Tag Archives: Lungs

Experimental decoy provides long-term protection from SARS-Cov-2 infection

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An experimental “decoy” provided long-term protection from infection by the pandemic virus in mice, a new study finds.

Led by researchers at NYU Grossman School of Medicine, the work is based on how the virus that causes COVID-19, SARS-CoV-2, uses its spike protein to attach to a protein on the surface of the cells that line human lungs. Once attached to this cell surface protein, called angiotensin converting enzyme 2 (ACE2), the virus spike pulls the cell close, enabling the virus to enter the cell and hijack its machinery to make viral copies.

Earlier in the pandemic, pharmaceutical companies designed monoclonal antibodies to glom onto the spike and neutralize the virus. Treatment of patients soon after infection was successful in preventing hospitalization and death. However the virus rapidly evolved through random genetic changes (mutations) that altered the spike’s shape enough to evade even combinations of therapeutic monoclonal antibodies. Thus, such antibodies, which neutralized early variants, became about 300 times less effective against more recent delta and omicron variants.

Published online this week in the Proceedings of the National Academy of Sciences, the study describes an alternative approach from which the virus cannot escape. It employs a version of ACE2, the surface protein to which the virus attaches, which, unlike the natural, cell-bound version, is untethered from the cell surface. The free-floating “decoy” binds to the virus by its spikes so that it can no longer attach to ACE2 on cells in airways. Unlike the monoclonal antibodies, which are shaped to interfere with a certain spike shape, the decoy mimics the spike’s main target, and the virus cannot easily evolve away from binding to ACE2 and still invade cells.

Treatment with the decoy, either by injection or droplets in the nose, protected 100 percent of the study mice when they were infected in the lab with an otherwise lethal dose of SARS-CoV-2. The decoy lowered the virus load in the mice by 100,000-fold, while mice exposed to a non-active control treatment died. Decoy treatment of mice that were already infected with SARS-CoV-2 caused a rapid drop in viral levels and return to health. This suggests that the decoy could be effective as a therapy post-infection, similar to monoclonal antibodies, the researchers say.

What is remarkable about our study is that we delivered the decoy using a harmless, adeno-associated virus or AAV vector, a type of gene therapy that has been found in previous studies to be safe for use in humans. The viral vector instructs cells in the body to produce the decoy so that the mouse or person is protected long-term, without the need for continual treatment.”

Nathanial Landau, PhD, senior study author, professor, Department of Microbiology at NYU Langone Health

Administered with the vector, says Landau, the treatment caused cells, not only to make the decoy, but to continue making it for several months, and potentially for years.

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Importantly, vaccines traditionally include harmless parts of a virus they are meant to protect against, which trigger a protective immune response should a person later be exposed. Vaccines are less effective, however, if a person’s immune system has been compromised, by diseases like cancer or in transplant patients treated with drugs that suppress the immune response to vaccination. Decoy approaches could be very valuable for immunocompromised patients globally, adds Landau.

Future pandemics

For the new study, the research team made key changes to a free ACE2 receptor molecule, and then fused the spike-binding part of it to the tail end of an antibody with the goal of strengthening its antiviral effect. Attaching ACE2 to the antibody fragment to form what the team calls an “ACE2 microbody” increases the time that the molecule persists in tissues (its half-life). The combination also causes the molecules to form dimers, mirror-image molecular pairs that increase the strength with which the decoy attaches to the viral spike.

Whether administered via injection into muscle, or through droplets in the nasal cavity, the study’s AAV vectors provided mice with long-lasting protection COVID infection, including the current Omicron variants.

The approach promises to be effective even if another coronavirus, a type of virus common in birds and bats or apes, were to be transferred to humans in the future, an event termed “zoonosis.” As long as the future virus also uses ACE2 to target cells, the decoy would be ready for “off-the-shelf” soon after an outbreak. If the virus were to somehow switch its receptor a different protein on the surface of lung cells, the decoy could be modified to target the new virus, says Landau.

Along with Landau, the study authors were Takuya Tada and Julia Minnee in the Department of Microbiology at NYU Grossman School of Medicine. The study was supported by a grant from the National Institutes of Health.

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Journal reference:

Tada, T., et al. (2023) Vectored immunoprophylaxis and treatment of SARS-CoV-2 infection in a preclinical model. PNAS. doi.org/10.1073/pnas.2303509120.

Mouse study offers clues to developing an effective vaccine for Klebsiella bacteria

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A mouse study at Washington University School of Medicine in St. Louis points to data that could be key to developing an effective vaccine for the bacterium Klebsiella pneumoniae. The bug is often resistant to antibiotics, making it difficult to treat in some.

In the U.S., the bacterium Klebsiella pneumoniae is a common cause of urinary tract infection, bloodstream infection and pneumonia. While infections with the bacterium can be easily treated in some, Klebsiella has a dangerous flip side: It also is frequently resistant to antibiotics, making it extraordinarily difficult to treat in others. About half of people infected with a hypervirulent, drug-resistant strain of the bacterium die.

Scientists are working on vaccines for Klebsiella, but the optimal vaccine design is still unknown. However, a new study in mice by scientists at Washington University School of Medicine in St. Louis and Omniose, a St. Louis startup company specializing in vaccine production, provides critical data that could be key to developing an effective vaccine for Klebsiella. The findings, published in PLoS Pathogens, are a step toward taming the superbug.

When you think about the bugs that can be resistant to almost all antibiotics — the scary superbugs in the news — a lot of them are strains of Klebsiella. For a long time, the bacterium wasn’t even a pressing issue. But now it is, due to an explosion in antibiotic-resistant Klebsiella. Our goal is to diminish Klebsiella’s superbug status by developing a vaccine before hypervirulent or resistant strains sicken and kill even more people.”

David A. Rosen, MD, PhD, study’s senior author, assistant professor of pediatrics and of molecular microbiology at Washington University

Hypervirulent Klebsiella strains have spread globally, often causing community-acquired infections.

In the U.S., Klebsiella infections primarily occur in health-care facilities where medically vulnerable patients are immunocompromised, require long courses of antibiotics to treat other conditions, have chronic diseases, or are elderly people or newborns. “But now we’re seeing the emergence of hypervirulent strains dangerous enough to cause serious disease or death among healthy people in the community,” Rosen said.

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Most concerning among scientists are the strains of Klebsiella impervious to carbapenems, a class of broad-spectrum antibiotics used to treat the most severe bacterial infections. For this reason, the World Health Organization and the U.S. Centers for Disease Control and Prevention have identified carbapenem-resistant Klebsiella as an urgent threat to public health.

The rod-shaped bacterium is immobile and, like chocolate-covered candies, encapsulated in sugar coatings. In the new study, researchers created two experimental vaccines based on two different sugars, or polysaccharides, on Klebsiella’s surface: the terminal sugars on lipopolysaccharide, called O-antigen, and a capsular polysaccharide, or K-antigen. Since sugars by themselves tend to produce weak immune responses, the researchers linked each of the sugars to a protein to boost the immune response, creating so-called conjugate vaccines. Sugar-protein conjugate vaccines have proven successful in combating several bacteria including Streptococcus pneumoniae, the most common cause of pneumonia. Historically, this connection between the sugar and protein carrier has been achieved using synthetic chemistry in a test tube; however, the vaccines created for this study are called bioconjugate vaccines, because the researchers connected the sugar to the protein all within an engineered bacteria system.

Once the vaccines were created, the researchers tested the experimental bioconjugate vaccines’ ability to protect mice from disease caused by Klebsiella.

“It turned out that the capsule vaccine was far superior to the O-antigen vaccine,” said the study’s first author, Paeton Wantuch, PhD, a postdoctoral associate in Rosen’s lab. “Mice that received the capsule vaccine were significantly more likely to survive Klebsiella infection in their lungs or their bloodstream than mice that received the O-antigen vaccine.”

Both vaccines elicited high levels of antibodies against their respective targets. But the antibodies against the O-antigen just weren’t as effective as the ones against the capsule. In some strains of Klebsiella, the O-antigen may be obscured by other sugars, so the antibodies that target the O-antigen cannot make contact with their target.

“Our findings suggest that we may also need to include the capsule-based antigens in vaccine formulations developed against Klebsiella,” Rosen said. “This is why it’s so important for us to continue studying antibody-antigen interactions in the different strains, with the goal of identifying the ideal vaccine composition for clinical trials soon. The need has never been more imperative, especially as Klebsiella’s drug-resistant, hypervirulent strains become stronger, bolder and more dangerous to human health.”

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Journal reference:

Wantuch, P. L., et al. (2023) Area-deprivation, social care spending and the rates of children in care proceedings in local authorities in Engl Capsular polysaccharide inhibits vaccine-induced O-antigen antibody binding and function across both classical and hypervirulent K2:O1 strains of Klebsiella pneumoniae. PLOS Pathogens. doi.org/10.1371/journal.ppat.1011367.

Scarring to the collagen framework causes dysfunction in Duchenne muscular dystrophy

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Muscles that ache after a hard workout usually don’t hurt for long, thanks to stem cells that rush to the injured site along “collagen highways” within the muscle and repair the damaged tissue. But if the cells can’t reach their destination, the damaged tissue can’t regenerate. Over time, it breaks down completely and ceases to function.

In a study recently published in npj Regenerative Medicine, a group of researchers led by biochemists at UCLA show for the first time that scarring to the collagen framework that carries these healing cells causes muscles to gradually stop working in Duchenne muscular dystrophy. The discovery in mice illuminates one reason stem cell therapy has not been effective for the disorder: The cells simply can’t get where they’re needed most.

Duchenne muscular dystrophy is the most common -; and one of the most severe -; hereditary muscular dystrophies. The muscle-wasting disease, which usually affects boys, begins in childhood and inevitably ends in death as the muscles that power the heart, lungs and other vital organs fail. It is caused by a mutation in the gene for the dystrophin protein, which regulates the organization of muscle cells. In healthy people, dystrophin helps bundles of muscle cells called myofibers attach to the collagen framework -; the extracellular matrix that gives muscles their shape, holds them together and provides the “highway” for stem cells to repair and regenerate damaged tissue.

Rachelle Crosbie, a UCLA professor of integrative biology and physiology who is looking for ways to treat Duchenne muscular dystrophy, suspected that the dysfunction caused by this mutation led to scarring and stiffening of the extracellular matrix, a process known as fibrosis.

Crosbie and Kristen Stearns-Reider, a postdoctoral fellow in Crosbie’s laboratory, designed a unique experiment to find out. Using facilities at UCLA’s California NanoSystems Institute, they devised a process to “wash” all the cells off the collagen extracellular matrix in healthy mice and those with Duchenne muscular dystrophy.

Under a microscope, the two cell-free matrices, which Crosbie calls “myoscaffolds,” appeared very different: The healthy one looked like delicate lace, while the Duchenne one looked more like a dense sponge.

Next, the researchers seeded each myoscaffold with stem cells and watched as the cells tried to grow muscle tissue. Muscle stem cells grew on the myoscaffolds exactly as they would in healthy and diseased muscle: In the healthy, lacy myoscaffold, cells migrated along the smooth threads and deposited themselves in evenly spaced holes. However, the bumpy, thickened surfaces of the Duchenne myoscaffold made travel difficult and threw up roadblocks that caused the cells to pile up in clumps; the cells were stressed an unable to progress efficiently.

Like suburban commuters, resident stem cells live on outskirts of the muscle fiber and travel along the muscle fiber to damaged areas and regenerate muscle. The extracellular matrix is the highway they use. It’s like the difference between driving to work on a regular day versus the day a landslide fell on the freeway.”

Rachelle Crosbie, UCLA professor of integrative biology and physiology

This is the first time scientists have imaged living cells in a fibrotic myoscaffold, revealing specifically how fibrosis disrupts cell behavior, Crosbie said.

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The thin, supple threads of the healthy scaffold also yielded slightly as stem cells attached to them, a deformation critical to the successful development of muscle tissue. The stem cells were unable to deform the thick, stiff fibers of the Duchenne scaffold. Tissue grown on the Duchenne scaffold showed large clumps of myofibers interspersed with even larger clumps of collagen instead of the evenly distributed myofibers seen in the healthy sample.

Protein sarcospan offers a potential way forward

The research team then tested cell behavior on a Duchenne myoscaffold that was created using a therapeutic protein called sarcospan, which is known to stabilize the extracellular matrix. Stem cell function improved once sarcospan had minimized the formation of fibrotic scars.

“The results made it really clear why stem cell therapies have proven challenging for Duchenne muscular dystrophy,” Crosbie said. “Finding ways to prevent or reduce scarring on the extracellular matrix could make them more effective.”

These myoscaffolds offer several broad possibilities for studying stem cell–extracellular matrix interactions, stem cell niche formation, the microenvironments that influence stem cell behavior, muscle maturation and disease modeling, said study co-authors Michael Hicks, a UCLA postdoctoral fellow, and April Pyle, a UCLA professor of microbiology, immunology, and molecular genetics.

Crosbie also noted that because the new method requires only very small samples, these studies could potentially be extended to include individual patients, using tissue from a muscle biopsy to study treatments before they are administered and identifying ones more likely to be effective.

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Journal reference:

Stearns-Reider, K. M., et al. (2023). Myoscaffolds reveal laminin scarring is detrimental for stem cell function while sarcospan induces compensatory fibrosis. Npj Regenerative Medicine. doi.org/10.1038/s41536-023-00287-2.

“Cytokine Storm” Debunked: Machine Learning Exposes the True Killer of COVID-19 Patients

Machine learning finds no evidence of cytokine storm in critically ill patients with COVID-19.

Secondary bacterial infection of the lung (pneumonia) was extremely common in patients with COVID-19, affecting almost half the patients who required support from mechanical ventilation. By applying machine learning to medical record data, scientists at Northwestern University Feinberg School of Medicine have found that secondary bacterial pneumonia that does not resolve was a key driver of death in patients with COVID-19, results published in The Journal of Clinical Investigation.

Bacterial infections may even exceed death rates from the viral infection itself, according to the findings. The scientists also found evidence that COVID-19 does not cause a “cytokine storm,” so often believed to cause death.

“Our study highlights the importance of preventing, looking for, and aggressively treating secondary bacterial pneumonia in critically ill patients with severe pneumonia, including those with COVID-19,” said senior author Benjamin Singer, MD, the Lawrence Hicks Professor of Pulmonary Medicine in the Department of Medicine and a Northwestern Medicine pulmonary and critical care physician.

The investigators found nearly half of patients with COVID-19 develop a secondary ventilator-associated bacterial pneumonia.

“Those who were cured of their secondary pneumonia were likely to live, while those whose pneumonia did not resolve were more likely to die,” Singer said. “Our data suggested that the mortality related to the virus itself is relatively low, but other things that happen during the ICU stay, like secondary bacterial pneumonia, offset that.”

The study findings also negate the cytokine storm theory, said Singer, also a professor of Biochemistry and Molecular Genetics.

“The term ‘cytokine storm’ means an overwhelming inflammation that drives organ failure in your lungs, your kidneys, your brain and other organs,” Singer said. “If that were true, if cytokine storm were underlying the long length of stay we see in patients with COVID-19, we would expect to see frequent transitions to states that are characterized by multi-organ failure. That’s not what we saw.”

The study analyzed 585 patients in the intensive care unit (ICU) at Northwestern Memorial Hospital with severe pneumonia and respiratory failure, 190 of whom had COVID-19. The scientists developed a new machine learning approach called CarpeDiem, which groups similar ICU patient-days into clinical states based on electronic health record data. This novel approach, which is based on the concept of daily rounds by the ICU team, allowed them to ask how complications like bacterial pneumonia impacted the course of the illness.

These patients or their surrogates consented to enroll in the Successful Clinical Response to Pneumonia Therapy (SCRIPT) study, an observational trial to identify new biomarkers and therapies for patients with severe pneumonia. As part of SCRIPT, an expert panel of ICU physicians used state-of-the-art analysis of lung samples collected as part of clinical care to diagnose and adjudicate the outcomes of secondary pneumonia events.

“The application of machine learning and artificial intelligence to clinical data can be used to develop better ways to treat diseases like COVID-19 and to assist ICU physicians managing these patients,” said study co-first author Catherine Gao, MD, an instructor in the Department of Medicine, Division of Pulmonary and Critical Care and a Northwestern Medicine physician.

“The importance of bacterial superinfection of the lung as a contributor to death in patients with COVID-19 has been underappreciated, because most centers have not looked for it or only look at outcomes in terms of presence or absence of bacterial superinfection, not whether treatment is successful or not,” said study co-author Richard Wunderink, MD, who leads the Successful Clinical Response in Pneumonia Therapy Systems Biology Center at Northwestern.

The next step in the research will be to use molecular data from the study samples and integrate it with machine learning approaches to understand why some patients go on to be cured of pneumonia and some don’t. Investigators also want to expand the technique to larger datasets and use the model to make predictions that can be brought back to the bedside to improve the care of critically ill patients.

Reference: “Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19” by Catherine A. Gao, Nikolay S. Markov, Thomas Stoeger, Anna E. Pawlowski, Mengjia Kang, Prasanth Nannapaneni, Rogan A. Grant, Chiagozie Pickens, James M. Walter, Jacqueline M. Kruser, Luke V. Rasmussen, Daniel Schneider, Justin Starren, Helen K. Donnelly, Alvaro Donayre, Yuan Luo, G.R. Scott Budinger, Richard G. Wunderink, Alexander V. Misharin and Benjamin D. Singer, 27 April 2023, The Journal of Clinical Investigation.
DOI: 10.1172/JCI170682

Other Northwestern authors on the paper include Nikolay Markov; Thomas Stoeger, PhD; Anna Pawlowski; Mengjia Kang, MS; Prasanth Nannapaneni; Rogan Grant; Chiagozie Pickens ’14 MD ’17 GME, assistant professor of Medicine in the Division of Pulmonary and Critical Care; James Walter, MD, assistant professor of Medicine in the Division of Pulmonary and Critical Care; Jacqueline Kruser, MD; Luke Rasmussen, MS; Daniel Schneider, MS; Justin Starren, MD, PhD, chief of Health and Biomedical Informatics in the Department of Preventive Medicine; Helen Donnelly; Alvaro Donayre; Yuan Luo, PhD, director of the Center for Collaborative AI in Healthcare and associate professor of Preventive Medicine; Scott Budinger, MD, chief of Pulmonary and Critical Care in the Department of Medicine; and Alexander Misharin, MD, PhD, associate professor of Medicine in the Division of Pulmonary and Critical Care.

The study was supported by the Simpson Querrey Lung Institute for Translational Sciences and grant U19AI135964 from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health.

Diet has a much stronger impact on intestinal microbiota than defensins

Researchers at Umeå University, Sweden, have found that among the many factors that shape the intestinal microbiota composition, diet has a much stronger impact than defensins, which are intestinal defence molecules produced by the body. Instead, they identified a possible role for these molecules in preventing increased blood glucose levels after consumption of high-caloric “Western-style diet”.

While the effect of defensins in shaping the adult microbiota composition is rather minor when compared to diet, defensins still have a very important role in protecting us against microbial infections; and our research highlights their protective role against the metabolic complications that can arise after the intake of a high-fat and high-sugar Western-style diet.”

Fabiola Puértolas Balint, PhD Student at the Department of Molecular Biology at Umeå University

She is working in Björn Schröder’s research group, which is also affiliated to Umeå Centre of Microbial Research, UCMR, and The Laboratory for Molecular Infection Medicine Sweden, MIMS, at Umeå University.

The gut microbiota refers to the community of trillions of microorganisms that live inside everyone’s gut. Over the past decades, the abundance of specific bacteria in this community has been extensively studied due to its connection to many diseases, including inflammatory bowel diseases, obesity and diabetes, and even psychological disorders. The microbial community is seeded during birth, after which several internal and external factors help shaping the community to its final composition. These factors include, among others, diet (especially fibre), genetics, medication, exercise, and defence molecules, the so-called antimicrobial peptides.

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Antimicrobial peptides can be regarded as the body´s own naturally produced antibiotic molecules. In particular, the largest group of antimicrobial peptides – the defensins – is produced by all body surfaces, including the skin, the lungs and the gastrointestinal tract. Defensins are considered the immune system´s first line of defence against infections but at the same time they have also been thought to be essential in shaping the microbiota composition in the small intestine. However, it was so far unclear how big their effect was as compared to diet, which is known to have a major impact.

To investigate this, the researchers from Björn Schröder lab used normal healthy mice and compared their microbiota composition in the small intestine to mice that could not produce functional defensins in the gut, and then both mouse groups were fed either a healthy diet or a low-fibre Western-style diet.
“When we analysed the microbiota composition inside the gut and at the gut wall of two different regions in the small intestine, we were surprised – and slightly disappointed – that defensins had only a very minor effect on shaping the overall microbiota composition,” says Björn Schröder.
However, the intestinal defensins still had some effect directly at the gut wall, where the defensins are produced and secreted. Here, a few distinct bacteria seemed to be affected by the presence of defensins, among them Dubosiella and Bifidobacteria, likely due to selective antimicrobial activity of the defensins.

“To our surprise, we also found that the combination of eating a Western-style diet and lacking functional defensins led to increased fasting blood glucose values, which indicated that defensins may help to protect against metabolic disorders when eating an unhealthy diet,” says Björn Schröder.
The results suggest that strategies that aim to positively modulate the microbiota composition should rather focus on diet, as modulation of the composition via increased production of own host defense molecules, such as defensins, may have only a small impact on the overall composition. However, it is possible that especially early in life, when the microbiota community is not fully matured yet, defensins may have a stronger effect on the microbial composition. Still, increasing the production of defensins may be a valuable option to prevent the development of metabolic disorders.

The results have been published in the scientific journal Microbiology Spectrum.

Journal reference:

Puértolas-Balint, F., & Schroeder, B. O. (2023). Intestinal α-Defensins Play a Minor Role in Modulating the Small Intestinal Microbiota Composition as Compared to Diet. Microbiology Spectrum. doi.org/10.1128/spectrum.00567-23.

Smoking alters lung microbiome, leading to loss of diversity and community structure

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In a recent study published in the journal Access Microbiology, researchers explore the composition of the microbiome and interactions in the lower respiratory tract (LRT) in smokers. 

Study: Lower respiratory tract microbiome composition and community interactions in smokers. Image Credit: vchal / Shutterstock.com

The impact of smoking on the respiratory microbiome

Smoking has been shown to impact resident microbial communities present in different bodily regions. Previous studies have proposed various mechanisms responsible for this association, such as immunosuppression related to smoking, an increase in biofilm formation for specific species, and selection of species by the influence of local oxygen tension.

The upper airways and oral cavities may also directly interact with smoking chemicals, microbes, and heat from cigarettes, which can alter microbiome content. Recent studies have hypothesized that dysbiosis noted in the oral microbiome related to smoking may lead to a greater likelihood of experiencing complications in the respiratory tract among smokers. 

About the study

In the present study, researchers compare the LRT microbiome profiles of active smokers (AS), former smokers (FS), and non-smokers (NS) to describe the bacterial communities present in the lung.

The study involved volunteer subjects aged over 40 years of age who were either smokers of a minimum of 10 pack-years throughout their life or non-smokers. Former smokers qualified for the study if they had abstained from using tobacco for a minimum of 12 months, while AS smoked a minimum of one cigarette within three days of recruitment.

All study participants were required to complete a pulmonary function examination and thorough demographic and clinical questionnaire. The sampling process was standardized for all participants. The team extracted total deoxyribonucleic acid (DNA) from the bronchoalveolar lavages (BALs) specimens.

A single polymerase chain reaction (PCR) assessment was conducted to amplify the V6-V8 region present on the 16S ribosomal ribonucleic acid (rRNA) gene from the metagenomic DNA extracts of the BAL samples. Alpha diversity was estimated using Chao richness and inverse Simpson diversity indices. The DESeq2 algorithm was also used to detect differentiating taxa for each cohort.

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Study findings

All 46 smokers reported similar smoking exposure in terms of pack-years, including the FS quitting smoking on an average of about 10 years prior to enrollment. AS and FS exhibited reduced forced vital capacity (FVC), diffusing capacity for carbon monoxide (DL-CO), and forced expiratory volume at second 1 (FEV1); however, these variations were not remarkable according to the analysis of variance (ANOVA).

Over 3,600 reads with an average length of about 479 nucleotides were documented in each participant’s BAL, which facilitated the description of almost 400 operational taxonomic units (OTUs) per participant. The NS profile was sufficiently balanced between the prevalent phyla Bacteroides, Firmicutes, Proteobacteria, and Actinobacteria with comparatively slightly higher proportions. The FS cohort had a significant increase in Proteobacteria with reduced Bacteroides and Firmicutes levels. This pattern was also true for AS, with Proteobacteria increasing to 75% and Firmicutes declining to 11%.

Genus-level assessments indicated that most of the enhancement in Proteobacteria in AS and FS in comparison to its high proportion in NS was due to the genus Ralstonia, which increased from 2% in the NS, 28% in AS, and 21% in FS.

From the Firmicutes phylum, the Streptococcus and Veillonella genera, as well as Prevotella from the Bacteroidetes phyla exhibited the greatest decline in comparative abundance. Furthermore, the Propionibacterium genus of the Actinobacteria phylum exhibited a slight improvement from 3% in AS and FS to 0.8% in NS.

With respect to the NS profile, a greater number of upper-quartile taxa were distinguished from AS, whereas lower-quartile taxa were distinguished from FS.

NS exhibited a considerably higher mean diversity as compared to AS and FS. The mean diversity further increased when the participants were placed by declining richness, thus indicating that NS reported higher richness. Yet, the diversity evaluated with the inverse Simpson index had only an intermediate association with richness estimates and the participant’s smoking status.


The current study provides new insights into the complicated microbial communities found in the LRT and how this microbiome can be changed under different smoking conditions. The researchers also observed that the oral microbiota can settle in the lungs of smokers, which makes the study of the upper airway microbiome interesting for future research.

The microbiomes of former smokers appear to exhibit similar properties to those of both AS and NS. In the future, integration of the present findings with next-generation analytical techniques would help establish the effect of such microbial communities on human health.

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Journal reference:
  • Campos, M., Cickovski, T., Fernandez, M., et al. (2023). Lower respiratory tract microbiome composition and community interactions in smokers. Access Microbiology. doi:10.1099/acmi.0.000497.v3

New Study: Brazilian Cachaça Yeast Can Prevent Asthma

According to a recent study conducted in Brazil, a daily serving of the yeast strain used in the production of cachaça, a distilled spirit made from fermented sugarcane juice, may act as a preventive measure against asthma. The findings were published in the journal Probiotics and Antimicrobial Proteins and were authored by researchers from the University of São Paulo and the Federal University of Minas Gerais. The specific yeast strain used in the study was Saccharomyces cerevisiae UFMG A-905.

Asthma is a prevalent pulmonary disorder that leads to challenges in breathing. This condition impacts approximately 334 million individuals across all age groups around the globe. Frequently beginning in childhood, asthma is marked by airway inflammation, restricted airflow, and alterations in the bronchial structure.

Despite increasing interest in the use of probiotics to prevent or treat allergies and various skin, gastrointestinal and neurological diseases, more research is needed to determine the ideal dose and administration regime to assure the desired benefits.

S. cerevisiae UFMG A-905, widely used in the production of beer and bread as well as cachaça, is a well-known probiotic and can attenuate the symptoms of asthma in animal models. This has been known for some time, but details of how best to use it have been lacking. The new study shows that the ideal daily dose is 10 billion (109) colony-forming units per milliliter (CFU/mL). For comparison, there are 16 billion CFUs in 65 mL of Yakult fermented milk.

“It’s important to understand that probiotics work like medication. Taking them occasionally or in the wrong amount is useless,” said Marcos de Carvalho Borges, a professor of clinical medicine at the Ribeirão Preto Medical School (FMRP-USP) and last author of the article.

The study, which was supported by FAPESP, involved analysis of the effects of administering a daily dose of 100 microliters (μL) for 27 consecutive days as a solution containing the probiotic at three different concentrations: 107, 108, and 109 CFU/mL. The researchers also investigated the effects of administering 100 μL of the solution with 109 UFC/mL of S. cerevisiae UFMG A-905 three times a week on alternate days for five weeks.

Male laboratory mice were intraperitoneally sensitized and nasally challenged with ovalbumin to induce allergic airway inflammation. They were fed the yeast via a tube leading down the throat to the stomach (gavage).

The researchers, who are affiliated with FMRP-USP and UFMG’s Institute of Biological Sciences, discovered that both daily administration of the probiotic and administration on alternate days significantly reduced bronchial hypersensitivity in comparison with the control group, which was given only saline solution. Bronchial hypersensitivity is excessive constriction of the airways in response to a stimulus and is one of the main characteristics of asthma.

However, only daily administration of the highest dose reduced airway inflammation in the asthmatic mice. “We measured the degree of inflammation in terms of eosinophil count and interferon levels,” Borges said. Eosinophils are immune system cells, and interferons also help the body fight infection. Both are markers of asthmatic inflammation. “They were both considerably reduced in the mice treated with the probiotic. We concluded that S. cerevisiae isolated from artisanal cachaça has significant potential to prevent asthma only if a high dose is taken every day.”

Airway and lung inflammation was not significantly reduced by administration of the probiotic either daily or on alternate days at concentrations of 107 and 108 UFC/mL. “From the public policy standpoint, having a natural product like a probiotic, which has practically no side-effects, with the potential to prevent a health problem as widespread as asthma is very important,” Borges said.

Following the trial in an animal model, the researchers plan to find out whether the probiotic has the same beneficial effects in humans and, if so, to investigate the mechanisms involved using fermented food products rather than a simple capsule with the solution.

Bread containing the yeast has been developed and found to have a similar preventive effect in master’s research supervised by Borges in partnership with colleagues at UFMG and the State University of Campinas (UNICAMP). The product has been patented and will soon be reported on in scientific journals.

Reference: “Dose–Response Effect of Saccharomyces cerevisiae UFMG A-905 on the Prevention of Asthma in an Animal Model” by Thamires M. S. Milani, Camila M. Sandy, Ana Paula Carvalho Thiers Calazans, Rosana Q. Silva, Vanessa M. B. Fonseca, Flaviano S. Martins and Marcos C. Borges, 29 November 2022, Probiotics and Antimicrobial Proteins.
DOI: 10.1007/s12602-022-10014-w

The study was funded by the São Paulo Research Foundation.

Nasal SARS-CoV-2 vaccine outperforms existing vaccines in preclinical trial

In a recent study published in the journal Nature Microbiology, researchers assess the role of the live-attenuated vaccine (LAV) sCPD9 in inducing systemic and mucosal immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com


Coronavirus disease 2019 (COVID-19) vaccines, currently administered through the intramuscular route, effectively stimulate the production of neutralizing antibodies, effector and central memory T-cells, germinal center B-cells, long-lived plasma cells, and nasal-resident CD8+ T-cells. The intramuscular route has lower efficacy in promoting long-lasting mucosal immunoglobulin A (IgA) and IgG responses, as well as pulmonary tissue-resident memory cell responses.

Notably, mucosal antibodies are important in reducing viral infectivity and transmission at the site of entry. Tissue-resident memory cells have faster recall responses and can recognize cognate antigens earlier due to their local positioning.

About the study

In the present study, researchers compare the immune responses and preclinical efficacy of the Pfizer-BioNTech BNT162b2 messenger ribonucleic acid (mRNA) COVID-19 vaccine, adenovirus-vectored spike vaccine Ad2-spike, and LAV sCPD9 in Syrian hamsters.

The efficiency and mechanism of action of the evaluated vaccines were evaluated in a heterologous SARS-CoV-2 Delta variant challenge condition. To this end, Syrian hamsters received one vaccine dose and were exposed to the SARS-CoV-2 Delta variant 21 days after vaccination to evaluate its effectiveness. Hamsters were administered two vaccine doses 21 days apart and were later infected with the virus 14 days after booster administration.

Histopathology was used to examine challenged hamsters and determine any lung damage caused by infection. Single-cell RNA sequencing (scRNA-seq) was performed on lung specimens to establish a correlation between inflammation levels and cellular responses.

The humoral responses of hamsters were assessed by analyzing their sera collected before and after vaccination and determining their neutralizing ability against SARS-CoV-2 variants at different time points.


All vaccinations protected hamsters from weight loss induced by SARS-CoV-2 infection. However, the vaccines did not provide complete protection against SARS-CoV-2 Delta infection after a single dose, as viral RNA was still present in the respiratory tract. The sCPD9 vaccine was the only tested vaccine that successfully reduced replicating viral titers to undetectable levels within two days post-challenge (dpc).

The overall efficacy of the SARS-CoV-2 vaccine was enhanced through prime-boost vaccination. Despite a significant reduction after prime-boost vaccination, all groups exhibited detectable viral RNA in oropharyngeal specimens and lungs. Nevertheless, sCPD9-based vaccination was more effective in decreasing viral RNA levels.

Vaccinated animals exhibited a significant reduction in replication-competent vial levels in their lungs two days post-challenge (dpc). Only the sCPD9 booster vaccine effectively reduced replicating virus proportions below the detection threshold, irrespective of whether the entire vaccination series was heterologous or homologous.

Furthermore, sCPD9 was highly effective in preventing inflammation and pneumonia after a single vaccination. This was demonstrated by the reduced levels of consolidated lung areas, along with lower scores for bronchitis, edema, and lung inflammation.

Animals with different vaccination schedules showed more significant bronchial hyperplasia. Prime-boost regimens showed a similar trend, with the mRNA vaccine displaying better histological outcomes with a homologous boost.

Homologous sCPD9 prime-boost vaccination offered better lung protection against inflammation. Both heterologous and homologous sCDP9 vaccinated hamsters exhibited reduced inflammation- and infection-related genes in their lung transcriptome.

Sera from sCPD9 vaccine recipients showed higher neutralization capacity against the ancestral SARS-CoV-2 variant B.1 compared to other groups. The sCPD9 sera effectively neutralized the Beta and Delta variants, as well as the Omicron BA.1 sublineage.

The neutralization capacity against Omicron BA.1 was reduced in all cohorts, with sCPD9 sera associated with significant neutralization. Neutralizing antibodies increased over time in all cohorts by five dpc due to challenge infection.

Hamsters that received the sCPD9 or mRNA vaccine, along with the prime-only vaccination, produced more neutralizing antibodies than those that only received the prime-only vaccination. Booster vaccination improved the serum neutralization capacity for various variants, with Omicron BA.1 exhibiting the highest neutralization evasion capacity among the tested variants.

Hamsters vaccinated with mRNA+sCDP9 and prime-boost sCDP9 produced notable IgG antibody responses against the SARS-CoV-2 spike, nucleocapsid protein, and open reading frame (ORF)-3a. Comparatively, hamsters vaccinated with prime-boost mRNA and Ad2 only exhibited IgG reactivity against the spike protein.


The study findings presented a comparison of vaccines across different platforms, including a novel LAV that provided better protection against SARS-CoV-2 infection than other types of COVID-19 vaccines. Importantly, these findings on enhanced immunity through heterologous prime-boost vaccination align with other recent studies that utilize systemic priming and intranasal boosting with Ad-2 vector or mRNA vaccines.

Anti-SARS-CoV-2 IgA levels in the nasal mucosa are significantly higher among sCPD9-vaccinated animals. Animals vaccinated with sCPD9 showed significant improvement in protection against virus replication, lung inflammation, and tissue damage. Animals that received sCPD9 had a broader antigen recognition, likely due to the key features of LAV.

Journal reference:
  • Nouailles, G., Adler, J. M., Pennitz, P., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology 1-15. doi:10.1038/s41564-023-01352-8

Live attenuated nasal vaccine elicits superior immunity to SARS-CoV-2 variants in hamsters

Since the beginning of the COVID-19 pandemic, researchers have been working on mucosal vaccines that can be administered through the nose. Now, scientists in Berlin have developed a live attenuated vaccine for the nose. In “Nature Microbiology”, they describe the special immune protection it induces.

Coronaviruses spread primarily through the air. When infected people speak, cough, sneeze or laugh, they expel droplets of saliva containing the virus. Other people then breathe in these airborne pathogens and become infected themselves. A research team in Berlin decided to try to fight the virus that causes COVID-19 where it first takes hold: the mucous membranes of the nose, mouth, throat, and lungs. To do so, the scientists developed a live attenuated SARS-CoV-2 vaccine that is administered through the nose. In the latest issue of the journal “Nature Microbiology“, the interdisciplinary team describes how this live attenuated vaccine confers better immunity than vaccines injected into muscle.

Already in the fall of last year, two nasal vaccination formulations were approved for use in India and China. These contain modified adenoviruses – which typically cause respiratory or gastrointestinal illnesses – that are self-attenuating, meaning they either replicate poorly or stop replicating altogether, and therefore never trigger disease. Other live nasal vaccines are currently undergoing development and testing around the world.

Protection at the site of infection

The benefits of a nasal vaccine go far beyond just providing an alternative for people afraid of needles. When a vaccine is injected, it infers immunity primarily in the blood and throughout the entire body. However, this means that the immune system only detects and combats coronaviruses relatively late on in an infection, as they enter the body via the mucous membranes of the upper respiratory tract. “It is here, therefore, that we need local immunity if we want to intercept a respiratory virus early on,” explains the study’s co-last author Dr. Jakob Trimpert, a veterinarian and research group leader at the Institute of Virology at Freie Universität Berlin.

“Nasal vaccines are far more effective in this regard than injected vaccines, which fail or struggle to reach the mucous membranes,” emphasizes Dr. Emanuel Wyler, another co-last author. He has been researching COVID-19 since the start of the pandemic as part of the RNA Biology and Posttranscriptional Regulation Lab, which is led by Professor Markus Landthaler at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB).

In an ideal scenario, a live intranasal vaccine stimulates the formation of the antibody immunoglobulin A (IgA) directly on site, thus preventing infection from occurring in the first place. IgA is the most common immunoglobin in the mucous membranes of the airways. It is able to neutralize pathogens by binding to them and preventing them from infecting respiratory tract cells. At the same time, the vaccine stimulates systemic immune responses that help provide effective overall protection from infection.

Memory T cells that reside in lung tissue play a similarly useful role to antibodies in the mucosa. These white blood cells remain in affected tissue long after an infection has passed and remember pathogens they have encountered before. Thanks to their location in the lungs, they can respond quickly to viruses that enter through the airways.” The co-first author draws attention to one of the observations the team made during their study: “We were able to show that prior intranasal vaccination results in the increased reactivation of these local memory cells in the event of a subsequent SARS-CoV-2 infection. Needless to say, we were particularly pleased with this result.”

Dr. Geraldine Nouailles, immunologist and research group leader at the Department of Pneumology, Respiratory Medicine, and Intensive Care Medicine at Charité

Local immunity impedes viral infection

The scientists tested the efficacy of the newly developed intranasal COVID-19 vaccine on hamster models that had been established by Trimpert and his team at Freie Universität Berlin at the beginning of the pandemic. These rodents are currently the most important non-transgenic model organisms for research into the novel coronavirus, as they can be infected with the same virus variants as humans and develop similar symptoms. They found that after two doses of the vaccine, the virus could no longer replicate in the model organism. “We witnessed strong activation of the immunological memory, and the mucous membranes were very well protected by the high concentration of antibodies,” Trimpert explains. The vaccine could therefore also significantly reduce the transmissibility of the virus.

In addition, the scientists compared the efficacy of the live attenuated vaccine with that of vaccines injected into the muscle. To do so, they vaccinated the hamsters either twice with the live vaccine, once with the mRNA and once with the live vaccine, or twice with an mRNA or adenovirus-based vaccine. Then, after the hamsters were infected with SARS-CoV-2, they used tissue samples from the nasal mucosa and lungs to see how strongly the virus was still able to attack the mucosal cells. They also determined the extent of the inflammatory response using single-cell sequencing. “The live attenuated vaccine performed better than the other vaccines in all parameters,” Wyler summarizes. This is probably due to the fact that the nasally administered vaccine builds up immunity directly at the viral entry site. In addition, the live vaccine contains all components of the virus – not just the spike protein, as is the case with the mRNA vaccines. While spike is indeed the virus’s most important antigen, the immune system can also recognize the virus from about 20 other proteins.

Better than conventional vaccines

The best protection against the SARS-CoV-2 was provided by double nasal vaccination, followed by the combination of a muscular injection of the mRNA vaccine and the subsequent nasal administration of the live attenuated vaccine. “This means the live vaccine could be particularly interesting as a booster,” says the study’s co-first author Julia Adler, a veterinarian and doctoral student at the Institute of Virology at Freie Universität Berlin.

The principle of live attenuated vaccines is old and is already used in measles and rubella vaccinations, for example. But in the past, scientists generated the attenuation by chance – sometimes waiting years for mutations to evolve that produced an attenuated virus. The Berlin researchers, on the other hand, were able to specifically alter the genetic code of the coronaviruses. “We wanted to prevent the attenuated viruses from mutating back into a more aggressive variant,” explains Dr. Dusan Kunec, a scientist at the Institute of Virology at Freie Universität Berlin and another co-last author of the study. “This makes our live vaccine entirely safe and means it can be tailored to new virus variants,” stresses Kunec, who was instrumental in developing the vaccine.

The next step is safety testing: The researchers are collaborating with RocketVax AG, a Swiss start-up based in Basel. The biotech company is developing the live attenuated SARS-CoV-2 vaccine and preparing a phase 1 clinical trial in humans. “We are thrilled to be at the forefront of developing and manufacturing the live attenuated SARS-CoV-2 vaccine as a nasal spray at RocketVax. Our goal is to rapidly scale-up production and advance clinical development towards market access to provide protection against post-COVID symptoms for all. We see great potential in the market for seasonal nasal vaccines”, says Dr. Vladimir Cmiljanovic, CEO of RocketVax.

The future will show which nasal vaccine will ultimately provide better protection. The manufacturers of the nasal adenovirus vaccines developed in India and China have not yet applied for approval in Europe. But one thing is clear to the scientists: since they are administered as nasal sprays or drops, nasal vaccines are a good option for use in places with limited access to trained medical staff. They are also inexpensive to produce and easy to store and transport. Last but not least, live attenuated vaccines such as this one have been proven to provide cross-protection against related viral strains, and thus presumably also against future SARS-CoV-2 variants.

Journal reference:

Nouailles, G., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology. doi.org/10.1038/s41564-023-01352-8

Scientists identify a distinct role of retinoic acid during immune response of the gut

A team of scientists from the Renaissance School of Medicine (RSOM) at Stony Brook University have identified a distinct role of retinoic acid, a metabolite of vitamin A, during the immune response of the gut. This finding, detailed in a paper published in the Journal of Experimental Medicine, and highlighted in a broader piece in the journal, could help lead to ways to control the retinoic acid response and therefore be used as a therapy or for vaccine development against infection or even to treat GI tumors.

Led by Brian Sheridan, PhD, Associate Professor in the Department of Microbiology and Immunology and Center for Infectious Diseases, the study involves basic research that centers on unraveling the factors that control the generation of cytotoxic memory CD8 T cells, which are an important arm of the body’s anti-pathogen immune response as they kill pathogen-infected cells and produce anti-pathogen cytokines. In fact, memory CD8 T cells provide long-lived and frontline protection at barrier tissues, highlighting their importance in vaccine design.

To date scientists have known that retinoic acid in the gut-draining lymph nodes promotes effector CD8 T cell migration to the intestines, enhancing the immune response. Additionally, vitamin A deficiency is associated with increased infections and poor vaccine efficiency.

Sheridan and his co-authors, including Zhijuan Qiu, PhD, a post-doctoral fellow in the department, identified a new role for retinoic acid, which is a key part of the immune process in the gut. They demonstrated in the lab that T cell activation in gut-associated lymph nodes regulates memory CD8 T cell differentiation in the intestine. They also demonstrated in contrast that T cells activated at other sites were impaired in the ability to differentiate into memory CD8 T cells after entry into the intestine.

During this process, they demonstrated that activation within the gut-associated lymph nodes, but not in other sites, promotes intestinal memory CD8 T cell development and that retinoic acid signals provided during this window of T cell activation in the lymph nodes enhances intestinal memory CD8 T cell development to a wider degree.

Our study highlights a fundamental new role of T cell activation on the generation of the intestinal memory CD8 T cells that appears distinct from other barrier sites like the lungs and skin. Remarkably, we can alter intestinal T cell development by promoting or limiting retinoic acid signals during T cell activation, independent of the role of retinoic acid on T cell migration.”

Brian Sheridan, PhD, Associate Professor in the Department of Microbiology and Immunology and Center for Infectious Diseases

Because the research team was able to replicate this limiting or promoting of retinoic acid signals in the gut, they believe that manipulating retinoic acid signals during T cell activation may provide a strategy for clinicians to promote or limit intestinal CD8 T cells to improve vaccine outcomes or limit immunopathology.

This research is supported in part by a grant (R01AI172919) from the National Institutes of Health’s National Institute of Allergy and Infectious Diseases (NIAID) to Brian Sheridan.

Journal reference:

Qiu, Z., et al. (2023). Retinoic acid signaling during priming licenses intestinal CD103+ CD8 TRM cell differentiation. Journal of Experimental Medicine. doi.org/10.1084/jem.20210923.