Phage structure captured for the first time, to benefit biotech applications

Phage image
Image Credit: Dr Vicki Gold et al, Nature Communications

New insights into the structure of phages will enable researchers to develop new uses for viruses in biotechnology.

Phages are viruses that infect bacteria, which enables them to be exploited as tools in biotechnology and medicine. Now, for the first time, researchers at the University of Exeter, in collaboration with Massey University and Nanophage Technologies, New Zealand, have mapped out what a commonly-used form of phage looks like, which will help researchers design better uses in future.

One common use for phage is phage display, which is a useful tool in drug discovery. Phage display works by linking a gene fragment of interest to a phage gene that makes one of the phage coat proteins. The new coat protein with the linked protein of interest appears on the surface of the phage, where it can be assayed and tested for biological activity.

Billions of types of phages exist. Phage display often uses a type of phage known as filamentous, so called because they are long and thin, making the display of many proteins across its surface possible. Although phage display and other applications have proved successful, until now, scientists have not known what this type of phage looks like.

Resistant mushroom species spreads

Candida auris infections are difficult to treat and potentially life-threatening. The picture shows yeast cells from C. auris on the left and a fluconazole-resistant C. auris strain on the right.
Image Credit: Alexander Aldejohann

In Germany, too, the number of infections with the Candida auris fungus is increasing. This is shown by a new study by research teams from Würzburg, Jena and Berlin. Despite the low numbers, those involved advise precautionary measures.

Among the yeasts from the genus Candida, that cause infections in humans is the type Candida auris still relatively new: this species was only described in 2009, and no evidence is known before the 1990s. It is unclear which ecological niche C. auris populated and why human infections have increased since the turn of the millennium.

The treatment of C. auris infections are made considerably more difficult by the potential of the pathogen to develop resistance to all available antifungals classes. In addition, C. auris unlike others Candida- Types, are efficiently transmitted from patient to patient via direct and indirect contact, thus leading to hospital outbreaks that are difficult to control.

Brain-Belly Connection: Gut Health May Influence Likelihood of Developing Alzheimer’s

UNLV study pinpoints 10 bacterial groups associated with Alzheimer’s disease, provides new insights into the relationship between gut makeup and dementia.
Illustration Credit: Julien Tromeur

Could changing your diet play a role in slowing or even preventing the development of dementia? We’re one step closer to finding out, thanks to a new UNLV study that bolsters the long-suspected link between gut health and Alzheimer’s disease.

The analysis — led by a team of researchers with the Nevada Institute of Personalized Medicine (NIPM) at UNLV and published this spring in the Nature journal Scientific Reports — examined data from dozens of past studies into the belly-brain connection. The results? There’s a strong link between particular kinds of gut bacteria and Alzheimer’s disease.

Between 500 and 1,000 species of bacteria exist in the human gut at any one time, and the amount and diversity of these microorganisms can be influenced by genetics and diet.

The UNLV team’s analysis found a significant correlation between 10 specific types of gut bacteria and the likelihood of developing Alzheimer’s disease. Six categories of bacteria — Adlercreutzia, Eubacterium nodatum group, Eisenbergiella, Eubacterium fissicatena group, Gordonibacter, and Prevotella9 — were identified as protective, and four types of bacteria — Collinsella, Bacteroides, Lachnospira, and Veillonella — were identified as a risk factor for Alzheimer’s disease.

Like ancient mariners, ancestors of Prochlorococcus microbes rode out to sea on exoskeleton particles

New research suggests the Prochlorococcus microbe’s ancient coastal ancestors colonized the ocean by rafting out on chitin particles.
Illustration Credit: Jose-Luis Olivares/MIT
(CC BY-NC-ND 3.0)

Throughout the ocean, billions upon billions of plant-like microbes make up an invisible floating forest. As they drift, the tiny organisms use sunlight to suck up carbon dioxide from the atmosphere. Collectively, these photosynthesizing plankton, or phytoplankton, absorb almost as much CO2 as the world’s terrestrial forests. A measurable fraction of their carbon-capturing muscle comes from Prochlorococcus — an emerald-tinged free-floater that is the most abundant phytoplankton in the oceans today.

But Prochlorococcus didn’t always inhabit open waters. Ancestors of the microbe likely stuck closer to the coasts, where nutrients were plentiful and organisms survived in communal microbial mats on the seafloor. How then did descendants of these coastal dwellers end up as the photosynthesizing powerhouses of the open oceans today?

MIT scientists believe that rafting was the key. In a new study they propose that ancestors of Prochlorococcus acquired an ability to latch onto chitin — the degraded particles of ancient exoskeletons. The microbes hitched a ride on passing flakes, using the particles as rafts to venture further out to sea. These chitin rafts may have also provided essential nutrients, fueling and sustaining the microbes along their journey.

Ancestral mitoviruses discovered in mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi in the Glomeromycotina colonize plant roots (left, micrograph) and deliver water and nutrients from soil (right).
Image Credit: Tatsuhiro Ezawa

A new group of mitochondrial viruses confined to the arbuscular mycorrhizal fungi Glomeromycotina may represent an ancestral lineage of mitoviruses.

Mitochondria are organelles in the cells of almost all eukaryotes — organisms with cells that have a nucleus. They were originally free-living bacteria capable of generating energy in the presence of oxygen; then engulfed by an ancestral eukaryotic cell where they became mitochondria, the site of cellular respiration and many important metabolic processes. In humans, dysfunctions of mitochondria are associated with aging and many diseases.

Bacteriophages are viruses that infect bacteria. As former bacteria, there are also viruses that infect mitochondria, known as mitoviruses, which evolved from bacteriophages. While mitoviruses have been found in fungi, plants, and invertebrates, they are not well studied.

Associate Professor Tatsuhiro Ezawa at Hokkaido University, Professor Luisa Lanfranco at University of Torino, and Dr. Massimo Turina at National Research Council of Italy (CNR) Torino led an international team to discover a new group of mitoviruses, called large duamitoviruses. Their findings were published in the journal mBio.

Essential mechanism for bacterial gut colonization discovered

Tomogram of a Bacteroides thetaiotaomicron cell.
Image Credit: Matthew Swulius / Pennsylvania State University
(CC BY-NC-ND 4.0)

New light has been shed on a key event that contributes to the successful colonization of bacteria in the gut of mice, according to a new study from Yale University and Penn State. The study, published in Science, reveals that a physical process called "liquid-liquid phase separation" is essential for the survival and colonization of the beneficial bacteria Bacteroides thetaiotaomicron in the gut.

“In our field we are trying to understand how bacteria can colonize your gut and what the molecular components are that allow these organisms to reside in your intestines, because not all bacteria can,” said Guy Townsend, assistant professor of biochemistry and molecular biology at the Penn State College of Medicine and an author on the paper. Prior to this work, researchers did not understand the mechanisms that allowed B. thetaiotaomicron to thrive in the gut of mammals.

The researchers demonstrated the crucial role played by an “intrinsically disordered domain” (IDR) within a particular protein in the bacterium, called Rho, that facilitates liquid-liquid phase separation.

Liquid-liquid phase separation is when two liquids that don't mix well separate into different parts because of their chemical differences. This process helps cells create structures that don't have a membrane and are important for many cell functions.

Near-universal T cell immunity towards a broad range of bacteria

Neutralizing the bacterially derived cytotoxic bomb: the pneumococci lie in the background, an array of macrophages and dendritic cells are arranged around the central image of a T cell. Rows of TCRs interacting with the identified pneumolysin epitope bound to HLA (white) cross the length and breadth of the artwork, emphasizing their centrality in the immune response.
Illustration Credit: Dr. Erica Tandori.

Typically, T cells of the immune system respond to a specific feature (antigen) of a microbe, thereby generating protective immunity. As reported in the journal Immunity, an international team of scientists have discovered an exception to this rule. Namely, a group of divergent bacterial pathogens, including pneumococci, all share a small highly conserved protein sequence, which is both presented and recognized by human T cells in a conserved population-wide manner.

The study set out to understand immune mechanisms that protect against pneumococcus, a bacterial pathobiont that can reside harmlessly in the upper respiratory mucosae but can also cause infectious disease, especially in infants and older adults, which can range from middle ear and sinus infections to pneumococcal pneumonia and invasive bloodstream infections.

Most currently used pneumococcal polysaccharide-based conjugate vaccines (PCVs) are effective against 10–13 serotypes, but growing serotype replacement becomes a problem.

Hunting for microbes in the global ocean

Hunting for microbes in the global ocean. Sampling of seawater is performed with Niskin Bottles, which are cylindrical container used in oceanography to collect water samples containing microbes at various depths, triggered to snap shut at the desired depth.
Photo Credit: © 2022 Federico Baltar

A team of international researchers led by Federico Baltar of the University of Vienna and José M González of the University of La Laguna has identified a previously unknown group of bacteria, called UBA868, as key players in the energy cycle of the deep ocean. They are significantly involved in the biogeochemical cycle in the marine layer between 200 and 1000 meters. The results have now been published in the journal Nature Microbiology.

The deep sea, the marine layer at depths of 200 meters and more, accounts for about 90 percent of the world's ocean volume. It forms the largest habitat on Earth and is home to the largest number of microorganisms. These microorganisms contribute significantly to the biogeochemical cycles. They extract organic material, for example from phytoplankton and zooplankton, transform it and make it available again to the ecosystem as nutrients. In this way, they play a major role in the fixation and cycling of carbon. Dissolved sulfur compounds are also converted by bacteria and returned to the material cycle. 

Antimicrobial use in agriculture can breed bacteria resistant to first-line human defenses

E. coli bacteria
Image Credit: itstheeighthhorcrux

A new study led by the University of Oxford has shown that overuse of antimicrobials in livestock production can drive the evolution of bacteria more resistant to the first line of the human immune response. The results, published today in the journal eLife, indicate that farmed pigs and chickens could harbor large reservoirs of cross-resistant bacteria, capable of fueling future epidemics.

Drug-resistant infections are one of the most serious threats to global health, and there is an urgent need to develop new, effective antimicrobials. One promising solution could be antimicrobial peptides (AMPs). These are compounds naturally produced by most living organisms, including animals, and have important roles in innate immunity, our first line of defense against bacterial infections.

However, some AMPs are also used widely in livestock production, both to control infections and as growth promoters. This has raised concerns that agricultural AMP use may generate cross-resistant bacteria that could then overcome the human innate immune response.

 In this new study, led by the University of Oxford, researchers have demonstrated that evolution of such cross-resistant bacteria is not only possible, but also highly likely.

Earliest animal likely used chemical signaling to evolve into multicellular organism

J.P. Gerdt is an assistant professor of chemistry in the IU Bloomington College of Arts and Sciences.
 Photo Credit: Courtesy of J.P. Gerdt

The earliest animal likely used chemical signaling to evolve from a single cell to a multicellular organism, according to a study led by an Indiana University Bloomington scientist. The findings provide new information about how one of the biggest transitions in the history of life on earth likely occurred.

J.P. Gerdt, assistant professor of chemistry in the IU Bloomington College of Arts and Sciences, led the study, along with Núria Ros-Rocher of the Institute of Evolutionary Biology in Barcelona, Spain. Their findings are published in the Proceedings of the National Academy of Sciences.

“The general view is that animals evolved from a unicellular organism, and this research helps explain how that may have happened and how those cells chose whether to be together or on their own,” Gerdt said. “Our results help us understand more about the first animals and their ancestors.”

Study Finds Significant Variation in Anatomy of Human Guts

Photo Credit: Lauren Nichols.

New research finds there is significant variation in the anatomy of the human digestive system, with pronounced differences possible between healthy individuals. The finding has implications for understanding the role that the digestive tracts anatomy can play in affecting human health, as well as providing potential insights into medical diagnoses and the microbial ecosystem of the gut.

“There was research more than a century ago that found variability in the relative lengths of human intestines, but this area has largely been ignored since then,” says Amanda Hale, co-first author of the study and a Ph.D. candidate at North Carolina State University. “When we began exploring this issue, we were astonished at the extent of the variability we found.”

“If you’re talking to four different people, odds are good that all of them have different guts, in terms of the relative sizes of the organs that make up that system,” says Erin McKenney, corresponding author of the study and an assistant professor of applied ecology at NC State. “For example, the cecum is an organ that’s found at the nexus of the large and small intestine. One person may have a cecum that is only a few centimeters long, while another may have a cecum the size of a coin purse. And we found similar variability for many digestive organs.”

Algae in Swedish lakes provide insights to how complex life on Earth developed

Lönsboda, Sweden
Photo Credit: Johanna Nilsson

By studying green algae in Swedish lakes, a research team, led by Lund University in Sweden, has succeeded in identifying which environmental conditions promote multicellularity. The results give us new clues to the amazing paths of evolution.

The evolution of multicellular life has played a pivotal role in shaping biological diversity. However, we have up until now known surprisingly little about the natural environmental conditions that favor the formation of multicellular groups.

The cooperation between cells within multicellular organisms has enabled eyes, wings and leaves to evolve. The predominant explanation for why multicellularity evolves is that being in a group enables species to better cope with environmental challenges – where being in a large group can, for instance, protect cells against being eaten.

"Our results challenge this idea, showing that multicellular groups form, not because they are inherently beneficial, but rather as a by-product of single-celled strategies to reduce environmental stress. In particular, cells produce a range of substances to protect themselves from the environment and these substances appear to prevent daughter cells from dispersing away from their mother cell", says Charlie Cornwallis, biology researcher at Lund University.

UC Irvine biologists discover bees to be brew masters of the insect world

The UCI study found that the cellophane bee (pictured) ‘brew’ a liquid food for their offspring.
Photo Credit: Tobin Hammer

Scientists at the University of California, Irvine have made a remarkable discovery about cellophane bees – their microbiomes are some of the most fermentative known from the insect world. These bees, which are named for their use of cellophane-like materials to line their subterranean nests, are known for their fascinating behaviors and their important ecological roles as pollinators. Now, researchers have uncovered another aspect of their biology that makes them even more intriguing.

According to a study published in Frontiers in Microbiology, cellophane bees “brew” a liquid food for their offspring, held in chambers called brood cells. The microbiome of these brood cells is dominated by lactobacilli bacteria, which are known for their role in fermenting foods like yogurt, sauerkraut and sourdough bread. The researchers found that these bacteria are highly active in the food provisions of cellophane bees, where they likely play an important role as a source of nutrients for developing larvae.

Massive Caribbean sea urchin die-off caused by parasite

In a study led by Cornell microbiology professor Ian Hewson, scientists have discovered that a parasite is behind a severe die-off of long-spined sea urchins across the Caribbean Sea, which has had devastating consequences for coral reefs and surrounding marine ecosystems.

Video Credit: Noël Heaney/Cornell University 

Scientists have discovered that a parasite is behind a severe die-off of long-spined sea urchins across the Caribbean Sea, which has had devastating consequences for coral reefs and surrounding marine ecosystems.

The long-spined sea urchins (Diadema antillarum) serve as vital herbivores that graze on algae, which if left unchecked will outcompete corals for resources and space and blanket them, block light and kill them. By feeding on algae, the sea urchins are essential to maintaining coral health and balance in the marine ecosystem.

Diadema mortalities were first reported in St. Thomas in the U.S. Virgin Islands in late January 2022. By late March, the condition was found across the Lesser Antilles, Jamaica and the Mexican Caribbean. And by June of last year, it had been detected in most of the Greater Antilles, Florida and Curacao.

Prior to an experiment designed to verify the source of infections, a healthy sea urchin was swabbed to ensure it had never been exposed to the ciliate parasite.

Scientists have been trying to identify the cause of the mysterious illness, which has led to declines of between 85% and 95% compared to pre-mortality numbers in affected areas. When sea urchins die, they lose their spines and detach from their anchors.

Revealed: Molecular “superpower” of antibiotic-resistant bacteria

Scanning electron micrograph of en:Clostridioides difficile bacteria from a stool sample
Photo Credit: Public Health Image Library

A species of ordinary gut bacteria that we all carry flourishes when the intestinal flora is knocked out by a course of antibiotics. Since the bacteria is naturally resistant to many antibiotics, it causes problems, particularly in healthcare settings. A study led from Lund University in Sweden now shows how two molecular mechanisms can work together make the bacterium extra resistant. “Using this knowledge, we hope to be able to design even better medicines,” says Vasili Hauryliuk, senior lecturer at Lund University, who led the study.

The threat from antibiotic resistant bacteria is as well-known as it is grave. Last year, The Lancet reported that an estimated 1.27 million people died in 2019 as a result of bacterial infection that could not be treated with existing medicines. To tackle this threat is it is essential to understand the underpinning molecular mechanisms.

New study finds that microplastics can help dangerous bacteria survive on beaches

Microplastics on the beach
Photo Credit: Vera Kratochvil

New research from the University of Stirling has found that dangerous bacteria are able to survive the journey from sewage treatment plants to beaches on microplastic pollution.

During their study, scientists from the University’s Faculty of Natural Sciences found drug-resistant bacteria colonizing microplastics on Scottish beaches.  

The findings could have global consequences, with an estimated 2.3 million tons of plastic pollution thought to be floating in the world’s oceans.

Lead researcher Rebecca Metcalf, supervised by Professor Richard Quilliam, conducted her research by subjecting microplastics colonized by bacteria in wastewater to the different environments that they would likely pass through on their way to our beaches. She found that not only could the bacteria such as E. coli survive the entire journey, but that viable bacteria also survived for seven days on the sand. 

Microscopic Syringes for Stressed Out Strep

Slide culture of a Streptomyces
Photo Credit: Public Domain 

Researchers from the University of Tsukuba find that Streptomyces phage tail-like particles are located intracellularly, unlike other contractile injections systems, and protect the bacterium against osmotic stress

Everyone can use a little stress relief, even bacteria. Now, researchers from Japan have found that a bacterial nanomachine with an unusual cellular location can protect cells from stressful environments.

In a study published recently in mSphere, researchers from the University of Tsukuba have revealed that a protein complex related to phage tail-like secretion systems is expressed intracellularly in a model Gram-positive organism and protects it from osmotic stress.

Many types of bacteria contain genes encoding phage tail-like nanomachines called contractile injection systems (CISs). These systems are essentially little syringes that the bacteria produce and release into their environment to contact other cells and inject their contents.

Hundreds of thousands of fungi are denied scientific names

Drying soil samples immediately upon collection under field conditions in Norway.
Photo Credit: Sten Anslan

Fungi that do not form fruiting bodies and that we can’t cultivate in the laboratory cannot be given scientific names. This has left them essentially ignored by science. In a study coordinated from the university of Gothenburg, researchers analyzed a large dataset of fungal DNA sequences from global soil samples and found that these intangible fungi seem to dominate the fungal kingdom.

The concept of dark biodiversity denotes species that are recovered through DNA sequencing of substrates such as soil and water – but where no individuals of those species have ever been observed.

It has been known for more than a decade that the fungal kingdom is home to dark biodiversity, but the magnitude of this dark fungal diversity has been the subject of much speculation. A new study from the University of Gothenburg, published in the journal MycoKeys, addresses the question based on 8 million fungal DNA sequences from global soil sampling. The study turns our understanding of the fungi on its head by showing that the fungal kingdom may be almost exclusively dark.

Ambrosia beetles can recognize their food fungi by their scents

Nest of a black stem borer (Xylosandrus germanus) in a hazelnut branch with adult females (large), a male (small) and individual larvae. The greyish fungal coating of the food fungus is visible on the walls of the tunnel system.
Photo Credit: Antonio Gugliuzzo

Experiments at the University of Freiburg provide evidence for the first time of the ability of ambrosia beetles to distinguish between food and harmful fungi

Certain ambrosia beetles species engage in active agriculture. As social communities, they breed and care for food fungi in the wood of trees and ensure that so-called weed fungi spread less. Researchers led by Prof. Dr. Peter Biedermann, professor of Forest Entomology and Forest Protection at the University of Freiburg, now demonstrates for the first time that ambrosia beetles can distinguish between different species of fungi by their scents. "The results can contribute to a better understanding of why beetles selectively colonize trees with conspecifics and how exactly their fungiculture works," says Biedermann. "In addition, the scents of the fungi could be used to develop attractants to control non-native ambrosia beetles."

Scientists track evolution of microbes on the skin’s surface

An SEM image showing four yellow-colored, spheroid shaped, Staphylococcus aureus bacteria.
Image Credit: National Institute of Allergy and Infectious Diseases (NIAID)

Human skin is home to millions of microbes. One of these microbes, Staphylococcus aureus, is an opportunistic pathogen that can invade patches of skin affected by eczema, also known as atopic dermatitis.

In a new study, researchers at MIT and other institutions have discovered that this microbe can rapidly evolve within a single person’s microbiome. They found that in people with eczema, S. aureus tends to evolve to a variant with a mutation in a specific gene that helps it grow faster on the skin.

This study marks the first time that scientists have directly observed this kind of rapid evolution in a microbe associated with a complex skin disorder. The findings could also help researchers develop potential treatments that would soothe the symptoms of eczema by targeting variants of S. aureus that have this type of mutation and that tend to make eczema symptoms worse.

“This is the first study to show that Staph aureus genotypes are changing on people with atopic dermatitis,” says Tami Lieberman, an assistant professor of civil and environmental engineering and a member of MIT’s Institute for Medical Engineering and Science. “To my knowledge, this is the most direct evidence of adaptive evolution in the skin microbiome.”

Lieberman and Maria Teresa García-Romero, a dermatologist and assistant professor at the National Institute of Pediatrics in Mexico, are the senior authors of the study, which appears today in Cell Host and Microbe. Felix Key, a former MIT postdoc who is now a group leader at the Max Planck Institute for Infection Biology, is the lead author of the paper.