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

Monday, March 18, 2024

Alzheimer’s Drug Fermented with Help from AI and Bacteria Moves Closer to Reality

Photo-Illustration Credit: Martha Morales/The University of Texas at Austin

Galantamine is a common medication used by people with Alzheimer’s disease and other forms of dementia around the world to treat their symptoms. Unfortunately, synthesizing the active compounds in a lab at the scale needed isn’t commercially viable. The active ingredient is extracted from daffodils through a time-consuming process, and unpredictable factors, such as weather and crop yields, can affect supply and price of the drug. 

Now, researchers at The University of Texas at Austin have developed tools — including an artificial intelligence system and glowing biosensors — to harness microbes one day to do all the work instead. 

In a paper in Nature Communications, researchers outline a process using genetically modified bacteria to create a chemical precursor of galantamine as a byproduct of the microbe’s normal cellular metabolism.  Essentially, the bacteria are programmed to convert food into medicinal compounds.

“The goal is to eventually ferment medicines like this in large quantities,” said Andrew Ellington, a professor of molecular biosciences and author of the study. “This method creates a reliable supply that is much less expensive to produce. It doesn’t have a growing season, and it can’t be impacted by drought or floods.” 

Tuesday, March 12, 2024

Researchers discover a coral superhighway in the Indian Ocean

A coral reef in the Seychelles.
Photo Credit: Christophe Mason-Parker

Despite being scattered across more than a million square kilometers, new research has revealed that remote coral reefs across the Seychelles are closely related. Using genetic analyses and oceanographic modelling, researchers at Oxford University demonstrated for the first time that a network of ocean currents scatter significant numbers of larvae between these distant islands, acting as a ‘coral superhighway.’ These results have been published today in Nature Scientific Reports.

"This study couldn’t come at a timelier moment. The world is once again watching, as El Niño devastates coral reefs throughout the Indian Ocean. Now we know which reefs will be crucial to coral recovery, but we can’t pause in our commitment to reducing greenhouse gas emissions and stopping climate change."
Senior author of the study, Professor Lindsay Turnbull 
Department of Biology, University of Oxford

Dr April Burt (Department of Biology, University of Oxford, and Seychelles Islands Foundation), lead author of the study, said: ‘This discovery is very important because a key factor in coral reef recovery is larval supply. Although corals have declined alarmingly across the world due to climate change and a number of other factors, actions can be taken at local and national scale to improve reef health and resilience. These actions can be more effective when we better understand the connectivity between coral reefs by, for instance, prioritizing conservation efforts around coral reefs that act as major larval sources to support regional reef resilience.’

Monday, March 11, 2024

“Molecular Rosetta Stone” Reveals How our Microbiome Talks to Us

Bacteria in the gut convert bile acids produced by the liver into a wide array of new compounds. These molecules are akin to the language of the gut microbiome, allowing them to influence distant organ systems.
Photo Credit: Lakshmiraman Oza

Researchers from Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego have uncovered thousands of previously unknown bile acids, a type of molecule used by our gut microbiome to communicate with the rest of the body.

“Bile acids are a key component of the language of the gut microbiome, and finding this many new types radically expands our vocabulary for understanding what our gut microbes do and how they do it,” said senior author Pieter Dorrestein, Ph.D., professor at Skaggs School of Pharmacy and Pharmaceutical Sciences and professor of pharmacology and pediatrics at UC San Diego School of Medicine. “It’s like going from ‘See Spot Run’ to Shakespeare.”

The results, as described by study co-author and bile acids expert Lee Hagey, Ph.D, are akin to a molecular Rosetta stone, providing previously unknown insight into the biochemical language microbes use to influence distant organ systems.

Tuesday, March 5, 2024

Possible ‘Trojan Horse’ found for treating stubborn bacterial infections

Transmission electron microscope (TEM) image of the bacterial cell with an extracellular vesicle attached.
Image Credit: Courtesy of Washington State University

Bacteria can be tricked into sending death signals to stop the growth of their slimy, protective homes that lead to deadly infections, a new study demonstrates.

The discovery by Washington State University researchers could someday be harnessed as an alternative to antibiotics for treating difficult infections. Reporting in the journal Biofilm, the researchers used the messengers, which they named death extracellular vesicles (D-EVs), to reduce growth of the bacterial communities by up to 99.99% in laboratory experiments.

“Adding the death extracellular vesicles to the bacterial environment, we are kind of cheating the bacteria cells,” said Mawra Gamal Saad, first author on the paper and a graduate student in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering. “The cells don’t know which type of EVs they are, but they take them up because they are used to taking them from their environment, and with that, the physiological signals inside the cells change from growth to death.”

Monday, February 26, 2024

Scientists assemble a richer picture of the plight and resilience of the foothill yellow-legged frog

Foothill yellow-legged frogs live in the flowing water of rivers and streams, so are especially vulnerable when these shrink to isolated pools.
Photo Credit: Brome McCreary / USGS

Up to only a few inches in length, with a lemon-hued belly, the foothill yellow-legged frog may seem unassuming. But its range once stretched from central Oregon to Baja California. In 2023, it was listed under the federal Endangered Species Act. Its rapidly decreasing range is due in part to a fungal pathogen called Batrachochytrium dendrobatidis, or Bd, that has devastated amphibians around the world.

A team of researchers, including UC Santa Barbara’s Andrea Adams, has conducted the most comprehensive study to date of disease dynamics in foothill yellow-legged frogs. The team’s data — sourced from both wild frogs and specimens in museum collections — enabled them to track patterns of infection across a large geographic range. In a study published in Royal Society Open Science, the researchers reveal that drought, rising temperatures and the increasing conversion of land for agriculture appear to be the largest factors driving Bd infection in this species.

The researchers aimed to assemble as much data as they could, both in space and time. They surveyed in the creeks and rivers of California and Oregon, where they swabbed wild yellow-legged frogs for the presence of Bd. It also led them into fluorescent-lit museum collections to sample specimens from as far back as the 1890s.

Friday, February 23, 2024

Research reveals new insights into marine plastic pollution

Photo Credit: Lucien Wanda

A groundbreaking study led by researchers at the University of Stirling has uncovered the crucial role of bacteria living on plastic debris.

The research also identifies rare and understudied bacteria that could assist in plastic biodegradation, offering new insights for tackling plastic pollution.

Plastic pollution is a worldwide problem, with up to two million tons estimated to enter oceans every year, damaging wildlife and ecosystems.

In a pioneering study, experts at the University of Stirling’s Faculty of Natural Sciences and the University of Mons (Belgium) analyzed the proteins in plastic samples taken from Gullane Beach in Scotland.

Unlike previous studies carried out in warmer climates that focus on the genetic potential of biofilms inhabiting plastics, this research led by Dr Sabine Matallana-Surget took a unique approach by analyzing the proteins expressed by active microorganisms.

Their findings have unveiled a remarkable discovery of enzymes actively engaged in degrading plastic. Moreover, the team has pioneered new methodologies for enhanced predictions in marine microbiology research.

Thursday, February 22, 2024

Mice study suggests metabolic diseases may be driven by gut microbiome, loss of ovarian hormones

Mice that received fecal implants from donors that had their ovaries removed gained more fat mass and had greater expression of liver genes associated with inflammation, Type 2 diabetes, fatty liver disease and atherosclerosis. The findings may shed light on the greater incidence of metabolic dysfunction in postmenopausal women. The team members included, from left: molecular and integrative physiology professor Erik R. Nelson; Kelly Swanson, the director of the Division of Nutritional Sciences and the Kraft Heinz Endowed Professor in Human Nutrition; and animal sciences professor Brett R. Loman.
  Photo Credit: Fred Zwicky

The gut microbiome interacts with the loss of female sex hormones to exacerbate metabolic disease, including weight gain, fat in the liver and the expression of genes linked with inflammation, researchers found in a new rodent study.

The findings, published in the journal Gut Microbes, may shed light on why women are at significantly greater risk of metabolic diseases such as obesity and Type 2 diabetes after menopause, when ovarian production of female sex hormones diminishes.

“Collectively, the findings demonstrate that removal of the ovaries and female hormones led to increased permeability and inflammation of the gut and metabolic organs, and the high-fat diet exacerbated these conditions,” said Kelly S. Swanson, the director of the Division of Nutritional Sciences and the Kraft Heinz Endowed Professor in Human Nutrition at the University of Illinois Urbana-Champaign who is a corresponding author of the paper.  “The results indicated that the gut microbiome responds to changes in female hormones and worsens metabolic dysfunction.”

Monday, February 19, 2024

Discovery about bacterial cell walls can lead to new antibiotics

Felipe Cava is Professor of Infection Biology, Department of Molecular Biology, Umeå University and affiliated group leader with the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR) and the Integrated Science Lab (Icelab) and SciLifeLab.
Photo Credit: 
Mattias Pettersson, simon ohman jonsson inhousebyran

Researchers at Umeå University in Sweden, led by Professor Felipe Cava, have identified a new family of enzymes that creates a unique type of cross-linking between the building blocks of bacterial cell walls. This discovery could help develop new antibiotics against infectious diseases.

Bacterial cell walls form mesh-like structures, shielding cells from rupturing under high internal pressure and safeguarding against external threats. The cell wall is comprised of sugar and amino acid molecules interconnected by various types of cross-links. These cross-links play a crucial role in providing strength and stability to the cell wall, while also enabling bacteria to adapt to diverse environments and stressors.

In a groundbreaking study recently published in the esteemed journal Nature Communications, researchers from Umeå University and international institutions have unveiled a novel family of enzymes responsible for generating a unique cross-linkage between L-alanine and meso-diaminopimelic acid. These amino acids are integral components of the peptide chains constituting the cell wall of numerous bacterial species. Termed LD1,3-transpeptidase, this enzyme has been identified across various groups of alpha and beta proteobacteria, including opportunistic pathogens such as Burkholderia and Achromobacter.

Thursday, February 15, 2024

Scientists are unraveling the secrets of red and grey squirrel competition

Image Credit: Gemini Advance AI

In a first of its kind study, researchers have identified significant differences between the diversity of gut bacteria in grey squirrels compared to red squirrels which could hold the key to further understanding the ability of grey squirrels to outcompete red squirrels in the UK. 

New research, published in the Journal of Medical Microbiology, looked to understand more about the mechanisms by which grey squirrels are able to gain an advantage over red squirrels. Chris Nichols, Conservation Evidence Manager at the Woodland Trust, and co-author of the study, said:

“The more we know about grey squirrels, the more equipped we’re going to be in the future to tackle the threats they pose to red squirrels and our native trees, which is one of the biggest problems for forest conservation in the UK.”

Grey squirrels are an invasive, non-native species introduced from North America to sites in Great Britain and Ireland between 1876 to 1929. They out-compete the native red squirrels and multiply thanks to various traits including their ability to access a broader range of food sources including the bark of UK broadleaved trees. This causes significant damage to the trees, and is a behavior that, prior to this research, was not completely understood. 

Wednesday, February 14, 2024

Better diagnosis and treatment of cryptococcosis

Photo Credit: Courtesy of University of Cologne

Global guideline for the management of cryptococcosis, a fungal infection that can have serious health consequences, published in the journal ‘The Lancet Infectious Diseases

A group of international mycology experts led by Professor Dr Oliver A. Cornely at the University of Cologne has jointly drafted a guideline for the diagnosis and treatment of cryptococcosis, which aims at improving infection management and thus the survival rate of patients. Cryptococcosis is a fungal infection of mainly the lungs that might lead to meningitis. The article ‘Global guideline for the diagnosis and management of cryptococcosis’ was published in the journal The Lancet Infectious Diseases.

Cryptococcosis, especially cryptococcal meningitis (CM) as the most fatal form, is responsible for a high fatality rate among patients. It is one of the most widespread invasive fungal infections in the world and is a major threat particularly to people suffering from immunodeficiencies. For example, around one million cases of cryptococcal meningoencephalitis are diagnosed worldwide every year in people with HIV alone, and more than 600,000 people die from the disease each year. Patients who have undergone a bone marrow transplant or organ transplant are also at high risk of infection. It is transmitted through the inhalation of spores from soil. Other organs are then also infected via the bloodstream. The lungs, brain, skin and bones are most frequently affected.

Compounds released by bleaching coral reefs promote bacteria

Field site in Moʻorea, French Polynesia.
Photo Credit: Milou Arts of NIOZ

On healthy reefs, corals, algae, fishes and microbes live interconnected and in balance—exchanging nutrients, resources and chemical signals. New research led by the University of Hawaiʻi at Mānoa and the Royal Netherlands Institute for Sea Research (NIOZ) revealed that when coral bleaching occurs, corals release unique organic compounds into the surrounding water that not only promote bacterial growth overall, but also promote bacteria that may further stress reefs and pose the risk for more damage.

“Our results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend beyond coral and into the water column,” said Wesley Sparagon, co-lead author, postdoctoral researcher in the UH Mānoa College of Tropical Agriculture and Human Resources and previous doctoral student with the UH Mānoa School of Ocean and Earth Science and Technology (SOEST).

The research team, which included scientists from UH Mānoa, NIOZ, Scripps Institution of Oceanography and University of California, Santa Barbara, conducted experiments on bleached and unbleached corals gathered during a bleaching event in Moorea, French Polynesia in 2019.

“Although coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, there has been relatively little research on the implications for reef water column microbiology and biogeochemistry,” said Craig Nelson, senior author on the study and professor in SOEST.

Thursday, December 21, 2023

Multitasking microbes: UW–Madison scientists engineer bacteria to make two valuable products from plant fiber

Ben Hall, Genetics Ph.D. Student, holds a mixed sample of microbes and carotenoids, in Tim Donohue’s lab.
Photo Credit: Chelsea Mamott

We often look to the smallest lifeforms for help solving the biggest problems: Microbes help make foods and beverages, cure diseases, treat waste and even clean up pollution. Yeast and bacteria can also convert plant sugars into biofuels and chemicals traditionally derived from fossil fuels — a key component of most plans to slow climate change.

Now University of Wisconsin–Madison researchers have engineered bacteria that can produce two chemical products at the same time from underutilized plant fiber. And unlike humans, these multitasking microbes can do both things equally well.

“To my knowledge, it’s one of the first times you can make two valuable products simultaneously in one microbe,” says Tim Donohue, UW–Madison professor of bacteriology and director of the Great Lakes Bioenergy Research Center.

The discovery, detailed in a paper in the December issue of the journal Applied and Environmental Microbiology, could help make biofuels more sustainable and commercially viable.

“In principle, the strategy lowers the net greenhouse gas emissions and improves the economics,” Donohue says. “The amount of energy and greenhouse gas that you need to make two products in one pot is going to be less than running two pots to make one product in each pot.”

Wednesday, December 20, 2023

Discovery: plants use “trojan horse” to fight mold invasions

Photo Credit: Gábor Adonyi

UC Riverside scientists have discovered a stealth molecular weapon that plants use to attack the cells of invading gray mold. 

If you’ve ever seen a fuzzy piece of fruit in your fridge, you’ve seen gray mold. It is an aggressive fungus that infects more than 1,400 different plant species: almost all fruits, vegetables, and many flowers. It is the second most damaging fungus for food crops in the world, causing billions in annual crop losses.

A new paper in the journal Cell Host & Microbe describes how plants send tiny, innocuous-seeming lipid “bubbles” filled with RNA across enemy lines, into the cells of the aggressive mold. Once inside, different types of RNA come out to suppress the infectious cells that sucked them in.

“Plants are not just sitting there doing nothing. They are trying to protect themselves from the mold, and now we have a better idea how they’re doing that,” said Hailing Jin, Microbiology & Plant Pathology Department professor at UCR and lead author of the new paper.

Previously, Jin’s team discovered that plants are using the bubbles, technically called extracellular vesicles, to send small RNA molecules able to silence genes that make the mold virulent. Now, the team has learned these bubbles can also contain messenger RNA, or mRNA, molecules that attack important cellular processes, including the functions of organelles in mold cells. 

Monday, December 18, 2023

Giant bacterium powers itself with unique processes

Micrograph of a group of Epulopiscium viviparus bacteria.
Image Credit: Esther Angert

Not all bacteria are created equal.

Most are single-celled and tiny, a few ten-thousandths of a centimeter long. But bacteria of the Epulopiscium family are large enough to be seen with the naked eye and 1 million times the volume of their better-known cousins, E. coli.

In a study published Dec. 18 in Proceedings of the National Academy of Sciences, researchers from Cornell and Lawrence Berkeley National Laboratory have for the first time described the full genome of one species of the family of giants, which they’ve named Epulopiscium viviparus.

“This incredible giant bacterium is unique and interesting in so many ways: its enormous size, its mode of reproduction, the methods by which it meets its metabolic needs and more,” said Esther Angert, professor of microbiology in the College of Agriculture and Life Sciences, and corresponding author of the study. “Revealing the genomic potential of this organism just kind of blew our minds.”

The first member of the Epulopiscium family was discovered in 1985. All members of the species live symbiotically within the intestinal tracts of certain surgeonfish in tropical marine coral reef environments, such as the Great Barrier Reef and in the Red Sea.

Genetic sequencing uncovers unexpected source of pathogens in floodwaters

A NASA image containing visible and infrared data revealing the presence of dissolved organic matter – including potential antibiotic-resistant pathogens – in the waterways along coastal North Carolina after Hurricane Florence.
Image Credit: Courtesy NASA

Researchers report in the journal Geohealth that local rivers and streams were the source of the Salmonella enterica contamination along coastal North Carolina after Hurricane Florence in 2018 – not the previously suspected high number of pig farms in the region. 

These findings have critical implications for controlling the spread of disease caused by antibiotic-resistant pathogens after flooding events, particularly in the coastal regions of developing countries that are being highly impacted by the increase in tropical storms. 

The study, led by civil and environmental engineering professor Helen Nguyen and graduate student Yuqing Mao, tracks the presence and origin of S. enterica from environmental samples from coastal North Carolina using genetic tracing. 

“Infections caused by antibiotic-resistant pathogens are responsible for approximately 2.8 million human illnesses and 36,000 deaths per year in the U.S. alone,” Nguyen said. “These infections spread easily across the globe and are a major burden on burgeoning health care systems, but they are preventable through mitigation.”

Dramatic rise in antibiotic use in first year of pandemic in primary care

Excessive use of antibiotics can give rise to bacterial resistance to these drugs, making bacterial infections increasingly hard to treat
Image Credit: Arek Socha

Antibiotics have no effect on viruses, and that includes the coronavirus. Yet in the first year of the pandemic, primary care physicians in Switzerland prescribed antibacterial medications twice as frequently as before, report researchers at the University of Basel. A risky practice, warns the research team.

It was a time of great uncertainty. When the first wave of the new coronavirus swept across Switzerland in winter and spring 2020, there were no diagnostic tests, no vaccines, and no effective medications. During this precarious phase, primary care physicians based in Switzerland seem to have increasingly resorted to treating patients with antibiotics, even though these medications have no effect on viruses. This was the conclusion reached by a research team led by Professor Heiner C. Bucher from the Department of Clinical Research at the University of Basel and University Hospital Basel.

As the team reports in the journal Clinical Microbiology and Infection, the use of antibiotics doubled from around eight to 16 prescriptions per 100 consultations. During the first wave of SARS-CoV-2 at the beginning of 2020, a massive rise in prescriptions of antibiotics became apparent. Prescriptions then remained at an above-average level throughout the year compared with previous years (2017-2019).

New possibilities for a healing toxin

Richard Kammerer and Oneda Leka in one of the PSI laboratories in front of an apparatus that is used, among other things, to purify proteins.
Photo Credit: Paul Scherrer Institute/Mahir Dzambegovic

PSI researchers have discovered a surprising trick that could expand the possibilities for medical use of botulinum toxin A1, better known under the name Botox, as an active agent. They have developed antibody-like proteins that speed up the enzyme’s effect on the transmission of nerve signals. This suggests that Botox might, for example, be able to relief pain more quickly than before. The study has now been published in the journal Nature Communications.

Botulinum neurotoxin A1, better known under the trademark Botox, is actually a nerve toxin produced by bacteria. It gained widespread public awareness through its use as a cosmetic aid. Many people have it injected into wrinkles to make them look younger. The substance blocks signal transmission from nerves to muscles, thus relaxing them so that facial features appear smooth. What is less well known: Botox is also used very often in therapeutic medicine to treat conditions that can be traced back to cramping muscles or faulty nerve signals, including pains, spasms, bladder weakness, grinding of teeth, and misalignments, for example of the eyes. Botox is even used in treating stomach cancer, to block the vagus nerve and thus slow down tumor growth.

In any therapy, it is crucial to use this highly effective medicine in a very targeted manner with careful dosage, since Botox is the most potent natural nerve toxin of all, which can lead to dangerous paralysis in a clinical picture called botulism. Just one hundred nanograms or so administered intravenously can be enough to kill a person, because the toxin paralyses the respiratory muscles, along with others.

Friday, December 15, 2023

The keto diet protects against epileptic seizures. Scientists are uncovering why

Photo Credit: Jenna Hamra

The high-fat, low-carbohydrate ketogenic diet is more than just a trendy weight-loss tactic. It has also been known to help control seizures in children with epilepsy, particularly those who don’t respond to first-line anti-seizure medications.

In a new UCLA study published in the journal Cell Reports, researchers demonstrate that the changes the diet causes in the human gut microbiome — the trillions of bacteria and other microorganisms that live in the digestive tract — can confer protection against seizures in mice.

Understanding how the function of the microbiome is altered by the diet could aid in the development of new therapeutic approaches that incorporate these beneficial changes while avoiding certain drawbacks of the diet, said the study’s lead author, Gregory Lum, a postdoctoral researcher in the laboratory of UCLA professor Elaine Hsiao.

The ketogenic diet is not recommended as a primary anti-seizure option because patients are often averse to drastic changes in their food intake or have trouble staying on the diet due to its strict requirements and potential side effects like, nausea, constipation and fatigue.

Revealed: Some microbiome species regulate their entire bacterial ecosystem

Image Credit: Scientific Frontline 

A team of mathematicians and biologists led by Carnegie’s Will Ludington and Technische Universität Berlin’s Michael Joswig developed a new approach to reveal key genes and species that regulate biological networks. Their work, published this week in Proceedings of the National Academy of Sciences, identifies genes in cells and species in ecosystems that sit at the top of a regulatory hierarchy and drive evolutionary and ecological trajectories.

Charles Darwin concluded On the Origin of Species with the famous “tangled bank” analogy to explain how organisms in an ecosystem affect one another’s fitness. “It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth,” Darwin wrote. “And to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us.” 

To map these interactions in ecosystems, ecologists use network analysis to study the connections. Keystone species, such as wolves, have a disproportionately large impact on their communities and the other organisms within them.

Thursday, December 14, 2023

Ribosomal protein exhibits remarkable evolutionary transformation

The cryo-EM maps and atomic models showing the structure of ribosomal protein msL1 in the ribosome from microsporidian parasites V. necatrix (first row), and protein msL2 in the ribosome from microsporidian parasites E. cuniculi (second row).
Illustration Credit: Leon Schierholz

A team of researchers from the Universities of Newcastle and Umeå has discovered that a ribosomal protein exhibits a remarkable evolutionary transformation, with its three-dimensional structure changing drastically while its sequence remains relatively conserved.

The protein, known as msL1/msL2, is found in ribosomes of parasitic microorganisms called microsporidia, and it is suggested to play a role in stabilizing the highly reduced protein synthesis machinery in these unique organisms. 

“Despite its conserved sequence, msL1/msL2 adopts distinct folds in two different microsporidian species, Encephalitozoon cuniculi, and Vairimorpha necatrix. This structural divergence is particularly striking given that the two proteins share approximately 41% sequence similarity,” comments Léon Schierholz, one of the authors from Umeå University.  

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