the strategy could eventually be adapted to other bacterial species affecting animals, humans, wildlife and plants. Goswami’s team is beginning to examine Enterococcus faecalis, a close relative of E. cecorum and a frequent cause of hospital-acquired infections in humans. They also plan to apply the pipeline to Escherichia coli and other bacteria to study how nonpathogenic lineages acquire the genomic configurations associated with disease. The study, published in Frontiers in Microbiology, demonstrates how machine learning and comparative genomics can reveal hidden signals in bacterial DNA and may help researchers track the evolution of emerging pathogens.

Subject of Research: Animals

Article Title: Genomic-island cassette architecture provides interpretable signal for exploratory classification of poultry-associated Enterococcus cecorum lineages

News Publication Date: 7-Jul-2026

Web References: https://doi.org/10.3389/fmicb.2026.1882753

References: Frontiers in Microbiology, DOI: 10.3389/fmicb.2026.1882753

Image Credits: UA University Relations photo by Chieko Hara

Keywords: artificial intelligence, machine learning, deep learning, computational biology, bacterial pathogens, Enterococcus cecorum, genomic islands, genomic architecture, antibiotic resistance, poultry disease, pathogen surveillance, comparative genomics

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The global expansion of chicken farming has created conditions that allow Campylobacter to spread, mix and adapt more readily. Commercial poultry farms now hold billions of chickens, creating a vast habitat where bacteria can move, mix and adapt. An analysis from the Ineos Oxford Institute for Antimicrobial Research at the University of Oxford found that [...]

What about attempts to test their virulence in humans? The approach in the Stanford lab sure sounds like a new form of gain-of-function research to me.

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Gut bacteria helped some adults tolerate peanuts in a first human trial.

Talk about homework: a large class of undergraduates at an unnamed university in Utah became the unfortunate subject of a severe public health response after an extraordinary bungle in a science lab.

In September of last year, the group of lab students were tasked with identifying a bacterium known as P. shigelloides, a relatively harmless pathogen known to cause diarrhea when ingested. But as lab results came in, students were alarmed to find the specimens handed out in class were actually the bacteria Neisseria meningitidis, a potentially deadly pathogen that causes meningitis.

Unlike P. shigelloides, the bacterium N. meningitidis calls for high-security practices, like double gloves, disposable clothes, and fit-tested N95 masks, as the bare minimum. (In one unfortunate case from 2012, a 25-year old microbiologist whose lab was ill equipped to handle N. meningitidis died mere hours after exposure to the aerosolized microbe.)

According to People, Utah public health authorities soon raided the Utah stockroom, finding samples labeled “N. meningitidis.” That discovery prompted a recommendation that all 33 of the exposed students begin a cautionary antibiotic regimen, especially given that the lab participants were only wearing gloves and lab coats at the time of exposure.

On top of the antibiotics dose, at least two people sought medical attention due to possible exposure symptoms, which included a painful and invasive spinal tap.

It was only after the frenzy that further professional lab tests identified the offending pathogen as Neisseria sicca, a bacterium “commonly found in the upper respiratory tract” that is “nonpathogenic in immunocompetent persons,” according to a recently-filed Center for Disease Control study of the Utah lab incident.

Student misidentification notwithstanding, the event underscores the importance of accurately labeling microbial cultures — lest aspiring biologists become victims of their own studies.

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The post 33 Students Treated for Deadly Bacteria Exposure When Classroom Experiment Goes Horribly Wrong appeared first on Futurism.

Scientists trained artificial intelligence on libraries of DNA and then asked the model to create recipes for viral genomes. Sixteen of them were viable, yielding new viruses.

Macrobiological features have been cited as irreducibly complex, including animal joints and the trap mechanisms of carnivorous plants, even the cell itself.

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Warming is expected to fuel the spread of food-borne pathogens. We might not be prepared.

© Melanie Moser/CDC, via Associated Press

In 1982, she led the research team that figured out how to genetically alter plants, a discovery that would eventually transform global agriculture.

A gum disease bacterium may contribute to aortic valve calcification through inflammation, according to preliminary human tissue and mouse research. A bacterium best known for damaging gums may also be involved in the hardening of the heart’s aortic valve. Preliminary research presented at the American Heart Association’s Basic Cardiovascular Sciences Scientific Sessions 2026 points to [...]

The microbes don't exactly digest uranium, but their metabolism made it far less mobile.

In a groundbreaking revelation that could reshape our understanding of plant-microbe interactions and agricultural biotechnology, researchers have unveiled a novel chemical communication mechanism between rice roots and beneficial soil bacteria. This newly discovered pathway centers on the secretion of heptadecanoic acid, a specific fatty acid, which effectively recruits Bacillus species to the rhizosphere, the densely populated soil region surrounding plant roots. Such a mechanism not only highlights the intricate biochemical dialogues that underpin plant-microbe symbioses but also opens promising avenues for sustainable crop management through microbiome engineering.

Rice, a staple food that sustains more than half of the world’s population, has long been studied for its interactions with the soil ecosystem. The rhizosphere harbors myriad microbial communities, some of which promote plant health by enhancing nutrient acquisition, defending against pathogens, or improving stress tolerance. Identifying the exact signals that facilitate recruitment of beneficial bacteria has presented a considerable scientific challenge. The recent study by Zeng, Wen, Zhao, and colleagues provides essential insights and fills a critical gap by pinpointing heptadecanoic acid as a chemical attractant secreted by rice roots, which acts as a molecular beacon for Bacillus.

Heptadecanoic acid, also known as margaric acid, is a saturated fatty acid containing 17 carbon atoms. Traditionally, plant root exudates—complex mixtures of organic acids, sugars, amino acids, and secondary metabolites—have been observed to influence microbial colonization, but the specific involvement of fatty acids as signals was less appreciated. The team’s meticulous biochemical analyses have now elucidated that rice roots not only exude heptadecanoic acid but do so strategically when recruiting beneficial Bacillus species. This revelation signifies a refined understanding of the selective microbial recruitment strategies employed by plants.

The team’s research employed an array of advanced techniques—ranging from root exudate profiling through gas chromatography-mass spectrometry (GC-MS) to microbial chemotaxis assays—to validate that Bacillus species detect and are attracted to gradients of heptadecanoic acid in the rhizosphere. Importantly, not all soil microbes respond equivalently, underscoring the specificity of this fatty acid signal. Functional studies further demonstrated that disrupting rice root production of heptadecanoic acid diminished Bacillus colonization, which correspondingly weakened the plant’s resistance to common soil-borne pathogens.

Understanding the biochemical basis for such recruitment enables scientists to rethink approaches to crop protection and enhancement. Bacillus species are well-known for their plant growth-promoting traits, including production of antimicrobial compounds, enhancement of nutrient solubilization, and induction of systemic resistance in plants. By harnessing the heptadecanoic acid signaling pathway, it is conceivable that agricultural inoculants could be optimized to improve colonization efficiency and consistency in field conditions, potentially reducing the need for chemical pesticides and fertilizers.

This molecular dialogue highlights a sophisticated communication network where plants actively shape their microbial environment. The discovery that a fatty acid functions not merely as a structural or energy-storage molecule but as a signaling compound redefines our conception of root exudate complexity. Moreover, heptadecanoic acid’s hydrophobic nature prompts questions about its diffusion dynamics in soil and the mechanisms by which Bacillus receptors detect it. Future exploration into bacterial chemoreceptors and downstream signaling pathways activated by this molecule could illuminate novel targets for microbiome manipulation.

Beyond direct agricultural implications, this finding resonates with broader ecological principles. The soil microbiome’s composition significantly influences plant community dynamics, ecosystem productivity, and resilience to environmental stresses. By uncovering a precise mediator of microbe recruitment, the work by Zeng and colleagues contributes to the fundamental ecological theory of plant-soil feedback loops, suggesting that plants possess active biochemical agency in curating their microbial consortia.

Interestingly, the secretion of heptadecanoic acid is not constant but modulated by environmental cues and plant developmental stages, emphasizing the dynamic nature of root exudation profiles. This temporal regulation indicates that plants might selectively recruit beneficial microbes in response to specific physiological needs or external threats, adding an adaptive dimension to this interaction. Understanding these controls could inform timing strategies for microbial inoculant application in agriculture to coincide with natural recruitment periods.

The authors also raise intriguing evolutionary considerations. The conserved ability among rice varieties to secrete heptadecanoic acid suggests selective pressure favoring plants capable of enlisting Bacillus partners. Parallel studies on other cereal crops could reveal whether this fatty acid signaling is a widespread mechanism or unique to rice. Such comparative analyses across plant taxa may unearth a broader family of fatty acid signals mediating symbioses and expand the toolkit for synthetic microbiome engineering.

This pioneering investigation underscores the necessity of interdisciplinary approaches combining plant biology, microbiology, analytical chemistry, and ecology to fully decipher plant-microbe interactions. It leverages cutting-edge omics technologies and bioinformatics pipelines to characterize metabolite profiles and microbial responses, illustrating the power of integrative science. The robust experimental design and reproducible methodologies set a new benchmark for future studies aiming to parse root exudate signaling.

As the global agricultural sector grapples with the challenges of increasing food production sustainably on finite arable land under climate change pressures, the discovery of a natural plant mechanism to recruit growth-promoting and protective microbes represents a potentially transformative tool. Strategies informed by such foundational knowledge could reduce reliance on synthetic inputs, lower environmental footprints, and enhance crop resilience, aligning with ambitious global sustainability goals.

In conclusion, the identification of heptadecanoic acid as a pivotal signaling molecule secreted by rice roots to attract beneficial Bacillus species marks an exciting advance in the field of plant-microbe research. It unravels a previously unrecognized layer of biochemical communication with profound implications for agriculture and ecology. Continued investigation into the molecular details, environmental regulation, and cross-species relevance of this signaling mechanism promises to unlock innovative avenues for crop improvement and sustainable farming practices worldwide.

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Subject of Research: Plant-microbe interactions focusing on the biochemical signaling between rice roots and Bacillus species mediated by heptadecanoic acid secretion.

Article Title: Author Correction: Rice roots recruit Bacillus via the secretion of heptadecanoic acid.

Article References: Zeng, J., Wen, T., Zhao, J. et al. Author Correction: Rice roots recruit Bacillus via the secretion of heptadecanoic acid. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02341-5

Image Credits: AI Generated

Scientists have uncovered a shared target used by multiple diarrhea-causing bacteria to invade the gut. Despite decades of research, scientists still do not have vaccines against two of the world’s most common causes of severe bacterial diarrhea: enterotoxigenic E. coli (ETEC) and Shigella. Together, these pathogens infect hundreds of millions of people each year and [...]

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The post 113-Million-Year-Old Pterosaur Fossil Reveals What Flying Reptiles Ate appeared first on Sci.News: Breaking Science News.

Researchers at Washington University School of Medicine in St. Louis have made a groundbreaking discovery that could revolutionize the prevention of diarrheal diseases caused by enterotoxigenic Escherichia coli (ETEC) and Shigella. These two bacterial pathogens are responsible for hundreds of millions of infections annually and are leading causes of diarrheal mortality worldwide, particularly among young children. Despite decades of efforts, vaccine development has encountered significant obstacles, primarily due to the extensive strain variability that hampers the identification of universal vaccine targets.

In a recent study published in the Proceedings of the National Academy of Sciences, the WashU team, collaborating with scientists at the University of Missouri and the International Centre for Diarrhoeal Disease Research in Bangladesh, identified a shared vulnerability within these pathogens that could open the door for a combined vaccine platform. This innovative approach hinges on targeting homologous enzymes that these bacteria use to degrade the mucus lining in the human gut, a critical step in establishing infection.

For bacterial pathogens like ETEC and Shigella to cause illness, they first need to overcome the intestinal mucus barrier. This thick layer of mucus serves as a physical and biochemical shield protecting the gut epithelium and regulating the microenvironment by keeping pathogenic entities at bay while preserving the beneficial microbiota. The ability to breach this barrier is a hallmark of pathogenicity, allowing bacteria to access the underlying tissues and deploy additional virulence factors, including enterotoxins that induce diarrhea.

The study’s focal point is a family of mucin-degrading enzymes that facilitate this breaching process. The researchers detail three closely related enzymes—EatA, SepA, and Pic—that are expressed by ETEC, Shigella, and other diarrheal pathogens. EatA, an acronym for “eat away,” is produced by ETEC and was previously identified by Fleckenstein’s laboratory as a critical mucinase targeting the primary structural protein within mucus. SepA and Pic, related enzymes produced by Shigella and some other bacteria, perform analogous roles. Their enzymatic activity effectively dismantles the mucosal barrier, clearing a path for bacterial invasion.

Intriguingly, the antibodies that the team isolated from individuals infected with ETEC or experimentally exposed to the bacteria displayed a functional cross-reactivity. The antibodies not only neutralized EatA but also inhibited SepA and Pic, indicating a conserved epitope region among these mucinases. This neutralization prevents the enzymes from degrading intestinal mucus, thereby blocking the pathogens’ entry into host tissues. The concept of a single antibody interfering with multiple bacterial targets underscores a significant breakthrough in vaccine strategy.

To unravel the structural mechanics behind this immune neutralization, the researchers leveraged cryo-electron microscopy—a state-of-the-art imaging method that preserves biomolecules in near-native states by flash-freezing samples. This technique enabled detailed visualization at atomic resolution, revealing the precise binding site of the neutralizing antibodies. Remarkably, the site of interaction was a structurally conserved region across EatA, SepA, and Pic, providing a rational basis for the design of vaccine antigens that elicit broadly neutralizing antibodies.

“The identification of this shared Achilles’ heel among diverse diarrhea-causing bacteria signifies a paradigm shift in vaccine development,” explains James M. Fleckenstein, MD, co-senior author of the study and professor of medicine at WashU. “It suggests we can target a common mechanism of gut colonization rather than chasing highly variable surface molecules, which has been the stumbling block in the field for so long.”

Further bolstering the translational potential of these findings, epidemiological data from children in Dhaka, Bangladesh, indicate that naturally acquired antibodies against EatA correlate with protection from diarrheal illness. This natural immunity validates EatA as a viable immunological target and encourages the pursuit of vaccines that induce similar protective responses.

The implications extend beyond the developing world, as enterotoxigenic E. coli has been implicated in recent foodborne outbreaks in industrialized countries such as the United States. The difficulty in distinguishing pathogenic ETEC from non-pathogenic strains in clinical settings further complicates diagnosis and containment. Moreover, reliance on antibiotics to treat infections caused by these bacteria accelerates the evolution of antibiotic resistance, posing a global public health threat.

Zachary Berndsen, PhD, assistant professor of biochemistry at the University of Missouri and co-senior author, emphasizes the rational approach to vaccine design enabled by these insights. “By pinpointing enzyme domains targeted by neutralizing antibodies, we provide a template for crafting precise immunogens that can stimulate protective immunity across multiple pathogens. This can streamline the production of vaccines that are both effective and broad-spectrum,” Berndsen says.

Development of such a vaccine could not only reduce the global burden of diarrheal diseases but also mitigate the spread of antibiotic resistance by decreasing the frequency of bacterial infections requiring treatment. Additionally, preserving the gut microbiota through targeted disruption of pathogenic mechanisms may alleviate some adverse consequences associated with broad-spectrum antibiotic use.

Going forward, the research team is focused on translating their molecular discoveries into practical vaccine candidates. This involves preclinical testing of immunogens incorporating the conserved epitopes identified, assessing their immunogenicity and protective efficacy in animal models, and progressing toward human clinical trials.

“In our ongoing battle with enteric pathogens that have coevolved with humans for millennia, blocking the enzymatic opening of the mucus gate represents a promising strategy,” Fleckenstein concludes. “If successful, this vaccine would preempt infection at its earliest and most vulnerable stage, changing the trajectory of diarrheal disease worldwide.”

The study was supported by grants from the National Institute of Allergy and Infectious Diseases and the Department of Veterans Affairs. The multidisciplinary collaboration brings together expertise in infectious diseases, structural biology, immunology, and clinical research, underscoring the necessity of integrated approaches to tackle complex global health challenges.

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Subject of Research: Human tissue samples

Article Title: Human enterotoxigenic Escherichia coli (ETEC) infections elicit antibodies that broadly neutralize mucinases of pathogenic Escherichia coli and Shigella

News Publication Date: 15-Jun-2026

References:
Buckley DP, Akhtar M, Thapa M, Schmitz A, Turner J, Vickers TJ, Khatoon N, Kaisar MH, Coggin JA, Ganguli D, Sheikh A, Laird RM, Poly F, Porter CK, Ruiz-Perez F, Miller MJ, Chowdhury F, Bhuiyan TR, Qadri F, Trillo-Muyo S, Dolan B, van der Post S, Ellebedy A, Berndsen ZT, Fleckenstein JM. Human enterotoxigenic Escherichia coli (ETEC) infections elicit antibodies that broadly neutralize mucinases of pathogenic Escherichia coli and Shigella. PNAS. June 15, 2026.

Image Credits: David Hasty

Keywords: Infectious diseases, Microbial infections, Diarrhea

The oldest known cases, discovered among hunter-gatherers in Siberian graves, contradict the theory that the disease once was mild.

New analysis of ancient frozen Greenland rubbish heaps, called middens, has revealed new insights into several ancient societies that have passed through the country over the last five millennia. The findings include insights into ancient diseases and animals that the inhabitants kept but didn’t eat.

Although the team noted the potential risk that climate change could release dangerous ancient microbes into the modern environment, their analysis found little evidence that the pathogens they identified could pose a threat beyond the immediate area around the middens.

Ancient Middens Offer Historical Insights Beyond Traditional Artifacts

Archaeologists have often excavated items discarded by ancient societies from trash heaps to learn more about the people who lived there. Although such excavations often unearth things like animal bones and mollusk shells, offering insights into diet and hunting habits, these ancient rubbish heaps can also contain human artifacts, such as discarded blades and other tools.

In a country like Greenland, where different peoples have settled the region since 2,500 BCE, the ancient middens may also contain microbes that could offer researchers an entirely different type of historical data. For example, microbial data from middens could reveal which diseases ancient populations had to survive. The team notes that microbes could also help determine what ancient societies kept “but perhaps didn’t eat.”

Still, studies of ancient midden microbes are limited, leaving a gap in historical knowledge. The authors of the new paper also highlight that rapidly increasing Arctic warming could release infectious diseases to which humans have lost immunity over the ensuing generations.

Over One Thousand New Species Were Identified

To bridge the information gap, Dr Frank Møller Aarestrup, a professor at the National Food Institute of Denmark Technical University and corresponding author of the article detailing the team’s research, examined samples collected during 2020 and 2021 expeditions in West and South Greenland. During those expeditions, scientists collected samples from middens locked in time by permafrost, dating back as far as 4,500 years.

Among the middens sampled were the ancient Norse sites of Kapisilit and Narsarsuaq, where researchers collected soil samples from what the new paper’s authors termed “historic winter enclosures.” The site also contained evidence that it was a summer grazing ground for livestock.

After selecting several soil samples, Dr. Aarestrup’s team sequenced the DNA of ancient microbes found in the midden samples. Next, they compared the data, including entire bacterial communities, to 143 soil samples previously collected from areas of permafrost far away from any known historical human settlements.

According to the team’s statement, the sequencing revealed a total of 1,207 species and differing ranges of bacterial species per midden. In denser areas, the team identified as many as 202 species, whereas less microbe-dense middens had as few as nine.

The team’s analysis also found several species that had not been previously identified. This resulted in the team labeling the unidentified microbes using what they termed “broad taxonomic categories” above the genus and species level, such as family and order.

Preserving the ‘Biological Legacy’ of Human Activity

When comparing the microbial communities in the ancient middens with those from samples collected away from human settlements, the team found a significantly richer community of ancient bacteria preserved in the middens. The team notes that this discrepancy confirms that the middens “preserved the biological legacy of human activity.”

The most soil-like bacterial communities were identified within the oldest Paleo-Inuit middens. The researchers said the finding suggests that the microbial “imprint” left behind by humans and animals diminishes over time.

Bacterial communities were also associated with the types of waste discarded in each ancient midden. For example, although most middens contained bacteria associated with human and animal hosts, middens from colonial-era Nuuk contained decomposing seal skins. The middens from colonial-era sites were also rich in the bacterium Clostridium perfringens, which the team notes is “a major cause of food poisoning.”

Risk of Ancient Pathogens is Low

Although the team identified strains of bacteria that can cause botulism or other life-threatening conditions, such as toxic shock syndrome, sepsis, and gangrene, they also found a diversity of antimicrobial-resistance genes in the genomes of bacteria collected from the same middens.

According to the study authors, finding the two sets of genes in ancient and modern soil layers “signaled that microbes resistant to antimicrobials can linger in permafrost for centuries.”

Fortunately, the team’s analysis found that most of the identified microbes, including potentially dangerous pathogens, don’t spread far from middens, even those undergoing defrosting. As a result, the team said that these ancient microbes  “pose little risk to public health,” at least for the time being.

“Here we show that the risk of release of ancient pathogens from ancient middens in Greenland is currently low,” Dr. Aarestrup explained.

Instead, the researcher noted that Arctic middens appear to function like “long-term natural experiments,” in which both human- and animal-associated bacteria, including “opportunistic” species carrying resistance genes, remain detectable centuries later as a broader “legacy of human activity.”

The study “Microbial composition of archaeological middens: Tracing Human Footprints Through Centuries in Greenland’s Ancient Settlements” was published in Frontiers in Microbiology.

Christopher Plain is a Science Fiction and Fantasy novelist and Head Science Writer at The Debrief. Follow and connect with him on X, learn about his books at plainfiction.com, or email him directly at christopher@thedebrief.org.

In a mouse study conducted by scientists at the Dasman Diabetes Institute in Kuwait, rodents fed a sucrose-free diet developed insulin resistance, gut microbial imbalances and signs of fatty liver disease despite maintaining similar body weight.

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Ancient Australian fossils indicate that the earliest eukaryotes depended on oxygen, providing new evidence that oxygen helped enable the evolution of complex life. Stored in an open-air warehouse in tropical Darwin, Australia, are dozens of trays containing cylindrical cores of rock. They are from drill holes bored hundreds of meters below the surface by mineral [...]