Tag Archives: Medical School

Identifying what makes some gut bacteria strains life-threatening in pre-term babies

Researchers from the Quadram Institute and University of East Anglia have identified what makes some strains of gut bacteria life-threatening in pre-term babies.

The findings will help identify and track dangerous strains and protect vulnerable neonatal babies.

A major threat to neonatal babies with extremely low birth weight is necrotizing enterocolitis (NEC).

Rare in full-term babies, this microbial infection exploits vulnerabilities destroying gut tissue leading to severe complications. Two out of five cases are fatal.

One bacterial species that causes especially sudden and severe disease is Clostridium perfringens. These are common in the environment and non-disease-causing strains live in healthy human guts.

So what makes certain strains so dangerous in preterm babies?

Prof Lindsay Hall and Dr Raymond Kiu from the Quadram Institute and UEA led the first major study on C. perfringens genomes from preterm babies, including some babies with necrotizing enterocolitis.

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The research team analyzed C. perfringens genomes from the faecal samples of 70 babies admitted to five UK Neonatal Intensive Care Units (NICUs).

Based on genomic similarities, they found one set had a lower capacity to cause disease. This allowed a comparison with the more virulent strains.

The less virulent group lacked genes responsible for production of a toxin called PFO and other factors needed for colonization and survival.

This study has begun to construct genomic signatures for C. perfringens associated with healthy preterm babies and those with necrotizing enterocolitis.

Exploring genomic signatures from hundreds of Clostridium perfringens genomes has allowed us potentially to discriminate between ‘good’ bacterial strains that live harmlessly in the preterm gut, and ‘bad’ ones associated with the devastating and deadly disease necrotizing enterocolitis.

We hope the findings will help with ‘tracking’ deadly C. perfringens strains in a very vulnerable group of patients – preterm babies.”

Prof Lindsay Hall, UEA’s Norwich Medical School and the Quadram Institute

Larger studies, across more sites and with more samples may be needed but this research could help identify better ways to control necrotizing enterocolitis.

The team previously worked alongside Prof Paul Clarke and clinical colleagues at the Norfolk and Norwich University Hospital NICU. And they demonstrated the benefits of providing neonatal babies with probiotic supplements.

The enterocolitis gut microbiome of neonatal infants is significantly disrupted, making it susceptible to C. perfringens overgrowth.

Prof Hall said: “Our genomic study gives us more data that we can use in the fight against bacteria that cause disease in babies – where we are harnessing the benefits of another microbial resident, Bifidobacterium, to provide at-risk babies with the best possible start in life.”

Dr Raymond Kiu, from the Quadram Institute, said: “Importantly, this study highlights Whole Genome Sequencing as a powerful tool for identifying new bacterial lineages and determining bacterial virulence factors at strain level which enables us to better understand disease.”

This research was supported by the Biotechnology and Biological Sciences Research Council, part of UKRI, and the Wellcome Trust.

The study was led by researchers at Quadram Institute and the University of East Anglia, in collaboration with colleagues at Imperial College, London, the University of Glasgow, the University of Cambridge, Newcastle University and Northumbria University.

‘Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains’ is published in Nature Microbiology.

Journal reference:

Kiu, R., et al. (2023). Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nature Microbiology. doi.org/10.1038/s41564-023-01385-z.

Long-ignored antibiotic could help fight against multi-drug resistant bacteria

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“The end of modern medicine as we know it.” That’s how the then-director general of the World Health Organization characterized the creeping problem of antimicrobial resistance in 2012. Antimicrobial resistance is the tendency of bacteria, fungus and other disease-causing microbes to evolve strategies to evade the medications humans have discovered and developed to fight them. The evolution of these so-called “super bugs” is an inevitable natural phenomenon, accelerated by misuse of existing drugs and intensified by the lack of new ones in the development pipeline.

Without antibiotics to manage common bacterial infections, small injuries and minor infections become potentially fatal encounters. In 2019, more than 2.8 million antimicrobial-resistant infections occurred in the United States, and more than 35,000 people died as a result, according to the Centers for Disease Control and Prevention (CDC). In the same year, about 1.25 million people died globally. A report from the United Nations issued earlier this year warned that number could rise to ten million global deaths annually if nothing is done to combat antimicrobial resistance.

For nearly 25 years, James Kirby, MD, director of the Clinical Microbiology Laboratory at Beth Israel Deaconess Medical Center (BIDMC), has worked to advance the fight against infectious diseases by finding and developing new, potent antimicrobials, and by better understanding how disease-causing bacteria make us sick. In a recent paper published in PLOS Biology, Kirby and colleagues investigated a naturally occurring antimicrobial agent discovered more than 80 years ago.

Using leading-edge technology, Kirby’s team demonstrated that chemical variants of the antibiotic, called streptothricins, showed potency against several contemporary drug-resistant strains of bacteria. The researchers also revealed the unique mechanism by which streptothricin fights off bacterial infections. What’s more, they showed the antibiotic had a therapeutic effect in an animal model at non-toxic concentrations. Taken together, the findings suggest streptothricin deserves further pre-clinical exploration as a potential therapy for the treatment of multi-drug resistant bacteria.

We asked Dr. Kirby to tell us more about this long-ignored antibiotic and how it could help humans stave off the problems of antimicrobial resistance a little longer.

Q: Why is it important to look for new antimicrobials? Can’t we preserve the drugs we have through more judicious use of antibiotics?

Stewardship is extremely important, but once you’re infected with one of these drug-resistant organisms, you need the tools to address it.

Much of modern medicine is predicated on making patients temporarily — and sometimes for long periods of time — immunosuppressed. When these patients get colonized with these multidrug-resistant organisms, it’s very problematic. We need better antibiotics and more choices to address multidrug resistance.

We have to realize that this is a worldwide problem, and organisms know no borders. So, a management approach for using these therapies may work well in Boston but may not in other areas of the world where the resources aren’t available to do appropriate stewardship.

Q: Your team investigated an antimicrobial discovered more than 80 years ago. Why was so little still known about it?

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The first antibiotic, penicillin, was discovered in 1928 and mass produced for the market by the early 1940s. While a game-changing drug, it worked on only one of the two major classes of bacteria that infect people, what we call gram-positive bacteria. The gram-positive bacteria include staphylococcal infections and streptococcal infections which cause strep throat, skin infections and toxic shock. There still was not an antibiotic for the other half of bacteria that can cause human infections, known as gram-negative organisms.

In 1942, scientists discovered this antibiotic that they isolated from a soil bacterium called streptothricin, possibly addressing gram-negative organisms. A pharmaceutical company immediately licensed the rights to it, but the development program was dropped soon after when some patients developed renal or kidney toxicity. Part of the reason for not pursuing further research was that several additional antibiotics were identified soon thereafter which were also active against gram-negatives. So, streptothricin got shelved.

Q: What prompted you to look at streptothricin specifically now?

It was partly serendipity. My research laboratory is interested in finding new, or old and forgotten, solutions to treat highly drug-resistant gram-negative pathogens like E. coli or Klebsiella or Acinetobacter that we commonly see in hospitalized, immunocompromised patients. The problem is that they’re increasingly resistant to many if not all of the antibiotics that we have available.

Part of our research is to understand how these superbugs cause disease. To do that, we need a way to manipulate the genomes of these organisms. Commonly, the way that’s done is to create a change in the organism linked with the ability to resist a particular antibiotic that’s known as a selection agent. But for these super resistant gram-negative pathogens, there was really nothing we could use. These bugs were already resistant to everything.

We started searching around for drugs that we could use, and it turns out these super resistant bugs were highly susceptible to streptothricin, so we were able to use it as a selection agent to do these experiments.

As I read the literature on streptothricin and its history, I had the realization that it was not sufficiently explored. Here was this antibiotic with outstanding activity against gram-negative bacteria – and we confirmed that by testing it against a lot of different pathogens that we see in hospitals. That raised the question of whether we could get really good antibiotic activity at concentrations that are not going to cause damage to the animal or person in treatment.

Q: But it did cause kidney toxicity in people in 1942. What would be different now?

What scientists were isolating in 1942 was not as pure as what we are working with today. In fact, what was then called streptothricin is actually a mixture of several streptothricin variants. The natural mixture of different types of streptothricins is now referred to as nourseothricin.

In animal models, we tested whether we could kill the harmful microorganism without harming the host using a highly purified single streptothricin variant. We used a very famous strain of Klebsiella pneumoniae called the Nevada strain which was the first pan-drug-resistant, gram-negative organism isolated in the United States, an organism for which there was no treatment. A single dose cleared this organism from an infected animal model while avoiding any toxicity. It was really remarkable. We’re still in the very early stages of development, but I think we’ve validated that this is a compound that’s worth investing in further studies to find even better variants that eventually will meet the properties of a human therapeutic.

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Q. How does nourseothricin work to kill gram-negative bacteria?

That’s another really important part of our study. The mechanism hadn’t been figured out before and we showed that nourseothricin acts in a completely new way compared to any other type of antibiotic.

It works by inhibiting the ability of the organism to produce proteins in a very sneaky way. When a cell makes proteins, they make them off a blueprint or message that tells the cell what amino acids to link together to build the protein. Our studies help explain how this antibiotic confuses the machinery so that the message is read incorrectly, and it starts to put together gibberish. Essentially the cell gets poisoned because it’s producing all this junk.

In the absence of new classes of antibiotics, we’ve been good at taking existing drugs like penicillin for example and modifying them; we’ve been making variations on the same theme. The problem with that is that the resistance mechanisms against penicillin and other drugs already exist. There’s a huge environmental reservoir of resistance out there. Those existing mechanisms of resistance might not work perfectly well against your new variant of penicillin, but they will evolve very quickly to be able to conquer it.

So, there’s recognition that what we really want is new classes of antibiotics that act in a novel way. That’s why streptothricin’s action uncovered by our studies is so exciting. It works in a very unique way not seen with any other antibiotic, and that is very powerful because it means there’s not this huge environmental reservoir of potential resistance.

Q. You emphasize these are early steps in development. What are the next steps?

My lab is working very closely with colleagues at Northeastern University who figured out a way to synthesize streptothricin from scratch in a way that will allow us to cast many different variants. Then we can look for ones that have the ideal properties of high potency and reduced toxicity.

We are also continuing our collaboration with scientists at Case Western Reserve University Medical Center, diving more deeply to understand exactly how this antibiotic works. Then we can use that fundamental knowledge in our designs of future variants and be smarter about how we try to make the best antibiotic.

We have great collaborators that have allowed us to pursue a project that crosses multiple fields. This work is an example of collaborative science really at its best.

Co-authors included first author Christopher E. Morgan and Edward W. Yuof Case Western Reserve; Yoon-Suk Kang,Alex B. Green, Kenneth P. Smith, Lucius Chiaraviglio, Katherine A. Truelson, Katelyn E. Zulauf, Shade Rodriguez, and Anthony D. Kang of BIDMC; Matthew G. Dowgiallo,Brandon C. Miller, and Roman Manetsch of Northeastern University.

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New compound with antibacterial activity shows promising results within one hour in laboratory trials

Resistance to antibiotics is a problem that alarms the medical and scientific community. Bacteria resistant to three different classes of antibiotics, known as multi-drug resistant (MDR) bacteria, are far from rare. Some are even resistant to all currently available treatments and are known as pan-drug resistant (PDR). They are associated with dangerous infections and listed by the World Health Organization (WHO) as priority pathogens for drug development with maximum urgency.

An article published in a special issue of the journal Antibiotics highlights a compound with antibacterial activity that presented promising results within one hour in laboratory trials.

The study was led by Ilana Camargo, last author of the article, and conducted during the doctoral research of first author Gabriela Righetto at the Molecular Epidemiology and Microbiology Laboratory (LEMiMo) of the University of São Paulo’s São Carlos Institute of Physics (IFSC-USP) in Brazil.

The compound we discovered is a new peptide, Pln149-PEP20, with a molecular framework designed to enhance its antimicrobial activity and with low toxicity. The results can be considered promising insofar as the trials involved pathogenic bacteria associated with MDR infections worldwide.”

Adriano Andricopulo, co-author of the article

Although novel antibacterial drugs are urgently needed, the pharmaceutical industry is notoriously uninterested in pursuing them, mainly because research in this field is time-consuming and costly, requiring very long lead times to bring viable active compounds to market.

The Center for Innovation in Biodiversity and Drug Discovery (CIBFar), a Research, Innovation and Dissemination Center (RIDC) set up and funded by FAPESP, looks for molecules that can be used to combat multidrug-resistant bacteria.

Camargo and Andricopulo are researchers at CIBFar, as are two other co-authors who study promising bactericidal compounds: Leila Beltramini and José Luiz Lopes.

For over a decade, the group formed by the collaboration between Beltramini and Lopes has analyzed Plantaricin 149 and its analogs. Plantaricins are substances produced by the bacterium Lactobacillus plantarum to combat other bacteria.

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Lactobacillus plantarum is commonly found in nature, especially in anaerobic plant matter, and in many fermented vegetable, meat and dairy products.

In the case of Plantaricin 149, Japanese researchers were the first to report its bactericidal action (in 1994) and since then scientists have been interested in obtaining more efficient synthetic analogs (molecules with small structural differences). In 2007, one of the first projects completed by the CIBFar team showed that the peptide inhibits pathogenic bacteria such as Listeria spp. and Staphylococcus spp. They then began studying synthetic analogs with stronger bactericidal activity than the original (causing more damage to the membrane of the combated microorganisms).

With the support of a scholarship from FAPESP, Righetto synthesized 20 analogs of Plantaricin 149, finding that Pln149-PEP20 had the best results so far and was also half the size of the original peptide. “The main advances in our research consist of the development of this smaller, more active and less toxic molecule, and the characterization of its action and propensity to develop resistance. It has proven to be highly promising in vitro – active against MDR bacteria and extensively resistant bacteria,” said Camargo, principal investigator for the project.

LEMiMo, the laboratory where the studies were conducted, has experience in characterizing bacterial isolates involved in outbreaks of hospital infections and holds a collection of bacteria selected for these trials in search of novel active compounds. The bacteria have the resistance profiles currently of greatest concern and were isolated during hospital outbreaks.

They are known in the scientific community by the term ESKAPE, an acronym for the scientific names of six highly virulent and antibiotic-resistant bacterial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.

Further research can now be conducted to investigate the molecule’s action mechanism in more depth, to look for formulations, and possibly to develop an application. “In terms of the action mechanism, it’s also possible to use the cell morphology of the bacteria to identify cellular pathways affected by the peptide,” Righetto said. “As for optimization, the molecule can be functionalized by being linked to macrostructures, and the amino acid sequence can be modified.” Research is also needed on its cytotoxicity and on its selectivity (whether it affects healthy cells).

“We’re living in times of major global public health hazards due to a lack of antimicrobials that can be used to treat infections caused by extremely resistant bacteria. Antimicrobial peptides are targets of great interest for the development of novel candidate drugs. This novel molecule has the potential to be used as an innovative antimicrobial therapy, but further modifications and molecular optimizations still need to be investigated,” Andricopulo said.

Publication of the article also involved Harvard Medical School’s Infectious Disease Institute in Boston (USA) via researchers Paulo José Martins Bispo and Camille André.

Journal reference:

Righetto, G. M., et al. (2023). Antimicrobial Activity of an Fmoc-Plantaricin 149 Derivative Peptide against Multidrug-Resistant Bacteria. doi.org/10.3390/antibiotics12020391.

How inert, sleeping bacteria spring back to life

Solving a riddle that has confounded biologists since bacterial spores -; inert, sleeping bacteria -; were first described more than 150 years ago, researchers at Harvard Medical School have discovered a new kind of cellular sensor that allows spores to detect the presence of nutrients in their environment and quickly spring back to life.

It turns out that these sensors double as channels through the membrane and remain closed during dormancy but rapidly open when they detect nutrients. Once open, the channels allow electrically charged ions to flow out through the cell membrane, setting in motion the shedding of protective spore layers and the switching on of metabolic processes after years -; or even centuries -; of dormancy.

The team’s findings, published April 28 in Science, could help inform the design of ways to prevent dangerous bacterial spores from lying dormant for months, even years, before waking up again and causing outbreaks.

This discovery solves a puzzle that’s more than a century old. How do bacteria sense changes in their environment and take action to break out of dormancy when their systems are almost completely shut down inside a protective casing?”

David Rudner, study senior author, professor of microbiology, Blavatnik Institute at HMS

How sleeping bacteria come back to life

To survive adverse environmental conditions, some bacteria go into dormancy and become spores, with biological processes put on hold and layers of protective armor around the cell.

These biologically inert mini fortresses allow bacteria to wait out periods of famine and shield themselves from the ravages of extreme heat, dry spells, UV radiation, harsh chemicals, and antibiotics.

For more than a century, scientists have known that when the spores detect nutrients in their environment, they rapidly shed their protective layers and reignite their metabolic engines. Although the sensor that enables them to detect nutrients was discovered almost 50 years ago, the means of delivering the wake-up signal, and how that signal triggers bacterial revival remained a mystery.

In most cases, signaling relies on metabolic activity and often involves genes encoding proteins to make specific signaling molecules. However, these processes are all shut off inside a dormant bacterium, raising the question of how the signal induces the sleeping bacteria to wake up.

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In this study, Rudner and team discovered that the nutrient sensor itself assembles into a conduit that opens the cell back up for business. In response to nutrients, the conduit, a membrane channel, opens, allowing ions to escape from the spore interior. This initiates a cascade of reactions that allow the dormant cell to shed its protective armor and resume growth.

The scientists used multiple avenues to follow the twists and turns of the mystery. They deployed artificial intelligence tools to predict the structure of the intricately folded sensor complex, a structure made of five copies of the same sensor protein. They applied machine learning to identify interactions between subunits that make up the channel. They also used gene-editing techniques to induce bacteria to produce mutant sensors as a way to test how the computer-based predictions played out in living cells.

“The thing that I love about science is when you make a discovery and suddenly all these disparate observations that don’t make sense suddenly fall into place,” Rudner said. “It’s like you’re working on a puzzle, and you find where one piece goes and suddenly you can fit six more pieces very quickly.”

Rudner described the process of discovery in this case as a series of confounding observations that slowly took shape, thanks to a team of researchers with diverse perspectives working together synergistically.

Along the way, they kept making surprising observations that confused them, hints that suggested answers that didn’t seem like they could possibly be true.

Stitching the clues together

One early clue emerged when Yongqiang Gao, an HMS research fellow in the Rudner lab, was conducting a series of experiments with the microbe Bacillus subtilis, commonly found in soil and a cousin to the bacterium that causes anthrax. Gao introduced genes from other bacteria that form spores into B. subtilis to explore the idea that the mismatched proteins produced would interfere with germination. Much to his surprise, Gao found that in some cases the bacterial spores reawakened flawlessly with a set of proteins from a distantly related bacterium.

Lior Artzi, a postdoctoral fellow in the lab at the time of this research, came up with an explanation for Gao’s finding. What if the sensor was a kind of receptor that acts like a closed gate until it detects a signal, in this case a nutrient like a sugar or an amino acid? Once the sensor binds to the nutrient, the gate pops open, allowing ions to flow out of the spore.

In other words, the proteins from distantly related bacteria would not need to interact with mismatched B. subtilis spore proteins, but instead simply respond to changes in the electric state of the spore as ions begin to flow.

Rudner was initially skeptical of this hypothesis because the receptor didn’t fit the profile. It had almost none of the characteristics of an ion channel. But Artzi argued the sensor might be made up of multiple copies of the subunit working together in a more complex structure.

AI has entered the chat

Another postdoc, Jeremy Amon, an early adopter of AlphaFold, an AI tool that can predict the structure of proteins and protein complexes, was also studying spore germination and was primed to investigate the nutrient sensor.

The tool predicted that a particular receptor subunit assembles into a five-unit ring known as a pentamer. The predicted structure included a channel down the middle that could allow ions to pass through the spore’s membrane. The AI tool’s prediction was just what Artzi had suspected.

Gao, Artzi, and Amon then teamed up to test the AI-generated model. They worked closely with a third postdoc, Fernando Ramírez-Guadiana and the groups of Andrew Kruse, HMS professor of biological chemistry and molecular pharmacology, and computational biologist Deborah Marks, HMS associate professor of systems biology.

They engineered spores with altered receptor subunits predicted to widen the membrane channel and found the spores awoke in the absence of nutrient signals. On the flip side, they generated mutant subunits that they predicted would narrow the channel aperture. These spores failed to open the gate to release ions and awake from stasis in the presence of ample nutrients to coax them out of dormancy.

In other words, a slight deviation from the predicted configuration of the folded complex could leave the gate stuck open or shut, rendering it useless as a tool for waking up the dormant bacteria.

Implications for human health and food safety

Understanding how dormant bacteria spring back into life is not just an intellectually tantalizing puzzle, Rudner said, but one with important implications for human health. A number of bacteria that are capable of going into deep dormancy for stretches of time are dangerous, even deadly pathogens: The powdery white form of weaponized anthrax is a made up of bacterial spores.

Another dangerous spore-forming pathogen is Clostridioides difficile, which causes life-threatening diarrhea and colitis. Illness from C. difficile typically occurs after use of antibiotics that kill many intestinal bacteria but are useless against dormant spores. After treatment, C. difficile awakens from dormancy and can bloom, often with catastrophic consequences.

Eradicating spores is also a central challenge in food-processing plants because the dormant bacteria can resist sterilization due to their protective armor and dehydrated state. If sterilization is unsuccessful, germination and growth can cause serious foodborne illness and massive financial losses.

Understanding how spores sense nutrients and rapidly exit dormancy can enable researchers to develop ways to trigger germination early, making it possible to sterilize the bacteria, or block germination, keeping the bacteria trapped inside their protective shells, unable to grow, reproduce, and spoil food or cause disease.

Journal reference:

Gao, Y., et al. (2023) Bacterial spore germination receptors are nutrient-gated ion channels. Science. doi.org/10.1126/science.adg9829.

Genomic study reveals Babesia duncani’s pathogenicity and virulence

‘Tis the season for hiking now that spring has arrived and temperatures are on the upswing. But with hikes come insect bites and on the increase in North America is babesiosis, a malaria-like disease spread especially between May and October by a tick.

Indeed, recent research suggests an increase in the incidence of diseases transmitted by ticks around the world, not just the United States and Canada, due likely to climate change and other environmental factors. Among the tick-borne pathogens, Babesia parasites, which infect and destroy red blood cells, are considered a serious threat to humans and animals. All cases of human babesiosis reported in the United States have been linked to either Babesia microti, B. duncani, or a B. divergens-like species.

Now a research team led by scientists at the University of California, Riverside, and Yale University reports the first high-quality nuclear genome sequence and assembly of the pathogen B. duncani. The team also determined the 3D genome structure of this pathogen that resembles Plasmodium falciparum, the malaria-causing parasite.

“Our data analysis revealed that the parasite has evolved new classes of multigene families, allowing the parasite to avoid the host immune response,” said Karine Le Roch, a professor of molecular, cell and systems biology at UC Riverside, who co-led the study with Choukri Ben Mamoun, a professor of medicine at Yale University.

According to Le Roch, who directs the UCR Center for Infectious Disease Vector Research, the study, published today in Nature Microbiology, not only identifies the molecular mechanism most likely leading to the parasite’s pathogenicity and virulence, but also provides leads for the development of more effective therapies.

By mining the genome and developing in vitro drug efficacy studies, we identified excellent inhibitors of the development of this parasite -; a pipeline of small molecules, such as pyrimethamine, that could be developed as effective therapies for treating and better managing human babesiosis. Far more scientific and medical attention has been paid to B. microti. The genome structure of B. duncani, a neglected species until now, will provide scientists with important insights into the biology, evolution, and drug susceptibility of the pathogen.”

Karine Le Roch, professor of molecular, cell and systems biology at UC Riverside

Human babesiosis caused by Babesia duncani is an emerging infectious disease in the U.S. and is often undetected because healthy individuals do not usually show symptoms. It has, however, been associated with high parasite burden, severe pathology, and death in multiple cases. Despite the highly virulent properties of B. duncani, little was known about its biology, evolution, and mechanism of virulence, and recommended treatments for human babesiosis against B. duncani are largely ineffective.

A strong immune system is required to fight the pathogen. A compromised immune system could lead to flu-like illness. The tick that spreads babesiosis is mostly found in wooded or grassy areas and is the same tick that transmits bacteria responsible for Lyme disease. As a result, around 20% of patients with babesiosis are co-infected with Lyme disease.

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B. duncani mostly infects deer, which serve as the reservoir host during the pathogen’s asexual development. The parasite’s sexual cycle occurs in the tick after the tick bites the infected deer. When this tick bites humans, infection begins. The full life cycle of Babesia parasites has not yet been determined. The tick that spreads babesiosis, called Dermacentor albipictus, lives longer than mosquitoes and could facilitate a long life cycle for B. duncani.

Even though scientists are discovering more Babesia species, diagnostics are mostly developed for B. microti. Le Roch is already working with Stefano Lonardi, a professor of computer science and engineering at UCR and co-first author of the study, on new Babesia strains that have evolved.

“The Babesia genomes are not very long,” said Lonardi, who assembled the B. duncani strain. “But they are challenging to assemble due to their highly repetitive content and can require years of research. Once the genome is assembled and annotated, it can provide valuable information, such as how the genes are organized, which genes are transcribed during infection, and how the pathogen avoids the host’s immune system.”

In older and immunocompromised people, if B. duncani is left unattended, babesiosis could worsen and lead to death. Once the pathogen enters the body and red blood cells start to get destroyed, fever, headache, and nausea can follow. People who get bitten by the ticks often don’t feel the bite, which complicates diagnosis. Skin manifestations of babesiosis are rare, Lonardi said, and difficult to separate from Lyme disease.

Le Roch and Lonardi urge people to be mindful of ticks when they go hiking.

“Check yourself for tick bites,” Le Roch said. “When you see your physician don’t forget to let them know you go hiking. Most physicians are aware of Lyme disease but not of babesiosis.”

Next the team plans to study how B. duncani survives in the tick and find novel vector control strategies to kill the parasite in the tick.

Le Roch, Mamoun, and Lonardi were joined in the study by colleagues at UCR, Yale School of Medicine, Université de Montpellier (France), Instituto de Salud Carlos III (Spain), Universidad Nacional Autónoma de México, and University of Pennsylvania. Pallavi Singh at Yale and Lonardi contributed equally to the study. The B. duncani genome, epigenome, and transcriptome were sequenced at UCR and Yale.

The study was supported by grants from the National Institutes of Health, Steven and Alexandra Cohen Foundation, Global Lyme Alliance, National Science Foundation, UCR, and Health Institute Carlos III.

Journal reference:

Singh, P., et al. (2023). Babesia duncani multi-omics identifies virulence factors and drug targets. Nature Microbiology. doi.org/10.1038/s41564-023-01360-8.

Mosquitoes’ saliva contains immune-dampening substances to increase infectivity of dengue viruses

The saliva of mosquitoes infected with dengue viruses contains a substance that thwarts the human immune system and makes it easier for people to become infected with these potentially deadly viruses, new research reveals.

Dengue has spread in recent years to Europe and the Southern United States in addition to longstanding hotspots in tropical and subtropical areas such as Southeast Asia, Africa and Latin America. The new discovery, from a University of Virginia School of Medicine scientist and his collaborators, helps explain why the disease is so easily transmitted and could eventually lead to new ways to prevent infection.

“It is remarkable how clever these viruses are – they subvert mosquito biology to tamp down our immune responses so that infection can take hold,” said Mariano A. Garcia-Blanco, MD, PhD, who recently joined UVA as chair of the Department of Microbiology, Immunology and Cancer Biology. “There is no doubt in my mind that better understanding of the fundamental biology of transmission will eventually lead to effective transmission-blocking measures.”

Further, Garcia-Blanco suspects that researchers will find similar immune-dampening substances accompanying other mosquito-borne infections such as Zika, West Nile and yellow fever.

Our findings are almost certainly going to be applicable to infections with other flaviviruses. The specific molecules here are unlikely to apply to malaria, but the concept is generalizable to viral infections.”

Mariano A. Garcia-Blanco, MD, PhD, UVA

Understanding dengue

Approximately half the world’s population is at risk for dengue, and roughly 400 million people are infected every year. Dengue’s symptoms, including fever, nausea and skin rash, are often mistaken for other diseases. Most people will have mild cases, but about 1 in 20 will develop severe illness that can lead to shock, internal bleeding and death. Unfortunately, it’s possible to contract dengue repeatedly, as it is caused by four related viruses transmitted primarily by the Aedes aegypti species of mosquito. There is no treatment, but the new discovery from Garcia-Blanco and his colleagues identifies an important contributor to the disease’s spread as researchers seek to find better ways to combat it.

Garcia-Blanco and his team found that infected mosquitoes’ saliva contained not just the expected dengue virus but a powerful conspirator: molecules produced by the virus that can blunt the body’s immune response. The injection of these molecules, called sfRNAs, during the mosquito bite makes it more likely that the victim will become infected with dengue, the scientists conclude.

“By introducing this RNA at the biting site, dengue-infected saliva prepares the terrain for an efficient infection and gives the virus an advantage in the first battle between it and our immune defenses,” the researchers write in a new scientific paper outlining their findings.

Scientists who study mosquitoes previously had suspected that the insects’ saliva might contain some type of payload to enhance the potential for infection. Garcia-Blanco’s team’s new findings pinpoints one weapon in the viruses’ arsenal and opens the door to finding new ways to help reduce transmission and control the disease’s spread. For now, the best way to avoid getting seriously sick with dengue remains to avoid getting bitten.

“It’s incredible that the virus can hijack these molecules so that their co-delivery at the mosquito bite site gives it an advantage in establishing an infection,” said researcher Tania Strilets, a graduate student with Garcia-Blanco and co-first author of the scientific paper. “These findings provide new perspectives on how we can counteract dengue virus infections from the very first bite of the mosquito.”

Findings published

The researchers have published their findings in the scientific journal PLOS Pathogens. The team consisted of Shih-Chia Yeh, Strilets, Wei-Lian Tan, David Castillo, Hacène Medkour, Félix Rey-Cadilhac, Idalba M. Serrato-Pomar, Florian Rachenne, Avisha Chowdhury, Vanessa Chuo, Sasha R. Azar, Moirangthem Kiran Singh, Rodolphe Hamel, Dorothée Missé, R. Manjunatha Kini, Linda J. Kenney, Nikos Vasilakis, Marc A. Marti-Renom, Guy Nir, Julien Pompon and Garcia-Blanco. Most of Garcia-Blanco’s work on the project was conducted while he was at Duke-NUS Medical School and the University of Texas Medical Branch.

Journal reference:

Yeh, S.-C., et al. (2023). The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLOS Pathogens. doi.org/10.1371/journal.ppat.1011224.

New study focuses on genetic diversity of E. coli bacteria in hospitalized patients

The human intestine is an environment inhabited by many bacteria and other microorganisms collectively known as the gut microbiome, gut microbiota or intestinal flora. In most people, it contributes to wellness. A healthy gut indicates a stronger immune system, improved metabolism, and a healthy brain and heart, among other functions.

Escherichia coli is one of the bacteria found in practically everyone’s gut microbiota, where it performs important functions, such as producing certain vitamins.

But there’s a vast amount of genetic diversity in the species. Some of its members are pathogenic and can cause diseases such as urinary tract infections. E. coli is the main agent of this type of infection among both healthy people and hospitalized patients or users of healthcare services.”

Tânia Gomes do Amaral, Head of the Experimental Enterobacterial Pathogenicity Laboratory (LEPE), Federal University of São Paulo’s Medical School (EPM-UNIFESP), Brazil

Amaral is first author of an article published in the journal Pathogens on the virulence of these bacteria and their resistance to antibiotics in hospitalized patients.

“Our study focused on hospitalized patients because patients who stay in hospital for a long period are more likely to undergo various procedures, such as urine catheter insertion or venous access. Although these procedures are performed to assure life support, they may facilitate the entry of bacteria into the organism and cause an infection,” Amaral explained.

She earned a PhD in microbiology from EPM-UNIFESP in 1988, conducting part of her research at New York University Medical School and the Center for Vaccine Development at the University of Maryland, Baltimore (UMB) in the United States.

The article reports the findings of a broader study led by Amaral, with 12 co-authors who are researchers and graduate students, on the virulence and drug resistance of E. coli strains associated with urinary tract infections. The study was supported by FAPESP via three projects (18/17353-7, 19/21685-8 and 17/14821-7).

The main aim of this part of the study, described in the master’s dissertation of José Francisco Santos Neto, was to evaluate the diversity and drug resistance of pathogenic E. coli strains isolated from the gut microbiota of inpatients, and to analyze the frequency of endogenous infection (caused by bacteria from the patient’s own microbiota).

The UNIFESP group first investigated the genetic diversity and drug resistance of E. coli strains isolated from the gut microbiota of hospitalized patients, sequencing these strains as well as others isolated from their urine and comparing the results in order to evaluate dissemination of the bacteria in the hospital environment.

“We also compared the genomes of these strains with those of E. coli strains isolated in different parts of the world in order to see if any globally disseminated pathogenic bacteria were present in the study sample,” said Ana Carolina de Mello Santos, a postdoctoral researcher working on the LEPE team.

Urinary tract infections proved to be endogenous for the vast majority of the patients in the study (more than 70%). The results also showed that the patients’ gut microbiota contained at least two genetically different populations of E. coli and that about 30% were colonized by non-lactose-fermenting E. coli strains, which are less common, with some of the patients studied having only such strains in their gut microbiota.

“This finding is most interesting because previous research conducted in other countries to analyze the composition of human gut microbiota didn’t investigate non-lactose-fermenting E. coli,” Santos said.

The authors also note the presence of bacteria with all the genetic markers required for classification as pathogenic and the detection of pathogenic bacteria in the gut microbiota of all patients that had not yet developed an infection. “Hospitalized patients are more susceptible to infection because by definition they are already unwell. Colonization by pathogens is the first step in the spread of hospital-acquired infections now so frequent worldwide,” Santos said.

With regard to antibiotics and other antimicrobials, the authors stress that drug resistance is also a growing global problem, and enterobacterial resistance to third-generation cephalosporins as well as colistin is critical. In all patients whose gut microbiota was colonized by drug-resistant bacteria, the same bacteria also caused endogenous urinary tract infections. In other words, the multidrug-resistant bacteria colonized the gut and traveled to the urinary tract, where they caused an infection.

“In light of these findings, early assessment of gut microbiota in hospitalized patients, at least in cases of E. coli infection, can facilitate and guide their treatment, while also identifying patients who risk progressing to extra-intestinal diseases such as urinary tract infections, which were part of the focus for our study,” Amaral said. “We don’t yet know whether the findings also apply to other bacteria found in gut microbiota, such as the genera Klebsiella, Enterobacter, Pseudomonas and others that can cause infections when they travel to extra-intestinal sites.”

These bacterial genera tend to be even more drug-resistant than E. coli, representing a major public health problem in the hospital environment. As the researchers noted, the World Health Organization (WHO) considers E. coli strains resistant to cephalosporin and colistin to be a critical global health threat. “The presence in human gut microbiota of drug-resistant bacteria associated with severe infectious disease is a matter of great concern, not least because they could spread to people outside the hospital environment,” Amaral said.

Another point raised by the study is the importance of finding out when colonization of the patient’s gut by drug-resistant virulent bacteria occurred. The authors of the article were unable to determine whether the bacteria resistant to cephalosporins and colistin colonized the patients before or after they were hospitalized.

By analyzing the genomes of the strains, however, the researchers were able to identify global risk clones that can cause severe disease and are associated with antimicrobial resistance. “One such clone found in the gut microbiota of two patients was identical to others isolated from urinary tract infections in Londrina, Paraná [a state in South Brazil], and in the United States, as well as European and Asian countries. This shows that some strains found in the study are clones generally associated with infections in all regions of the world,” Amaral said.

This type of information is important when patients are hospitalized. Knowledge of bacterial virulence and drug resistance can be used to prevent infection in parts of the organism outside the intestine and stop the bacteria from spreading to other patients in the same hospital.

Journal reference:

Santos-Neto, J.F., et al. (2023) Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens. doi.org/10.3390/pathogens11121528.

New analysis shows how convalescent plasma can be used as effective, low-cost COVID-19 treatment

Three years into the COVID-19 pandemic, new variant outbreaks continue to fuel economic disruptions and hospitalizations across the globe. Effective therapies remain unavailable in much of the world, and circulating variants have rendered monoclonal antibody treatments ineffective. But a new analysis shows how convalescent plasma can be used as an effective and low-cost treatment both during the COVID-19 pandemic and in the inevitable pandemics of the future.

In astudy published in Clinical Infectious Diseases, an international team of researchers analyzed clinical data and concluded that among outpatients with COVID-19, antibodies to SARS-CoV-2 given early and in high dose reduced the risk of hospitalization.

If the results of this meta-analysis had somehow been available in March of 2020, then I am certain that millions of lives would have been saved around the world.”

Dr. Adam C. Levine, study author, professor of emergency medicine at Brown University’s Warren Alpert Medical School

While several other early treatments for COVID-19 have had similar results, including antivirals like Paxlovid and monoclonal antibodies, only convalescent plasma, the researchers concluded, is likely to be both available and affordable for the majority of the world’s population both now and early in the next viral pandemic.

“These findings will be helpful for this pandemic, especially in places like China, India and other parts of the world that lack access to antiviral medications like Paxlovid,” Levine said. “And because it provides information on how to more effectively use convalescent plasma as a therapy, this will be even more helpful in the next pandemic. This study is essentially a roadmap for how to do this right the next time.”

Blood plasma from people who have recovered from COVID-19 and contains antibodies against SARS-CoV-2 was used as a treatment early in the pandemic, Levine said -; months before monoclonal antibody treatment or vaccines became available, and more than a year before an effective oral drug therapy was clinically available.

Although convalescent plasma seemed promising, outpatient research was limited, and studies that did exist showed mixed results. One problem was that most studies were conducted in patients already hospitalized with COVID-19, Levine said, largely due to the convenience of conducting research with this population. The objective in the new study was to review all available randomized controlled trials of convalescent plasma in non-hospitalized adults with COVID-19 to determine whether early treatment can reduce the risk of hospitalization.

The analysis included data from five studies conducted in four countries, including Argentina, the Netherlands, Spain, and two in the United States. Levine previously supervised enrollment at Rhode Island Hospital in a clinical trial led by Johns Hopkins Medicine and Johns Hopkins Bloomberg School of Public Health. Across the five studies, a total of 2,620 adult patients had received transfusions of convalescent plasma from January 2020 to September 2022. The researchers conducted an individual participant data meta-analysis to assess how the transfusion timing and dose impacted the patient’s risk of hospitalization during the 28 days after infection.

In their analysis, the researchers found that 160 (12.2%) of 1,315 control patients were hospitalized compared with 111 (8.5%) of 1,305 patients treated with COVID-19 convalescent plasma -; 30% fewer hospitalizations.

Notably, the strongest effects were seen in patients treated both early in the illness and with plasma with high levels of antibodies. In these patients, the reduction in hospitalization was over 50%.

For future pandemics, the goal is to use plasma from donors who have high levels of antibodies, said corresponding study author Dr. David J. Sullivan, a professor of molecular microbiology and immunology at Johns Hopkins Bloomberg School of Public Health and School of Medicine. “This research suggests that we have been underdosing convalescent plasma for many previous pathogens, which impacts effectiveness,” Sullivan said. “It bears repeating: Early and high levels of antibodies increased the beneficial efficacy.”

Levine explained that because convalescent plasma was the only treatment available at the beginning of the pandemic, it was used widely -; and often incorrectly, on hospitalized patients who were already experiencing severe symptoms late in the course of COVID-19. Those symptoms were due to a ramped-up immune response to the virus, not the virus itself, Levine explained.

“By the time the patient was at the point where they’d reached the inflammatory phase that caused severe symptoms, it was too late for treatments like convalescent plasma or even monoclonal antibodies to work,” he said.

What is now known is that convalescent plasma works best when given early in the course of illness. That’s when it can neutralize the virus and get ahead of the body mounting an intense immune response, thereby preventing hospitalization and death, Levine said.

The five drug treatment trials in the analysis took place at a variety of global health care sites, he noted, including nursing homes, outpatient clinics and emergency departments. The diversity across the studies is a sign that the data is likely generalizable to many other types of populations and settings around the world, said Levine, who also directs the Center for Human Rights and Humanitarian Studies at the Watson Institute for International and Public Affairs at Brown.

Levine cited another recently published study in JAMA Network Open that showed that convalescent plasma is effective in reducing mortality in immunocompromised patients. This new meta-analysis provides evidence that convalescent plasma can also be effective in the larger population of adults who are not immunocompromised.

The U.S. Food and Drug Administration allowed early convalescent plasma use in December 2021 for those patients with COVID-19 who were also immunocompromised, but not yet for patients with COVID-19 who are not immunocompromised. The authors said they hope the new study will push the FDA, and other countries around the world, to make early treatment with COVID-19 convalescent plasma available to a much larger group of patients at risk for hospitalization.

A treatment that evolves with the pandemic

The findings come at a time when monoclonal antibodies, the most commonly used treatment for COVID-19, have been shown to be ineffective against new variants of the virus. In November, the FDA revoked emergency authorization of the last monoclonal antibody treatment because it wasn’t expected to have much of an effect against Omicron sub-variants.

In contrast to monoclonal antibody therapies, Levine said, convalescent plasma donated by patients who have recovered from the virus is a treatment that evolves with the pandemic. Because it has antibodies that attach to multiple different parts of the virus, there are still opportunities to attach to a receptor even after the virus mutates and morphs some of its receptors. It’s also less expensive to produce than pharmaceutical antivirals.

In the first year of the pandemic, Levine said, before the development of vaccines and effective treatments, researchers tried many treatment strategies in order to quickly find something that worked to save lives.

“When the next big pandemic hits, we’re going to be in a very similar situation,” Levine said. “Yet at least next time, we’ll have research like this to inform our strategy.”

Journal reference:

Levine, A.C., et al. (2023) COVID-19 Convalescent Plasma Outpatient Therapy to Prevent Outpatient Hospitalization: A Meta-analysis of Individual Participant Data From Five Randomized Trials. Clinical Infectious Diseases. doi.org/10.1093/cid/ciad088.

Researchers find a way to block anaphylaxis caused by peanut allergies

Researchers from Indiana University School of Medicine have found a way to block anaphylaxis caused by peanut allergies. The groundbreaking discovery could lead to life-saving therapeutics for people with severe peanut allergies.

There are treatments for symptoms in patients with food allergies, but few preventive therapies other than strict dietary avoidance or oral immunotherapy. Neither of those options is successful in all patients.”

Mark Kaplan, PhD, chair of the Department of Microbiology and Immunology and senior author of the study

The team details their findings in a newly published article in Science Translational Medicine. When someone is allergic to a food, it is a result of allergen proteins cross-linking allergen specific immunoglobulin E (IgE) on the surface of mast cells and basophils. Activation of these cells can lead to anaphylaxis, a severe, life-threatening allergic reaction that can occur very quickly after exposure to an allergen.

Researchers developed peanut-specific inhibitors called covalent heterobivalent inhibitor (cHBI), that successfully blocked mast cell or basophil degranulation and anaphylaxis in an animal model.

“The inhibitor prevented allergic reactions for more than two weeks when given before allergen exposure,” said Nada Alakhras, lead author and a graduate student in the Department of Biochemistry and Molecular Biology. “The inhibitor also prevented fatal anaphylaxis and attenuated allergic reactions when given soon after the onset of symptoms.”

“These new findings suggest that cHBI has the potential to be an effective preventative for peanut-specific allergic responses in patients,” said Basar Bilgicer, PhD, professor of chemical and biomedical engineering at the University of Notre Dame and co-senior author of the study.

The inhibitor has not been tested in human patients yet. Researchers are now doing further testing in animal models to evaluate efficacy and toxicity before moving to clinical trials.

The research was funded in part by the Falk Medical Research Trust Award. Other authors include Anthony L. Sinn, Wenwu Zhang, PhD, MS, and Karen E. Pollok, PhD from IU School of Medicine as well as Gyoyeon Hwang, Jenna Sjoerdsma, Emily K. Bromley, and Jaeho Shin from the University of Notre Dame and Scott A. Smith, MD, PhD from Vanderbilt University Medical Center.

Journal reference:

Alakhras, N.S., et al. (2023) Peanut allergen inhibition prevents anaphylaxis in a humanized mouse model. Science Translational Medicine. doi.org/10.1126/scitranslmed.add6373.

Gut-dwelling bacteria can promote the desire to exercise, study shows

Some species of gut-dwelling bacteria activate nerves in the gut to promote the desire to exercise, according to a study in mice that was led by researchers at the Perelman School of Medicine at the University of Pennsylvania. The study was published today in Nature, and reveals the gut-to-brain pathway that explains why some bacteria boost exercise performance.

In the study, the researchers found that differences in running performance within a large group of lab mice were largely attributable to the presence of certain gut bacterial species in the higher-performing animals. The researchers traced this effect to small molecules called metabolites that the bacteria produce-;metabolites that stimulate sensory nerves in the gut to enhance activity in a motivation-controlling brain region during exercise.

If we can confirm the presence of a similar pathway in humans, it could offer an effective way to boost people’s levels of exercise to improve public health generally.”

Christoph Thaiss, PhD, Study Senior Author, Assistant Professor of Microbiology, Penn Medicine

Thaiss and colleagues set up the study to search broadly for factors that determine exercise performance. They recorded the genome sequences, gut bacterial species, bloodstream metabolites, and other data for genetically diverse mice. They then measured the amount of daily voluntary wheel running the animals did, as well as their endurance.

The researchers analyzed these data using machine learning, seeking attributes of the mice that could best explain the animals’ sizeable inter-individual differences in running performance. They were surprised to find that genetics seemed to account for only a small portion of these performance differences-;whereas differences in gut bacterial populations appeared to be substantially more important. In fact, they observed that giving mice broad-spectrum antibiotics to get rid of their gut bacteria reduced the mice’s running performance by about half.

Ultimately, in a years-long process of scientific detective work involving more than a dozen separate laboratories at Penn and elsewhere, the researchers found that two bacterial species closely tied to better performance, Eubacterium rectale and Coprococcus eutactus, produce metabolites known as fatty acid amides (FAAs). The latter stimulate receptors called CB1 endocannabinoid receptors on gut-embedded sensory nerves, which connect to the brain via the spine. The stimulation of these CB1 receptor-studded nerves causes an increase in levels of the neurotransmitter dopamine during exercise, in a brain region called the ventral striatum.

The striatum is a critical node in the brain’s reward and motivation network. The researchers concluded that the extra dopamine in this region during exercise boosts performance by reinforcing the desire to exercise.

“This gut-to-brain motivation pathway might have evolved to connect nutrient availability and the state of the gut bacterial population to the readiness to engage in prolonged physical activity,” said study co-author, J. Nicholas Betley, PhD, an associate professor of Biology at the University of Pennsylvania’s School of Arts and Sciences. “This line of research could develop into a whole new branch of exercise physiology.”

The findings open up many new avenues of scientific investigation. For example, there was evidence from the experiments that the better-performing mice experienced a more intense “runner’s high”-;measured in this case by a reduction in pain sensitivity-;hinting that this well-known phenomenon is also at least partly controlled by gut bacteria. The team now plans further studies to confirm the existence of this gut-to-brain pathway in humans.

Apart from possibly offering cheap, safe, diet-based ways of getting ordinary people running and optimizing elite athletes’ performance, he added, the exploration of this pathway might also yield easier methods for modifying motivation and mood in settings such as addiction and depression.

The study was led by Penn Medicine scientist Lenka Dohnalová. Other Penn Medicine authors include: Patrick Lundgren, Jamie Carty, Nitsan Goldstein, Lev Litichevskiy, Hélène Descamps, Karthikeyani Chellappa, Ana Glassman, Susanne Kessler, Jihee Kim, Timothy Cox, Oxana Dmitrieva-Posocco, Andrea Wong, Erik Allman, Soumita Ghosh, Nitika Sharma, Kasturi Sengupta, Mark Sellmyer, Garret FitzGerald, Andrew Patterson, Joseph Baur, Amber Alhadeff, and Maayan Levy.

The study was supported in part by the National Institutes of Health (S10-OD021750, DP2AG067492, R01-DK-129691, , P01-DK119130 and R01-DK115578), the Pew Charitable Trust, the Edward Mallinckrodt, Jr. Foundation, the Agilent Early Career Professor Award, the Global Probiotics Council, the IDSA Foundation, the Thyssen Foundation, the Human Frontier Science Program, and Penn Medicine, including the Dean’s Innovation Fund.

Journal reference:

Dohnalová, L., et al. (2022) A microbiome-dependent gut–brain pathway regulates motivation for exercise. Nature. doi.org/10.1038/s41586-022-05525-z.