Harmful bacteria can elude predators when in mixed colonies

 Colonies of the bacterium V. cholerae (purple) insulate E. coli (yellow) from its natural predator
Image Credit: James Winans

Efforts to fight disease-causing bacteria by harnessing their natural predators could be undermined when multiple species occupy the same space, according to a study by Dartmouth College researchers.

When growing in mixed colonies, some harmful bacteria may be able to withstand attacks from the bacteria and viruses that target them by finding protection inside groups of rival species, according to a report published in the Proceedings of the National Academy of Sciences.

The researchers found that the intestinal bacterium Escherichia coli became surrounded by tightly packed colonies of Vibrio cholerae — which causes the deadly disease cholera — when the species were grown together. These clusters protected E. coli from the bacteria Bdellovibrio bacteriovorus that preys on both species individually, but in the study could only kill the outer layer of V. cholerae. This left the unscathed cells of E. coli and V. cholerae insulated within the colonies free to multiply.

Like mushroom out ants

Argentine ant workers with brood. Ants react immediately to contamination with pathogens and not only to the later developing symptoms of a disease. The nest comrades efficiently clean colony members of infectious particles.
Photo Credit: Sina Metzler & Roland Ferrigato / ISTA

An Austrian-German research team discovered how disease-causing fungi adapt to the collective hygiene measures of ants.

Ants show many social behaviors. For example, they care for sick individuals and make it difficult to spread pathogens among the people with joint hygiene measures. Germs not only have to outsmart the immune system of individual ants, but also the health care of the whole group.

A new study, the journal, shows how the pathogens do this Nature Ecology & Evolution is published. It was presented by the team of Professor Sylvia Cremer from the Institute of Science and Technology Austria (ISTA) in cooperation with the animal ecologist Professor Thomas Schmitt from the Biozentrum of the Julius Maximilians University in Würzburg (JMU).

Molecular machines could treat fungal infections

Schematic representation of the mechanisms by which light-activated molecular machines kill fungi. Molecular machines bind to fungal mitochondria, decreasing adenosine triphosphate (ATP) production and impairing the function of energy-dependent transporters that control the movement of ions, such as calcium. This leads to the influx of water, which causes the organelles to swell and eventually the cells to burst.
Image Credit: Tour Group/Rice University

That stubborn athlete’s foot infection an estimated 70% of people get at some point in their life could become much easier to get rid of thanks to nanoscale drills activated by visible light.

Proven effective against antibiotic-resistant infectious bacteria and cancer cells, the molecular machines developed by Rice University chemist James Tour and collaborators are just as good at combating infectious fungi, according to a new study published in Advanced Science.

Based on the work of Nobel laureate Bernard Feringa, the Tour group’s molecular machines are nanoscale compounds whose paddlelike chain of atoms moves in a single direction when exposed to visible light. This causes a drilling motion that allows the machines to bore into the surface of cells, killing them.

More multi-resistant germs since the beginning of the Ukraine war

Martina Cremadus, Hans-Jörg Berthold and Niels Pfennigwerth (from left) monitor the occurrence of multi-resistant bacteria in the National Reference Center for Gram-negative Hospital Pathogens.
Photo Credit: RUB, Marquard

The pathogens reach German hospitals with refugees and war injuries. Researchers recommend clinics to screen as a precaution.

Since the outbreak of the war in Ukraine, certain hospital pathogens that are resistant to many antibiotics have been detected much more frequently in German hospitals. The pathogen Klebsiella pneumoniae is also resistant to the reserve antibiotics of carbapenems due to a combination of two enzymes. Together with the Robert Koch Institute (RKI), the National Reference Center (NRZ) for gram-negative hospital pathogens located at the Ruhr University Bochum has been able to demonstrate that many of the reported cases are related to patients from Ukraine. The researchers therefore recommend that this group be examined for the germ before being admitted to the hospital. They report in the journal Eurosurveillance.

Scientists Document Two Separate Reservoirs of Latent HIV in Patients

Rebound DNA sequences from the blood (red) and the CSF (blue)
Illustration Credit: Ron Swanstrom | UNC Center for AIDS Research | Swanstrom lab

This research, led by UNC School of Medicine scientists Laura Kincer, Sarah Joseph, PhD, and Ron Swanstrom, PhD, with international collaborators, shows that in addition to HIV’s ability to lay dormant in the blood/lymphoid system, the virus may also lay dormant in the central nervous system, delineating another challenge in creating a cure.

When people living with HIV take antiviral therapy (ART), their viral loads are driven so low that a standard blood test cannot detect the virus. However, once ART is stopped, detectable HIV re-emerges with new cells getting infected. This is called “rebound” virus, and the cells that release the virus to re-ignite the infection come from a small population of HIV-infected CD4+ T cells that had remained dormant in blood and lymph tissue while individuals were on ART.

It’s a problem called latency, and overcoming it remains a major goal for researchers trying to create curative therapies for HIV—the special focus of the UNC HIV Cure Center.

The increase of fungal infection

A strain of Candida auris cultured in a petri dish at a CDC laboratory.
Photo Credit: Shawn Lockhart / Centers for Disease Control / Public Domain

Late last year the WHO published a report highlighting the first-ever list of fungal "priority pathogens" – a catalogue of the 19 fungi that represent the greatest threat to public health. The premise behind the publication is both because fungi are a significant and increasing threat to public health and because there is little global R&D into fungi or their treatment.

According to Professor Ana Traven, from the Biomedicine Discovery Institute, fungi can range from the benign (skin and nail infections and vaginal thrush) to the deadly (Candida, Aspergillus), “and they have been largely ignored because deadly fungal infections predominantly target people who are immunosuppressed, they are generally not transmitted in human-to-human contact.”

Discovering Unique Microbes Made Easy with DOE Systems Biology Knowledgebase (KBase)

Overview of Metagenome-Assembled Genome Extraction data and analysis workflow using KBase apps.
Image courtesy of Chivian, D. et al. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols 18 (2022).

Microbes are foundational for life on Earth. These tiny organisms play a major role in everything from transforming sunlight into the fundamental molecules of life. They help to produce much of the oxygen in our atmosphere. They even cycle nutrients between air and soil. Scientists are constantly finding interactions between microbes and plants, animals, and other macroscopic lifeforms. As genomic sequencing has advanced, researchers can investigate not only isolated microbes, but also whole communities of microorganisms – known as microbiomes – based on DNA found in an environment. The genomes extracted from these communities (metagenomic sequences) can identify the organisms that carry out biogeochemical processes, contribute to health or disease in human gastrointestinal microbiomes, or interact with plant roots in the rhizosphere. The Department of Energy Systems Biology Knowledgebase (KBase) recently released a suite of features and a protocol for performing sophisticated microbiome analysis that can accelerate research in microbial ecology.

Humans have influenced the growth of blue-green algae in lakes for thousands of years

TERENO Monitoring Station on Lake Tiefer See, Germany (weather station, water probes, sediment traps).
Photo Credit: A. Brauer

In recent years, there have been increasing reports of toxic blue-green algae blooms in summer, even in German lakes, caused by climate warming and increased nutrient inputs. But humans have not only had an influence on the development of blue-green algae since modern times, but already since the Bronze Age from about 2,000 B.C. This is the result of a study by researchers from the German Research Centre for Geosciences GFZ and colleagues, published in the scientific journal “Communications Biology”. Since some blue-green algae, also known as cyanobacteria, leave no visible fossil traces in sediments due to their small size, little is known about how they evolved in our lakes during the last centuries and millennia. Using DNA from sediments, the researchers have now been able to decipher for the first time the history of blue-green algae over the last 11,000 years in the sediments of a lake in Mecklenburg.

Thermal motions and oscillation modes determine the uptake of bacteria in cells

Photo of a membrane bubble with different oscillation modes in the background and experimental scheme in the foreground. Optical tweezers (laser focus in red) bring a thermally fluctuating particle into contact with a membrane bubble (green) until the particle is invaginated into the membrane and taken up.
Graphic Credit: AG Rohrbach

How and with what effort does a bacterium - or a virus - enter a cell and cause an infection? Researchers from Freiburg have now made an important contribution to answering this question: A team led by physicist Prof. Dr. Alexander Rohrbach and his collaborator Dr. Yareni Ayala was able to show how thermal fluctuations of a model bacterium and membrane oscillation modes of a model cell influence the energy with which the model bacteria dock and enter the membrane. The results have just been published in the journal Nature Communications.

Like a sticky piece of candy on a wobbly balloon

“To understand how a bacterium or virus enters a cell, you can imagine a sticky candy on a floppy, wobbly balloon. When a child shakes the rubber balloon around, the candy sticks even tighter to its surface,” said Rohrbach, a professor of -Bio- and Nano-Photonics at the Department of Microsystems Engineering at the University of Freiburg. In his lab, the laser and bio-physicists set up a similar experiment to study the physics of infection processes. The wobbly balloon corresponds to a giant uni-lamellar vesicle (GUV), which serves as a biological model cell. The membrane vesicle is the size of a tiny grain of sand about 20 micrometers in diameter.

Parasite common in cats causes abortion in bighorn sheep

Bighorn sheep
Photo Credit: David Mark

A parasite believed to be present in more than 40 million people in the United States and often spread by domestic and wild cats could hamper ongoing conservation efforts in bighorn sheep.

A recent study led by Washington State University researchers at the Washington Animal Disease Diagnostic Laboratory found that Toxoplasma gondii, a parasite that infects most species of warm-blooded animals and causes the disease toxoplasmosis, is a cause of abortions, or pregnancy loss, as well as neonatal deaths in the sheep. Researchers documented five cases in bighorn sheep in a study published in the Journal of Wildlife Diseases, but additional studies are needed to determine the full scope of its impact, the authors said.

“We have seen Toxoplasma as a cause of fetal and neonate loss pretty commonly in domestic sheep, but we hadn’t seen pregnancy loss due to toxoplasmosis yet in bighorn sheep,” said Elis Fisk, the lead author of the study. “Unfortunately, it does appear to be causing abortions and some level of death in young bighorn lambs.”

Tracing the flow of water with DNA

Oliver Schilling analyzing spring water at Mount Fuji.
Photo Credit: T. Schilling

Environmental DNA analysis of microbial communities can help us understand how a particular region’s water cycle works. Basel hydrogeologist Oliver Schilling recently used this method to examine the water cycle on Mount Fuji. His results have implications for Switzerland as well.

Where does the water come from that provides drinking water to people in a particular region? What feeds these sources and how long does it take for groundwater to make its way back up to the surface? This hydrological cycle is a complex interplay of various factors. A better grasp of the system allows us to understand, for example, why pollution is worse in some spots than others, and it can help us implement sustainable water management policies and practices.

Environmental DNA (eDNA) provides some important data to improve our understanding. In combination with the evaluation of other natural tracers – noble gases, for example – this microbial data provides important glimpses into the flow, circulation and functioning of complex groundwater systems. “It’s a vast toolbox that’s new to our field of research,” says Oliver Schilling, Professor of Hydrogeology at the University of Basel and at Eawag, the Swiss Federal Institute of Aquatic Science and Technology. Quantitative hydrogeology maps out where and how quickly new groundwater will accumulate.

Harnessing the healing power within our cells

E. coli bacteria
Photo Credit: Public Domain 

University of Queensland researchers have identified a pathway in cells that could be used to reprogram the body’s immune system to fight back against both chronic inflammatory and infectious diseases.

Dr Kaustav Das Gupta and Professor Matt Sweet from UQ’s Institute for Molecular Bioscience discovered that a molecule derived from glucose in immune cells can both stop bacteria growing and dampen inflammatory responses.

Dr Das Gupta said the finding is a critical step towards future therapeutics that train immune cells.

“The effects of this molecule called ribulose-5-phosphate on bacteria are striking – it can cooperate with other immune factors to stop disease-causing strains of the E. coli bacteria from growing,” Dr Das Gupta said.

“It also reprograms the immune system to switch off destructive inflammation, which contributes to both life-threatening infectious diseases such as sepsis as well as chronic inflammatory diseases like respiratory diseases, chronic liver disease, inflammatory bowel disease, rheumatoid arthritis, heart disease, stroke, diabetes and dementia.”

Daylong wastewater samples yield surprises

Rice University engineers compared wastewater “grabs” to daylong composite samples and found the grab samples were more likely to result in bias in testing for the presence of antibiotic-resistant genes.
 Illustration Credit: Stadler Research Group/Rice University

Testing the contents of a simple sample of wastewater can reveal a lot about what it carries, but fails to tell the whole story, according to Rice University engineers.

Their new study shows that composite samples taken over 24 hours at an urban wastewater plant give a much more accurate representation of the level of antibiotic-resistant genes (ARGs) in the water. According to the Centers for Disease Control and Prevention (CDC), antibiotic resistance is a global health threat responsible for millions of deaths worldwide.

In the process, the researchers discovered that while secondary wastewater treatment significantly reduces the amount of target ARG, chlorine disinfectants often used in later stages of treatment can, in some situations, have a negative impact on water released back into the environment.

The lab of Lauren Stadler at Rice’s George R. Brown School of Engineering reported seeing levels of antibiotic-resistant RNA concentrations 10 times higher in composite samples than what they see in “grabs,” snapshots collected when flow through a wastewater plant is at a minimum.

New Research on Antibiotic Resistant Bacteria May Be A Step Toward New Treatments for Infections

 From left to right: NSU Students Gabriela Diaz Tang, Estefania Marin Meneses
Credit: Nova Southeastern University

Antibiotic resistant bacteria pose one of the greatest threats to global public health. In 2019, deaths due to antibiotic resistant bacteria outpaced deaths due to HIV and malaria. Given the lack of innovation in the discovery of new antibiotics, it is critical to determine the mechanisms by which bacteria tolerate existing antibiotics so that we can improve their effectiveness.

One way that bacteria can tolerate antibiotics is through the inoculum effect. Essentially, the higher the density of bacteria in an infection, the more antibiotics are required to treat the infection. While the inoculum effect has been observed for nearly all known antibiotics, and has been documented since the 1960s, a common mechanism to explain inoculum effect for multiple antibiotics has not been found.

Scientists recently discovered that interactions between how fast bacteria grow and the amount of energy (or metabolism) bacteria have can explain the inoculum effect for multiple antibiotics and bacteria species. This new research also shows that providing different nutrients to the bacteria that change growth rate and energy levels can eliminate the inoculum effect.

Antibody discovery paves way for new therapies against group A streptococcal infections

Pontus Nordenfelt Associate Professor, Infection Medicine Lund University
Source: Lund University

Researchers at Lund University in Sweden have discovered an antibody with the potential to protect against Strep A infection, as well as a rare form of antibody binding, that leads to an effective immune response against bacteria. The discovery could explain why so many Group A strep vaccines have failed.

The results are published in EMBO Molecular medicine.

Group A streptococci have several ways in which they evade the body's immune system and, when they infect us, can cause both common throat infections (strep throat), scarlet fever, sepsis, swine pox and skin infections. So far, antibiotics work against these bacteria, but should they become resistant, they will pose a major public health threat.

One strategy that the scientific community uses to find new ways of fighting bacterial infections is to create target-seeking antibodies. First, the antibodies that the body's immune system produces in the event of an infection are mapped, and then their effect on the immune system is studied. In this way, antibodies can be identified that can be used both for preventive treatment and for treatment during an ongoing infection. However, it's a challenging process, and many attempts to develop antibody-based treatments against Strep A have failed.

Molecules found in mucus could prevent cholera infection

Scanning electron microscope image of Vibrio cholerae bacteria, which infects the digestive system.
Image Credit: Zeiss DSM 962 SEM T.J. Kirn, M.J. Lafferty, C.M.P Sandoe and R.K. Taylor,

MIT researchers have identified molecules found in mucus that can block cholera infection by interfering with the genes that cause the microbe to switch into a harmful state.

These protective molecules, known as glycans, are a major constituent of mucins, the gel-forming polymers that make up mucus. The MIT team identified a specific type of glycan that can prevent Vibrio cholerae from producing the toxin that usually leads to severe diarrhea.

If these glycans could be delivered to the site of infection, they could help strengthen the mucus barrier and prevent cholera symptoms, which affect up to 4 million people per year. Because glycans disarm bacteria without killing them, they could be an attractive alternative to antibiotics, the researchers say.

“Unlike antibiotics, where you can evolve resistance pretty quickly, these glycans don’t actually kill the bacteria. They just seem to shut off gene expression of its virulence toxins, so it’s another way that one could try to treat these infections,” says Benjamin Wang PhD ’21, one of the lead authors of the study.

Monash researchers on the front line in fight against fungal infections

The fungal pathogen Candida albicans transformed with a green fluorescence protein (GFP) tagged iron sensor is engulfed by macrophages. Upon iron starvation induced by macrophages Candida will express GFP and make hyphal projections thereby escaping immune cells.
Source: Monash University

With fungal infections killing 1.5 million people each year, Monash University researchers are playing an important role as the World Health Organization recognizes this growing threat.

The world-leading Monash experts are among a small but determined group of researchers working to curb the growing impact of potentially dangerous fungal infections.

In late October, 2022, WHO published a report highlighting the first list of fungal "priority pathogens" – a catalogue of the 19 fungi that represent the greatest threat to public health.

The premise behind the publication is twofold: fungi are a significant and increasing threat to public health, and because there is little global research and development into fungi or their treatment.

Professor Ana Traven, from the Monash Biomedicine Discovery Institute, said fungi could range from benign (skin and nail infections and vaginal thrush) to the deadly (Candida, Aspergillus).

New branch on tree of life includes ‘lions of the microbial world’

On the left is a starving provoran. On the right, it has engulfed its prey.
Photo Credit: Tikhonenkov, Mikhailov, Gawryluk, Belyaev, Mathur, Karpov, Zagumyonnyi, Borodina, Prokina, Mylnikov, Aleoshin, and Keeling, Nature

There’s a new branch on the tree of life and it’s made up of predators that nibble their prey to death.

These microbial predators fall into two groups, one of which researchers have dubbed “nibblerids” because they, well, nibble chunks off their prey using tooth-like structures. The other group, nebulids, eat their prey whole. And both comprise a new ancient branch on the tree of life called “Provora,” according to a paper published today in the journal Nature.

Microbial lions

Like lions, cheetahs, and more familiar predators, these microbes are numerically rare but important to the ecosystem, says senior author Dr. Patrick Keeling, professor in the UBC department of botany. “Imagine if you were an alien and sampled the Serengeti: you would get a lot of plants and maybe a gazelle, but no lions. But lions do matter, even if they are rare. These are lions of the microbial world.”

Using water samples from marine habitats around the world, including the coral reefs of Curaçao, sediment from the Black and Red seas, and water from the northeast Pacific and Arctic oceans, the researchers discovered new microbes. “I noticed that in some water samples there were tiny organisms with two flagella, or tails, that convulsively spun in place or swam very quickly. Thus began my hunt for these microbes,” said first author Dr. Denis Tikhonenkov, senior researcher at the Institute for Biology of Inland Waters of the Russian Academy of Sciences.

Staph infection-induced kidney disease may be linked to bacterial gene mutation

Anjali Satoskar
Photo Credit: Ohio State University

Researchers aiming to predict which staph-infection patients might develop a related kidney disease have found a high frequency of gene mutations in the infecting bacteria of affected patients, which suggests these variants may play a role in the body’s initiation of the renal damage.

The kidney disorder is a fairly uncommon autoimmune complication to Staphylococcus aureus infection. Although it is potentially reversible with quick administration of appropriate antibiotics and effective treatment of the infection, it can also lead to kidney disease or kidney failure.

“There are many varieties of autoimmune nephritis. For most of them, suppressing the immune system is the first line of treatment, but this type is unique because you have both an ongoing severe infection as well as this autoimmune tissue-injury response happening at the same time. Immunosuppression is not an option while the infection is still active,” said study senior author Anjali Satoskar, clinical professor of pathology in the Ohio State University College of Medicine. “It can be a diagnostic as well as a therapeutic challenge.”

In an exploratory study, Satoskar and colleagues found a higher frequency of mutations affecting a group of Staphylococcus aureus genes in blood culture isolates from patients with staph-associated nephritis compared to patients having staph infections without development of autoimmune kidney disease.

How to Edit the Genes of Nature’s Master Manipulators

Scientists are using CRISPR to engineer the viruses that evolved to engineer bacteria
Illustration Credit: Davian Ho

CRISPR, the Nobel Prize-winning gene editing technology, is poised to have a profound impact on the fields of microbiology and medicine yet again.

A team led by CRISPR pioneer Jennifer Doudna and her longtime collaborator Jill Banfield has developed a clever tool to edit the genomes of bacteria-infecting viruses called bacteriophages using a rare form of CRISPR. The ability to easily engineer custom-designed phages – which has long eluded the research community – could help researchers control microbiomes without antibiotics or harsh chemicals, and treat dangerous drug-resistant infections. A paper describing the work was recently published in Nature Microbiology.

“Bacteriophages are some of the most abundant and diverse biological entities on Earth. Unlike prior approaches, this editing strategy works against the tremendous genetic diversity of bacteriophages,” said first author Benjamin Adler, a postdoctoral fellow in Doudna’s lab. “There are so many exciting directions here – discovery is literally at our fingertips!”

Bacteriophages, also simply called phages, insert their genetic material into bacterial cells using a syringe-like apparatus, then hijack the protein-building machinery of their hosts in order to reproduce themselves – usually killing the bacteria in the process. (They’re harmless to other organisms, including us humans, even though electron microscopy images have revealed that they look like sinister alien spaceships.)