“Molecular bodyguard” helps infections persist

Joram Waititu and Kemal Avican working together in the Avican Lab at the Department of Molecular Biology, Umeå University.
Photo Credit: Gabrielle Beans

Researchers at Umeå University have identified a key molecular player that helps bacteria survive the hostile environment inside the body. Their study reveals how the protein RfaH acts as a protective shield for bacterial genes — and points to new strategies for fighting persistent infections.

“The human body is a very stressful place for bacteria,” says Kemal Avican research group leader at Department of Molecular Biology and Icelab at Umeå University and leader of the study. “During infection, the immune system attacks, nutrients are scarce, and microbes are exposed to bile salts, acids and heat. We looked at how RfaH helps bacteria deal with that stress by turning on the right survival genes at the right time.”

Persistent bacterial infections pose a major challenge in medicine: bacteria can linger in the body long after acute symptoms fade, evading immune defenses and surviving antibiotic treatment. In diseases like tuberculosis, this leads to relapse and makes treatment difficult.

African Wildlife Poop Sheds Light on What Shapes the Gut Ecosystem

Photo Credit: James C. Beasley

A study of elephants, giraffes and other wildlife in Namibia’s Etosha National Park underscores the ways in which the environment, biological sex, and anatomical distinctions can drive variation in the gut microbiomes across plant-eating species. Because the gut microbiome plays a critical role in animal health, the work can be used to inform conservation efforts.

“This study is valuable because Etosha gave us the opportunity to sample such a large number of species under different environmental conditions,” says Erin McKenney, co-author of a paper on the work and an assistant professor of applied ecology at North Carolina State University. “That gives us meaningful insight into the role the environment plays in shaping the gut microbiome of herbivores.

“Unfortunately, this study may also be important for a second reason,” McKenney says. “Etosha is experiencing devastating wildfires affecting a huge section of the park. Because our samples were taken before the wildfires, these findings could inform recovery efforts by helping us understand how species’ microbiomes are adjusting to changes in diet that stem from the fire’s impact on the landscape.”

“Cocktails” of common pharmaceuticals in our waterways may promote antibiotic resistance

Photo Credit: Nana K.

New research has shown, for the first time, how mixtures of commonly used medications which end up in our waterways and natural environments might increase the development of antibiotic-resistant bacteria.

When humans or animals take medications, as much as 90 percent can pass through the body and into natural environments, via waste-water, or run-off from fields, ending up in the ocean. 

In the environment, this build-up of antibiotic medicines can accumulate to a strength sufficient to kill the bacteria that live there; this can result in bacteria evolving defenses that help them to survive these concentrations, which can mean they are also resistant to antibiotics used to treat them if they later infect humans. However, less is known about how build-up of other medicines also affects bacteria, and until now, scientists have largely investigated the effect of these medications on triggering this antibiotic resistance one-at-a-time. 

New research reveals the secret to ancient fish scales’ survival

Diplomystus dentatus, Fossil-Lake, Wyoming, USA
Photo Credit: Didier Descouens
(CC BY-SA 4.0)

A Curtin University-led international study has solved the mystery of how the skin of a fossilized fish was able to be preserved for 52 million years, extending our understanding of how even the most delicate of biological material can survive deep in time.

Published in Environmental Microbiology, the research examined a remarkably well-preserved specimen of Diplomystus dentatus complete with fossilized skin and scales, found in the ‘Fossil Basin’ region of Wyoming in the United States of America.

Despite being in an oxygen elevated micro-environment which would normally cause tissues to decay, the team discovered the initial degradation of the fish’s fatty skin also led to an environment where phosphate minerals could form and rapidly replace organic material – leading to fossilization.

As the skin broke down, it released fatty acids and hydrogen ions, altering the surrounding chemistry in a way that favored phosphate preservation by effectively blocking the usual carbonate deposits which would have otherwise caused the tissues to decay.

Climate change may increase the spread of neurotoxin in the oceans

The researchers’ findings raise concerns about how climate change may affect the levels of methylmercury in fish and shellfish.
Photo Credit: Johnér Bildbyrå AB

Climate-driven oxygen loss in the Black Sea thousands of years ago triggered the expansion of microorganisms capable of producing the potent neurotoxin methylmercury. That is shown in a new study published in Nature Water, led by Eric Capo at Umeå University, which suggests that similar processes could occur in today’s warming oceans.

Methylmercury is a highly toxic compound that accumulates in fish and seafood, posing severe health risks to humans. It is formed when certain microbes convert inorganic mercury under low-oxygen conditions.

Today, climate change is causing such oxygen-depleted areas to expand in coastal marine environments, including parts of the Baltic Sea. Warmer and more stagnant waters mix less efficiently, and increased algal blooms contribute to oxygen loss in deeper layers, creating ideal conditions for these microbes.

Researchers find key to stopping deadly infection

When rotavirus enters a cell without the FA2H enzyme, it becomes trapped in pockets called endosomes (indicated by red arrows). This prevents the virus from infecting the rest of the cell.
Image Credit: Ding Lab/WashU Medicine

Rotavirus causes severe dehydrating diarrhea in infants and young children, contributing to more than 128,500 deaths per year globally despite widespread vaccination efforts. Although rotavirus is more prevalent in developing countries, declining vaccination uptake in the United States has resulted in increasing cases in recent years.

New research from Washington University School of Medicine in St. Louis has identified a key step that enables rotavirus to infect cells. The researchers found that disabling the process in tissue culture and in mice prevented infection. This discovery opens up new avenues for therapeutic intervention to treat rotavirus and other pathogens that rely on the same infection mechanism.

“Rotavirus kills infants and children, young people who never had a chance at life,” said Siyuan Ding, an associate professor of molecular microbiology at WashU Medicine. “That’s why we want to develop effective therapeutics, even though we already have vaccines that we can use. Not all kids receive the vaccine, and this virus is very infectious. Once a child has the virus, there’s currently no treatment; we can only manage the symptoms.”

Changes in gut microbiota influence which patients get AIG-related neuroendocrine tumors

Researchers took biopsies of AIG patients with and without neuroendocrine tumor growth to understand their bacterial communities
Image Credit: Osaka Metropolitan University

Researchers from Osaka Metropolitan University have discovered how the balance of bacteria in the stomach affects the growth of neuroendocrine tumors (NETs). By identifying the specific bacteria involved and the biochemical reactions that cause tumor growth, the researchers hope to create a new diagnostic technique to detect which patients are most likely to develop cancer.

Autoimmune gastritis (AIG) is a long-term condition in which the body’s immune system mistakenly attacks the lining of the stomach. This ongoing immune response gradually damages the stomach, affecting how it functions and its ability to protect itself from harmful agents. Over time, these changes can increase the risk of developing NETs, a type of tumor that develops from hormone-producing cells in the stomach.

Researchers revive yoghurt made from... ants

Photo Credit: David Zilber

An old traditional recipe for yoghurt made from ants has been recreated by researchers at the University of Copenhagen. In a new study, they show how ants and the bacteria that live on them can transform milk into yoghurt. This provides new knowledge about the food traditions of the past and one of today's major food trends, and the study may also inspire new sustainable foods.

Take four live forest ants. Put them in a jar of warm milk. Cover with a piece of cloth, then place the jar in a colony overnight. Voila! Now you have tasty yoghurt. This is how yoghurt was made for generations in many parts of Turkey and the Balkans. Today, the tradition has largely died out. But what is actually the science behind the method? And what can modern research learn from this method?

A team of biologists, food scientists and anthropologists from the University of Copenhagen and DTU, among others, set out to investigate this in collaboration with chefs from the Michelin-starred restaurant The Alchemist. No one has ever described the biology behind this mysterious recipe.

Microbial DNA sequencing reveals nutrient pollution and climate change reinforce lake eutrophication

Lake 227 of the Experimental Lakes Area.
Photo Credit: Rebecca Garner

The algal blooms increasingly seen in Canadian lakes have been linked to both nutrient pollution from agricultural runoff and climate change. However, a new Concordia-led study using DNA sequencing of lakebed microbes reveals that these two drivers amplify each other in ways that profoundly affect the health of lake ecosystems.

Using records and samples from the International Institute for Sustainable Development Experimental Lakes Area (ELA), a group of 58 lakes in northwestern Ontario designated freshwater research facilities, the researchers paired environmental monitoring data dating back more than five decades with paleogenetic reconstructions from lakebed microbes dating back more than a century.

By sequencing DNA found in lake sediments, the researchers got insight into past algal communities’ composition and compare them to communities today. This provided critical insight into how those communities changed over decades.

“The sediment DNA archives gave us a chronology of these lakes’ history,” says lead author Rebecca Garner, PhD 2023, and currently a postdoctoral fellow at the University of California, Berkeley. “This is the first study to show that we can reconstruct the community dynamics of that ecosystem and dramatically expands the diversity of microorganisms that we were able to study.”

The study was published in the journal Environmental Microbiology.

Capturing 100 years of antibiotic resistance evolution

The team analysed the DNA from bacterial samples as far back as 1917, before antibiotics were discovered, to see how they had evolved since.
Photo Credit: Edward Jenner

Researchers have dived into the pre-antibiotic history of plasmids — one of bacteria’s tools of antimicrobial resistance — to understand how they have facilitated the spread of treatment-resistant infections worldwide.

Experts at the Wellcome Sanger Institute, the University of Bath, the UK Health Security Agency (UKHSA) and their collaborators, analyzed over 40,000 plasmids from historical and present-day bacterial samples taken across six continents, the largest dataset of its kind.

Plasmids are transferable structures in bacteria that allow different strains to share genetic information. In this study, published in Science, researchers found that a minority of plasmids causes most of the multidrug resistance in the world. In the future, developing ways to target these could lead to new therapies to combat treatment-resistant infections worldwide.

Currently, treatment-resistant infections cause at least one million deaths worldwide every year, with this number expected to rise. While some bacteria and fungi carry antimicrobial resistance (AMR) genes naturally, the emergence and spread of MDR and AMR genes has been consistently linked to the use of antibiotics.

Study shows mucus contains molecules that block Salmonella infection

MIT researchers have discovered how mucins found in the mucus that lines the digestive tract can disarm the bacterium that causes Salmonella (purple).
Image Credit: Courtesy of the researchers
(CC BY-NC-ND 4.0)

Mucus is more than just a sticky substance: It contains a wealth of powerful molecules called mucins that help to tame microbes and prevent infection. In a new study, MIT researchers have identified mucins that defend against Salmonella and other bacteria that cause diarrhea.

The researchers now hope to mimic this defense system to create synthetic mucins that could help prevent or treat illness in soldiers or other people at risk of exposure to Salmonella. It could also help prevent “traveler’s diarrhea,” a gastrointestinal infection caused by consuming contaminated food or water.

Mucins are bottlebrush-shaped polymers made of complex sugar molecules known as glycans, which are tethered to a peptide backbone. In this study, the researchers discovered that a mucin called MUC2 turns off genes that Salmonella uses to enter and infect host cells.

Influenza A viruses adapt shape in response to environmental pressures

Colorized transmission electron micrograph of influenza A virus particles, colorized red and gold, isolated from a patient sample and then propagated in cell culture. Influenza A can infect both humans and animals, including birds and pigs. More specifically, this image features the H3N2 influenza strain, isolated from a patient in Victoria, Australia, in 1975. Notable for forming both spheric
Image Credit: National Institute of Allergy and Infectious Diseases

Influenza A virus particles strategically adapt their shape—to become either spheres or larger filaments—to favor their ability to infect cells depending on environmental conditions, according to a new study from National Institutes of Health (NIH) scientists. This previously unrecognized response could help explain how influenza A and other viruses persist in populations, evade immune responses, and acquire adaptive mutations, the researchers explain in a new study published in Nature Microbiology.

The study, led by intramural researchers at NIH’s National Institute of Allergy and Infectious Diseases (NIAID), was designed to determine why many influenza A virus particles exist as filaments. The filament shape requires more energy to form than a sphere, they state, and its abundance has been previously unexplained. To find the answer, they developed a way to observe and measure real-time influenza A virus structure during formation.

Effects of Declining Diversity Documented in the World of Microbes

Phytoplankton, seen here inside a flask in the Jackrel Lab, are proving to be a valuable system for studying host-associated microbiomes
Photo Credit: Jackrel Lab / UCSD

Across the tree of life, human activities are accelerating declines in biological species diversity, from deserts to oceans to forests. But what about the microscopic world? Scientists in UC San Diego’s School of Biological Sciences recently investigated how declining biodiversity in tiny ecological systems unseen to the naked eye can carry significant consequences for the health of organisms and ecosystems.

Postdoctoral Scholar Jonathan Dickey and recent master’s graduate Nikki Mercer from Assistant Professor Sara Jackrel’s laboratory studied the implications of declining diversity within microbiomes — communities of microorganisms, such as bacteria, which can form tight associations with their hosts, such as plants and animals. Recent studies in microbial ecology have found that microbiomes can play a key role in regulating host health, leading researchers to believe that as our world changes it is imperative to understand the implications of biodiversity loss within the host microbiome.

Drawing a Line from the Gut Microbiome to Inflammation and Depression

Morganella morganii bacteria on a plate.
Photo Credit: Ajay Kumar Chaurasiya
(CC BY-SA 4.0)

It’s become increasingly clear that the gut microbiome can affect human health, including mental health. Which bacterial species influence the development of disease and how they do so, however, is only just starting to be unraveled.

For instance, some studies have found compelling links between one species of gut bacteria, Morganella morganii, and major depressive disorder. But until now no one could tell whether this bacterium somehow helps drive the disorder, the disorder alters the microbiome, or something else is at play.

Harvard Medical School researchers have now pinpointed a biologic mechanism that strengthens the evidence that M. morganii influences brain health and provides a plausible explanation for how it does so.

The findings, published in the Journal of the American Chemical Society, implicate an inflammation-stimulating molecule and offer a new target that could be useful for diagnosing or treating certain cases of the disorder. They also provide a roadmap for probing how other members of the gut microbiome influence human health and behavior.

“There is a story out there linking the gut microbiome with depression, and this study takes it one step further, toward a real understanding of the molecular mechanisms behind the link,” said senior author Jon Clardy, the Christopher T. Walsh, PhD Professor of Biological Chemistry and Molecular Pharmacology in the Blavatnik Institute at HMS.

First-of-its-kind integrated dataset enables genes-to-ecosystems research

DOE national laboratory scientists led by Oak Ridge National Laboratory have developed the first tree dataset of its kind, bridging molecular information about the poplar tree microbiome to ecosystem-level processes.
Illustration Credit: Andy Sproles/ORNL, U.S. Dept. of Energy

The first-ever dataset bridging molecular information about the poplar tree microbiome to ecosystem-level processes has been released by a team of Department of Energy scientists led by Oak Ridge National Laboratory. The project aims to inform research regarding how natural systems function, their vulnerability to a changing climate, and ultimately how plants might be engineered for better performance as sources of bioenergy and natural carbon storage.

The data, described in Nature Publishing Group’s Scientific Data, provides in-depth information on 27 genetically distinct variants, or genotypes, of Populus trichocarpa, a poplar tree of interest as a bioenergy crop. The genotypes are among those that the ORNL-led Center for Bioenergy Innovation previously included in a genome-wide association study linking genetic variations to the trees’ physical traits. ORNL researchers collected leaf, soil and root samples from poplar fields in two regions of Oregon — one in a wetter area subject to flooding and the other drier and susceptible to drought. 

Details in the newly integrated dataset range from the trees’ genetic makeup and gene expression to the chemistry of the soil environment, analysis of the microbes that live on and around the trees and compounds the plants and microbes produce.

The dataset “is unprecedented in its size and scope,” said ORNL Corporate Fellow Mitchel Doktycz, section head for Bioimaging and Analytics and project co-lead. “It is of value in answering many different scientific questions.” By mining the data with machine learning and statistical approaches, scientists can better understand how the genetic makeup, physical traits and chemical diversity of Populus relate to processes such as cycling of soil nitrogen and carbon, he said. 

Autism and ADHD are linked to disturbed gut flora very early in life

The researchers have found links between the gut flora in babies first year of life and future diagnoses.
Photo Credit: Cheryl Holt

Disturbed gut flora during the first years of life is associated with diagnoses such as autism and ADHD later in life. This is according to a study led by researchers at the University of Florida and Linköping University and published in the journal Cell.

The study is the first forward-looking, or prospective, study to examine gut flora composition and a large variety of other factors in infants, in relation to the development of the children's nervous system. The researchers have found many biological markers that seem to be associated with future neurological development disorders, such as autism spectrum disorder, ADHD, communication disorder and intellectual disability.

“The remarkable aspect of the work is that these biomarkers are found at birth in cord blood or in the child’s stool at one year of age over a decade prior to the diagnosis,” says Eric W Triplett, professor at the Department of Microbiology and Cell Science at the University of Florida, USA, one of the researchers who led the study.

Discovery could end global amphibian pandemic

Panamanian golden frog
Photo Credit: Brian Gratwicke/U.S. Fish & Wildlife Service

A fungus devastating frogs and toads on nearly every continent may have an Achilles heel. Scientists have discovered a virus that infects the fungus, and that could be engineered to save the amphibians.

The fungus, Batrachochytrium dendrobatidis or Bd, ravages the skin of frogs and toads, and eventually causes heart failure. To date it has contributed to the decline of over 500 amphibian species, and 90 possible extinctions including yellow-legged mountain frogs in the Sierras and the Panamanian golden frog. 

A new paper in the journal Current Biology documents the discovery of a virus that infects Bd, and which could be engineered to control the fungal disease.

The UC Riverside researchers who found the virus are excited about the implications of their discovery. In addition to helping them learn about how fungal pathogens rise and spread, it offers the hope of ending what they call a global amphibian pandemic. 

“Frogs control bad insects, crop pests, and mosquitoes. If their populations all over the world collapse, it could be devastating,” said UCR microbiology doctoral student and paper author Mark Yacoub. 

“They’re also the canary in the coal mine of climate change. As temperatures get warmer, UV light gets stronger, and water quality gets worse, frogs respond to that. If they get wiped out, we lose an important environmental signal,” Yacoub said. 

Scientists link certain gut bacteria to lower heart disease risk

Rod-shaped Oscillibacter sp. bacteria take up fluorescently labeled cholesterol (here shown in green).
Image Credit: Ahmed Mohamed 

Changes in the gut microbiome have been implicated in a range of diseases including type 2 diabetes, obesity, and inflammatory bowel disease. Now, a team of researchers at the Broad Institute of MIT and Harvard along with Massachusetts General Hospital has found that microbes in the gut may affect cardiovascular disease as well. In a study published in Cell, the team has identified specific species of bacteria that consume cholesterol in the gut and may help lower cholesterol and heart disease risk in people.

Members of Ramnik Xavier’s lab, Broad’s Metabolomics Platform, and collaborators analyzed metabolites and microbial genomes from more than 1,400 participants in the Framingham Heart Study, a decades-long project focused on risk factors for cardiovascular disease. The team discovered that bacteria called Oscillibacter take up and metabolize cholesterol from their surroundings, and that people carrying higher levels of the microbe in their gut had lower levels of cholesterol. They also identified the mechanism the bacteria likely use to break down cholesterol. The results suggest that interventions that manipulate the microbiome in specific ways could one day help decrease cholesterol in people. The findings also lay the groundwork for more targeted investigations of how changes to the microbiome affect health and disease.

“Our research integrates findings from human subjects with experimental validation to ensure we achieve actionable mechanistic insight that will serve as starting points to improve cardiovascular health,” said Xavier, who is a core institute member, director of the Immunology Program, and co-director of the Infectious Disease and Microbiome Program at the Broad. He is also a professor at Harvard Medical School and Massachusetts General Hospital.

Rice study identifies protein responsible for gas vesicle clustering in bacteria

Zongru Li (left) and George Lu
Photo Credit: Anna Stafford/Rice University

Gas vesicles are hollow structures made of protein found in the cells of certain microorganisms, and researchers at Rice University believe they can be programmed for use in biomedical applications.

“Inside cells, gas vesicles are packed in a beautiful honeycomb pattern. How this pattern is formed has never been thoroughly understood. We are presenting the first identification of a protein that can regulate this patterning, and we believe this will be a milestone in molecular microbiology,” said George Lu, assistant professor of bioengineering and a Cancer Prevention and Research Institute of Texas scholar.

Lu and colleagues have published their findings in a paper published in Nature Microbiology. The lead author is Zongru Li, a fourth-year bioengineering doctoral student in Lu’s Laboratory for Synthetic Macromolecular Assemblies.

“Gas vesicles are cylindrical tubes closed by conical end caps,” Li said. “They provide buoyancy within the cells of their native hosts.”

Researchers Identify Microbes That Help Plants Thwart Parasite

Sorghum crops in sub-Saharan Africa suffer heavy losses from the parasitic plant witchweed (Striga hermonthica). A new study shows how soil microbes can help protect sorghum from this pest and could be the basis for a soil probiotic treatment.
Photo Credit: Sabine

Bacteria that could help one of Africa’s staple crops resist a major pest have been identified by researchers at the University of California, Davis. Their findings, published in Cell Reports, could improve yields of sorghum, a mainstay of food and drink in West and East African countries.

About 20 percent of Africa’s sorghum crop is lost due to witchweed (Striga hermonthica), a parasitic plant that steals nutrients and water by latching onto the plant’s roots.

In a new study, UC Davis researchers show that soil microbes induce changes in sorghum roots that make the plant more resistant to infection by witchweed. They identified specific strains of bacteria that trigger these resistance traits and could be applied as a soil “probiotic” to improve sorghum yields in future.

“These microbes have great promise as soil additives that can help farmers grow sorghum successfully in sub-Saharan Africa,” said Siobhan Brady, a professor in the Department of Plant Biology and Genome Center and a senior author on the paper.