. Scientific Frontline: Microbiology
Showing posts with label Microbiology. Show all posts
Showing posts with label Microbiology. Show all posts

Thursday, December 1, 2022

Hibernating Corals and the Microbiomes That Sustain Them

A microscope image of Northern star coral with its polyps extended.
Photo Credit: Alicia Schickle, Roger Williams University

As winter approaches, many species of animals — from bears and squirrels to parasitic wasps and a few lucky humans — hunker down for some needed rest. The northern star coral (Astrangia poculata) also enters a hibernating state of dormancy, or quiescence, during this time. But what happens to its microbiome while it’s sleeping?

A study led by University of California, Davis, Assistant Professor Anya Brown found that microbial communities shift while this coral enters dormancy, providing it an important seasonal reset. The work may carry implications for coral in warmer waters struggling with climate change and other environmental issues.

“Dormancy, at its most basic, is a response to an environmental stressor — in this case, cold stress,” said Brown, who is part of the UC Davis Bodega Marine Laboratory in the Department of Evolution and Ecology. “If we understand more about this recovery period, it might help us understand what microbes may be responsible for recovering coral in warmer tropical systems.”

Commercial Dishwashers Destroy Protective Layer in Gut

Rinse aids in commercial dishwashers often contain alcohol ethoxylate. This substance damages the intestinal epithelium, which can lead to chronic diseases.

Residue from rinse agents is left behind on dishes after they are cleaned in professional-grade dishwashers. This damages the natural protective layer in the gut and can contribute to the onset of chronic diseases, as demonstrated by researchers working with organoids at the Swiss Institute of Allergy and Asthma Research.

Whether it’s at a restaurant, at school or in the barracks, commercial dishwashers help plates, glasses and cutlery become squeaky clean and dry in a matter of minutes. These practical appliances come with risks, however, as was recently discovered in a new study by researchers at the Swiss Institute of Allergy and Asthma Research (SIAF), an associated institute of the University of Zurich (UZH). One ingredient in particular found in commercial rinse agents has a toxic effect on the gastrointestinal tract.

Chemical residue on clean plates

A typical cycle in a commercial dishwasher involves circulating hot water and detergent for around 60 seconds at high pressure. Afterwards, there is a second 60-second washing and drying cycle in which water and a rinse agent are applied. “What’s especially alarming is that in many appliances, there’s no additional wash cycle to remove the remaining rinse aid,” says Cezmi Akdis, UZH professor of experimental allergology and immunology and director of the SIAF, who led the study. “This means that potentially toxic substances remain on the dishes, where they then dry in place.” When the dishes are used the next time, this dried chemical residue can easily end up in the gastrointestinal tract.

Tuesday, November 29, 2022

Gut Microbes Influence Binge-Eating of Sweet Treats in Mice

Sarkis Mazmanian, Luis B. and Nelly Soux Professor of Microbiology
Photo Credit: Caltech

We have all been there. You just meant to have a single Oreo as a snack, but then you find yourself going back for another, and another, and before you know it, you have finished off the entire package even though you were not all that hungry to begin with.

But before you start feeling too guilty for your gluttony, consider this: It might not be entirely your fault. Now, new research in mice shows that specific gut bacteria may suppress binge eating behavior.

Oreos and other desserts are examples of so-called "palatable foods"—food consumed for hedonistic pleasure, not simply out of hunger or nutritional need. Humans are not alone in enjoying this kind of hedonism: Mice like to eat dessert, too. Even when they have just eaten, they will still consume sugary snacks if available.

The new Caltech study shows that the absence of certain gut bacteria causes mice to binge eat palatable foods: Mice with microbiotas disrupted by oral antibiotics consumed 50 percent more sugar pellets over two hours than mice with gut bacteria. When their microbiotas were restored through fecal transplants, the mice returned to normal feeding behavior. Further, not all bacteria in the gut are able to suppress hedonic feeding, but rather specific species appear to alter the behavior. Bingeing only applies to palatable foods; mice with or without gut microbiota both still eat the same amount of their regular diet. The findings show that the gut microbiota has important influences on behavior and that these effects can be modulated when the microbiota is manipulated.

Thursday, November 24, 2022

Study sheds new light on the link between oral bacteria and diseases

Photo Credit: Quang Tri NGUYEN

Researchers at Karolinska Institutet have identified the bacteria most commonly found in severe oral infections. Few such studies have been done before, and the team now hopes that the study can provide deeper insight into the association between oral bacteria and other diseases. The study is published in Microbiology Spectrum.

Researchers at Karolinska Institutet have now analyzed samples collected between 2010 and 2020 at the Karolinska University Hospital in Sweden from patients with severe oral infections and produced a list of the most common bacteria.

This was a collaborative study that was performed by Professor Margaret Sällberg Chen and adjunct Professor Volkan Özenci’s research groups.

“We’re reporting here, for the first time, the microbial composition of bacterial infections from samples collected over a ten-year period in Stockholm County,” says Professor Sällberg Chen of the Department of Dental Medicine at Karolinska Institutet. “The results show that several bacterial infections with link to systemic diseases are constantly present and some have even increased over the past decade in Stockholm.”

Tuesday, November 22, 2022

A growing trend of antibody evasion by new omicron subvariants

Scanning electron micrograph of a cell (purple) infected with the omicron strain of SARS-CoV-2 virus particles (orange), isolated from a patient sample and colorized.
Image Credit: NIAID/NIH

Three currently circulating omicron subvariants of SARS-CoV-2 – including two that currently make up almost 50% of reported COVID-19 infections in the U.S. – are better at evading vaccine- and infection-generated neutralizing antibodies than earlier versions of omicron, new research suggests.

Scientists tested neutralizing antibodies in blood serum samples from vaccinated and once-boosted or recently infected health care professionals against several subvariants in circulation. Three subvariants stood out for their resistance to the antibody immune response: BQ.1, BQ.1.1 and BA.2.75.2.

BQ.1 and BQ.1.1 are subvariants of the BA.4/5 omicron variants that have been dominating the last few months in the U.S., and each now accounts for about a quarter of current infections, according to the Centers for Disease Control and Prevention (CDC). BA.2.75.2, a mutant of the BA.2 omicron variant, was the best of all variants tested at evading neutralizing antibodies, but currently accounts for only a very small proportion of reported illnesses in the United States.

“In general, the subvariants BQ.1 and BQ.1.1 are much better compared to prior variants at evading the booster-mediated antibody response – the neutralizing antibody titers are clearly much lower. And those two variants are becoming dominant,” said Shan-Lu Liu, senior author the study and a virology professor in the Department of Veterinary Biosciences at The Ohio State University.

Monday, November 21, 2022

Genetic ‘Hitchhikers’ Can Be Directed Using CRISPR

NC State researchers expand the CRISPR toolbox with possible agricultural implications.
Photo Credit: Atlas Green

In a new study, North Carolina State University researchers characterize a range of molecular tools to rewrite – not just edit – large chunks of an organism’s DNA, based on CRISPR-Cas systems associated with selfish genetic “hitchhikers” called transposons.

The researchers investigate diverse Type I-F CRISPR-Cas systems and engineer them to add genetic cargo – up to 10,000 additional genetic code letters – to the transposon’s cargo to make desired changes to a bacterium – in this case, E. coli.

The findings expand the CRISPR toolbox and could have significant implications in the manipulation of bacteria and other organisms at a time of need for flexible genome editing in therapeutics, biotechnology and more sustainable and efficient agriculture.

Bacteria use CRISPR-Cas as adaptive immune systems to withstand attacks from enemies like viruses. These systems have been adapted by scientists to remove or cut and replace specific genetic code sequences in a variety of organisms. The new finding shows that exponentially larger amounts of genetic code can be moved or added, potentially increasing CRISPR’s functionality.

Intestinal microorganisms influence white blood cell levels in blood

Under normal conditions (steady state) neutrophils regulate the gut microbiota. When the number of neutrophils drops (neutropenia), the composition of the gut microbiota changes, stimulating T cells to produce IL-17A. IL-17-A in turn stimulates the production of neutrophils in the bone marrow (reactive granulopoiesis).
Illustration Credit: Daigo Hashimoto

White blood cells, or granulocytes, are cells that are part of the innate immune system. The most common type of granulocyte is the neutrophil, a phagocyte that destroys microbes in the body. Low neutrophil counts in the blood is called neutropenia; this condition is commonly seen in cases of leukemia or following chemotherapy. It is known that neutropenia induces granulopoiesis, the process formation of granulocytes. However, the exact mechanisms by which neutropenia drives granulopoiesis are not fully understood.

A team of researchers led by Associate Professor Daigo Hashimoto and Professor Takanori Teshima at Hokkaido University’s Faculty of Medicine have discovered that the gut microbiome plays a critical role in driving granulopoiesis in mice models. Their findings were published in the journal Proceedings of the National Academy of Sciences.

Friday, November 18, 2022

Toxins force construction of ‘roads to nowhere’

This image shows the effects of the toxin VopF, depicted in green in the cell on the left, on actin filaments, depicted in magenta in both cells.
Image Credit: Elena Kudryashova

Toxins released by a type of bacteria that cause diarrheal disease hijack cell processes and force important proteins to assemble into “roads to nowhere,” redirecting the proteins away from other jobs that are key to proper cell function, a new study has found.

The affected proteins are known as actins, which are highly abundant and have multiple roles that include helping every cell unite its contents, maintain its shape, divide and migrate. Actins assemble into thread-like filaments to do certain work inside cells.

Researchers found that two toxins produced by the Vibrio genus of bacteria cause actins to start joining together into these filaments – which could be thought of as cellular highways on which cargo is delivered – at the wrong location inside cells, and headed in the wrong direction.

Friday, November 11, 2022

Friendly monkeys have friendly microbes


More sociable monkeys have a higher abundance of certain beneficial gut bacteria, and a lower abundance of potentially disease-causing bacteria, new research has found.

The study involved analyzing social network data from a population of non-captive macaques on the island of Cayo Santiago, off Puerto Rico, and combining this with sequencing data to assess their individual gut microbiota.

The researchers found that monkeys that engage in social interactions were more likely to have an abundance of gut microbes that are known to benefit the immune system, and were less likely to have an abundance of potentially harmful bacteria. The analyses controlled for other factors that could affect the microbiome, including age, season, sex and rank within the group’s hierarchy.

The study was conducted by Dr Katerina Johnson at the University of Oxford's Department of Psychiatry, in collaboration with Dr Karli Watson from the University of Colorado Boulder, alongside Oxford professors Robin Dunbar and Philip Burnet.

Thursday, November 10, 2022

Gut parasites may increase onward transmission of respiratory bugs in rabbits

Bordatella bronchiseptica shedding on BG-blood agar petri dishes. Examples of (a) supershedding event and (b) average shedding event.
Credit: Isabella Cattadori, Penn State

Rabbits co-infected with a respiratory bacterial infection and one or more gut helminth parasites are more likely to shed bacteria that can infect others, according to a report led by researchers at Penn State and published today in the journal eLife.

The study suggests that co-infection is an important source of variation in pathogen shedding between individual animals and could influence how likely a disease is to spread. Species similar to the ones used in this study infect humans and while the study was done in rabbits it has broad implications for human populations.

Individual variation in pathogen transmission can increase the basic reproduction number — the R value — of a pathogen, and determine whether an infection will spread or stutter and quickly fade away. One of the causes of this variation is differences in the amount and duration of pathogen shedding, as some individuals shed more and for longer than others — so-called super-shedders. Co-infection with other pathogens is thought to contribute to variation in host infection, and so transmission, because of interactions between pathogen species and the immune response they trigger.

Wednesday, November 9, 2022

A mysterious outbreak of bone-eating tb resembled an ancestral form


Tuberculosis is usually encountered as a disease of the lungs, but in 2 percent of cases in the U.S. it can also be found in the bones. The 9,000-year-old skeletons of some Egyptian mummies show signs of having tuberculosis infection in their bones, a painful condition that leaves the bones looking like they’ve been gnawed.

So, it was a weird puzzle when Duke physician Jason Stout M.D. encountered a Wake County TB outbreak in the mid-2000s in which the infection had spread beyond the lungs in six people. “Four out of six were in the bone,” Stout said. “That’s way more than 2 percent.”

The index case, the first person in Raleigh to have this strain of the disease, apparently contracted the bacterium in Vietnam, but he wasn’t feeling very sick and had been working around 400 people in his workplace.

“So, it was prolonged exposure in a workplace,” said Stout, a Duke professor of medicine who tracked down and identified seven subsequent infections through contact tracing and health department records.

All eight people were treated with antibiotics and other co-workers received preventative care and then the strange outbreak went away. But the mystery was never really solved. “I’m an epidemiologist and clinical trial specialist and I was left scratching my head,” Stout said.

How Pathogens Hijack Immune System to Cause Vaccine-Enhanced Disease

Associate Professor Steven Szczepanek (standing, left) with graduate students Tyler Gavitt (seated) and Arlind Mara (standing, right).
Photo Credit: Jason Sheldon/UConn

Researchers in the College of Agriculture, Health and Natural Resources are working to unlock a decades-long mystery that has hampered development of a walking pneumonia vaccine.

Associate Professor Steven Szczepanek and Professor Steven Geary from the Department of Pathobiology and Veterinary Science, along with former graduate students Tyler Gavitt and Arland Mara, published findings that help explain how Mycoplasma pneumoniae (Mp) hijacks our immune system following vaccination.

They shared their findings in two recent publications in Nature journal npj Vaccines.

Mp is a common pathogen that causes walking pneumonia. While this respiratory infection is not typically severe, it is a common co-pathogen with illnesses that spread in the same way, like the flu or COVID-19, which can cause more severe illnesses, especially in older or immunocompromised adults.

In the 1960s, scientists began working to develop an Mp vaccine. They killed the bacteria and injected it into human subjects, thinking it would provide protection from actual infection. But that’s not what happened.

Tuesday, November 8, 2022

Tracing tomatoes’ health benefits to gut microbes

The tomatoes used in the study were developed at Ohio State and are the type typically found in canned tomato products.
Photo Credit: Couleur

Two weeks of eating a diet heavy in tomatoes increased the diversity of gut microbes and altered gut bacteria toward a more favorable profile in young pigs, researchers found.

After observing these results with a short-term intervention, the research team plans to progress to similar studies in people, looking for health-related links between tomatoes in the diet and changes to the human gut microbiome – the community of microorganisms living in the gastrointestinal tract.

“It’s possible that tomatoes impart benefits through their modulation of the gut microbiome,” said senior author Jessica Cooperstone, assistant professor of horticulture and crop science and food science and technology at The Ohio State University.

“Overall dietary patterns have been associated with differences in microbiome composition, but food-specific effects haven’t been studied very much,” Cooperstone said. “Ultimately we’d like to identify in humans what the role is of these particular microorganisms and how they might be contributing to potential health outcomes.”

Monday, November 7, 2022

A Microbe's Local Environment Can Be the Difference Between Life and Death

Co-cultures of bacterial strains that produce (magenta) or consume (cyan) nitric oxide show range-dependent growth and lead to single cell intermixing in the absence of oxygen. Scale bar represents 10 µm.
Credit: S. Wilbert

The microbial world shapes essentially every facet of our lives. Whether they are in the soils where our food is grown, or the lungs of a person with an infection, or at the bottom of the ocean, microbes live in diverse communities made up of multiple species all working together and impacting each other. Just like in our own neighborhoods, the geography of how a microbial community is laid out affects how those microbes live and function together.

Now, Caltech researchers have discovered that changes in local oxygen concentration have drastic impacts on whether microbial neighbors live or die in the presence of a common microbial by-product, nitric oxide (NO). The results suggest that large-scale global models, such as those of the nitrogen cycle, ought to work toward representing the fact that chemical microscale environments affect microbial behavior.

Call it a CRISPR conundrum

Model grass Brachypodium distachyon plant grown on liquid media.
Photo courtesy of Marta Torres, m-CAFEs postdoctoral researcher, Deutschbauer lab, Environmental Genomics and Systems Biology "
Credit: University of California, Lawrence Berkeley National Laboratory."

Bacteria use CRISPR-Cas systems as adaptive immune systems to withstand attacks from enemies like viruses. These systems have been adapted by scientists to remove or cut and replace specific genetic code sequences in a variety of organisms.

But in a new study, North Carolina State University researchers show that viruses engineered with a CRISPR-Cas system can thwart bacterial defenses and make selective changes to a targeted bacterium – even when other bacteria are in close proximity.

“Viruses are very good at delivering payloads. Here, we use a bacterial virus, a bacteriophage, to deliver CRISPR to bacteria, which is ironic because bacteria normally use CRISPR to kill viruses,” said Rodolphe Barrangou, the Todd R. Klaenhammer Distinguished Professor of Food, Bioprocessing and Nutrition Sciences at NC State and corresponding author of a paper describing the research published today in Proceedings of the National Academy of Sciences. “The virus in this case targets E. coli by delivering DNA to it. It’s like using a virus as a syringe.”

The NC State researchers deployed two different engineered bacteriophages to deliver CRISPR-Cas payloads for targeted editing of E. coli, first in a test tube and then within a synthetic soil environment created to mimic soil – a complex environment that can harbor many types of bacteria.

University of Oxford study provides important insights into TB correlates of protection

Drug-resistant, Mycobacterium tuberculosis bacteria, the pathogen responsible for causing the disease tuberculosis (TB). A 3D computer-generated image.
Image Credit: CDC

Researchers from the University of Oxford have today reported findings from a study that investigated whether previously identified correlates of protection associated with risk of full-blown tuberculosis (TB) disease could also be associated with risk of infection from the bacteria that causes TB - highlighting certain correlates in the process.

In their paper on the TB020 study, published in Nature Communications, researchers identified that certain correlates of protection – inflammation and activation of the immune system (where the body responds to invading pathogens such as viruses and harmful bacteria) – were associated with the likelihood of becoming infected with Mycobacterium tuberculosis (M.tb), the bacteria that causes TB disease.

However, their previously identified correlates of risk of TB disease were not associated with an increased risk of M.tb infection in infants who became infected with the bacteria but did not progress to active TB.

Most individuals infected with M.tb do not progress to full TB disease. Instead, infection is either eliminated or contained by the infected individual. This study improves understanding of the immune-related factors that drive infection and disease – necessary for an effective TB vaccine that is yet to be developed.

Friday, November 4, 2022

A new weapon against antibiotic-resistant bacteria

This inoculated MacConkey agar culture plate cultivated colonial growth of Gram-negative, small rod-shaped and facultatively anaerobic Klebsiella pneumoniae bacteria. K. pneumoniae bacteria are commonly found in the human gastrointestinal tract, and are often the cause of hospital acquired, or nosocomial infections involving the urinary and pulmonary systems.
Credit: CDC

The unreasonable use of antibiotics has pushed bacteria to develop resistance mechanisms to this type of treatment. This phenomenon, known as antibiotic resistance, is now considered by the WHO as one of the greatest threats to health. The lack of treatment against multi-resistant bacteria could bring us back to a time when millions of people died of pneumonia or salmonella. The bacterium Klebsiella pneumoniae, which is very common in hospitals and particularly virulent, is one of the pathogens against which our weapons are becoming blunt. A team from the University of Geneva (UNIGE) has discovered that edoxudine, an anti-herpes molecule discovered in the 60s, weakens the protective surface of Klebsiella bacteria and makes them easier to eliminate for immune cells. These results can be read in the journal PLOS One.

Klebsiella pneumoniae causes many respiratory, intestinal and urinary tract infections. Due to its resistance to most common antibiotics and its high virulence, some of its strains can be fatal for 40% to 50% of infected people. There is an urgent need to develop new therapeutic molecules to counter it. “Since the 1930s, medicine has relied on antibiotics to get rid of pathogenic bacteria,” explains Pierre Cosson, professor in the Department of Cell Physiology and Metabolism at the UNIGE Faculty of Medicine, who led this research. “But other approaches are possible, among which trying to weaken the bacteria’s defense system so that they can no longer escape the immune system. This avenue seems all the more promising as the virulence of Klebsiella pneumoniae stems largely from its ability to evade attacks from immune cells.”

Thursday, November 3, 2022

Carnivore Gut Microbes Offer Insight into Health of Wild Ecosystems

wild American marten
Photo Credit: Cunigunde 

A new study finds the microbial ecosystem in the guts of wild marten (Martes americana) that live in relatively pristine natural habitat is distinct from the gut microbiome of wild marten that live in areas that are more heavily impacted by human activity. The finding highlights an emerging tool that will allow researchers and wildlife managers to assess the health of wild ecosystems.

“Specifically, we found that wild marten in relatively undisturbed environments have more carnivorous diets than martens in human-affected areas,” says Erin McKenney, co-lead author of a paper on the work and an assistant professor of applied ecology at North Carolina State University. Marten are small mammals, related to weasels, ferrets and mink.

“In conjunction with our other work on carnivore microbiomes, this finding tells us the microbial ecosystems in carnivore guts can vary significantly, reflecting a carnivore’s environment,” McKenney says. “Among other things, this means we can tell how much humans are impacting an area by assessing the gut microbiomes of carnivores that live in that area – which can be done by testing wild animal feces. In practical terms, this work reveals a valuable tool for assessing the health of wild ecosystems.”

“Our goal here was to determine how, if at all, human disturbance of a landscape affects the gut microbiome of American marten that live in that landscape,” says Diana Lafferty, co-lead author of the paper and an assistant professor of biology at Northern Michigan University. “And the answers here were pretty clear.”

Ocean microbes get their diet through a surprising mix of sources, study finds

Long thought to rely solely on photosynthesis, the microbe Prochlorococcus may get as much as one-third of its carbon through a second strategy: consuming the dissolved remains of other dead microbes. Illustration Credit: Jose-Luis Olivares, MIT

One of the smallest and mightiest organisms on the planet is a plant-like bacterium known to marine biologists as Prochlorococcus. The green-tinted microbe measures less than a micron across, and its populations suffuse through the upper layers of the ocean, where a single teaspoon of seawater can hold millions of the tiny organisms.

Prochlorococcus grows through photosynthesis, using sunlight to convert the atmosphere’s carbon dioxide into organic carbon molecules. The microbe is responsible for 5 percent of the world’s photosynthesizing activity, and scientists have assumed that photosynthesis is the microbe’s go-to strategy for acquiring the carbon it needs to grow.

But a new MIT study in Nature Microbiology today has found that Prochlorococcus relies on another carbon-feeding strategy, more than previously thought.

Organisms that use a mix of strategies to provide carbon are known as mixotrophs. Most marine plankton are mixotrophs. And while Prochlorococcus is known to occasionally dabble in mixotrophy, scientists have assumed the microbe primarily lives a phototrophic lifestyle.

The new MIT study shows that in fact, Prochlorococcus may be more of a mixotroph than it lets on. The microbe may get as much as one-third of its carbon through a second strategy: consuming the dissolved remains of other dead microbes.

Bacterial armor plating has implications for antibiotics

Magnified view of the E. coli outer membrane showing hexagonal clustering of proteins (red/green), alongside body armor for comparison. The black background represents lipids that are shared between neighboring proteins.
Image Credit: Dheeraj Prakaash and Syma Khalid Department of Biochemistry, University of Oxford

A new study published in the journal Science Advances sheds light on how Gram-negative bacteria like E. coli construct their outer membrane to resemble body armor, which has far-reaching implications for the development of antibiotics.

Professor Colin Kleanthous in the Department of Biochemistry at the University of Oxford led the interdisciplinary study, with contributions from colleagues in Oxford and University College London. They undertook a microscopic examination of the outer membrane of E. coli to understand the molecular basis for the protection it affords against many classes of antibiotics. E. coli causes infections such as pneumonia, UTIs and sepsis that are notoriously difficult to treat due to multidrug resistance.

The outer membrane is composed of two types of lipids that stack on top of each other, an unusual arrangement which, it was thought, is solely responsible for making the membrane resistant to antibiotics. As well as lipids, the outer membrane contains numerous proteins which the bacterium relies on to acquire nutrients and excrete waste products. Textbooks classically show these proteins dotted randomly in the membrane, contributing little to its stability or structure.

The discovery of Professor Kleanthous and colleagues came from them asking a simple question: do protein interactions play any role in the structural integrity of the outer membrane?

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