Tag Archives: Microbials

Microbiology

Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used …

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Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used types. As the threat of antibiotic resistance looms large, researchers have sought to find new antibiotics and other ways to destroy dangerous bacteria. But new antibiotics can be extremely difficult to identify and test. Bacteriophages, which are viruses that only infect bacterial cells, might offer an alternative. Bacteriophages (phages) were studied many years ago, before the development of antibiotic drugs, and they could help us once again.

Image credit: Pixabay

If we are going to use bacteriophages in the clinic to treat humans, we should understand how they work, and how bacteria can also become resistant to them. Microbes are in an arms race with each other, so while phages can infect bacteria, some bacterial cells have found ways to thwart the effects of those phages. New research reported in Nature Microbiology has shown that when certain bacteria carry a specific genetic mutation, phages don’t work against them anymore.

In this study, the researchers used a new technique so they could actually see a phage attacking bacteria. Mycobacteriophages infect Mycobacterial species, including the pathogens Mycobacterium tuberculosis and Mycobacterium abscessus, as well as the harmless Mycobacterium smegmatis, which was used in this research.

The scientists determined that Mycobacterial gene called lsr2 is essential for many mycobacteriophages to successfully infect Mycobacteria. Mycobacteria that carry a mutation that renders the Lsr2 protein non-functional are resistant to these phages.

Normally, Lsr2 aids in DNA replication in bacterial cells. Bacteriophages can harness this protein, however, and use it to reproduce the phage’s DNA. Thus, when Lsr2 stops working, the phage cannot replicate and it cannot manipulate bacterial cells.

In the video above, by first study author Charles Dulberger, a genetically engineered mutant phage infects Mycobacterium smegmatis. First, one phage particle (red dot at 0.42 seconds) binds to a bacterium. The phage DNA (green fluorescence) is injected into the bacterial cell (2-second mark). The bright green dots at the cells’ ends are not relevant. For a few seconds, the DNA forms a zone of phage replication, and fills the cell. Finally, the cell explodes at 6:25 seconds. (About three hours have been compressed to make this video.)

The approach used in this study can also be used to investigate other links between bacteriophages and the bacteria they infect.

“This paper focuses on just one bacterial protein,” noted co-corresponding study author Graham Hatfull, a Professor at the University of Pittsburgh. But there are many more opportunities to use this technique. “There are lots of different phages and lots of other proteins.”

Sources: University of Pittsburgh, Nature Microbiology


Carmen Leitch

Microbiology

The microbes of the world battle one another for domination, and some bacteria produce powerful molecules that can …

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The microbes of the world battle one another for domination, and some bacteria produce powerful molecules that can work against other microbes. Researchers have now discovered that some Pseudomonas bacteria generate strong antimicrobials that work against pathogenic fungi that affect humans, as well as plant fungal diseases. The findings have been reported in the Journal of the American Chemical Society.

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The chemicals that have been identified are called keanumycins, and these compounds can destroy a plant pest called Botrytis cinerea, which causes grey mold rot and leads to huge economic losses annually. Keanumycins can also inhibit pathogenic fungi that affect humans, including Candida albicans. Previous studies have indicated that it’s harmless to human and plant cells.

Keanumycins may offer an environmentally friendly way to protect plants without using chemical pesticides. They may also be a weapon in the battle against drug-resistant fungi.

“We have a crisis in anti-infectives,” noted first study author Sebastian Götze, a postdoc at Leibniz-HKI. “Many human pathogenic fungi are now resistant to antimycotics, partly because they are used in large quantities in agricultural fields.”

The research team has been investigating Pseudomonas bacteria for a long time, and they know that many types of Pseudomonas are toxic to amoeba. The deadly effect of the bacteria is due to a few compounds that the investigators have traced to the Pseudomonas genome. The natural products are lipopeptides called keanumycins A, B and C, which have soap-like characteristics.

One of those keanumycins was isolated so it could be studied further. “The lipopeptides kill so efficiently that we named them after Keanu Reeves because he, too, is extremely deadly in his roles,” quipped Götze.

Some fungi have a resemblance to amoeba, and the researchers suspected keanumycins would also kill fungi. Indeed, tests reveled that Keanumycin could kill grey mould rot on hydrangea leaves. With only the fluid collected from a culture of bacterial, fungal growth slowed.

Additional work will be needed to confirm the findings, but the liquid from Pseudomonas cultures could be used on plants, Götze noted.

Keanumycin is also biodegradable, which suggests that permanent residues from the compound won’t contaminate soil, and it could be an environmentally friendly pesticide alternative.

“In addition, we tested the isolated substance against various fungi that infect humans. We found that it strongly inhibits the pathogenic fungus Candida albicans, among others,” added Götze. There aren’t many antifungals on the market, so this would be a welcome addition to the pharmacy.

Sources: Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Journal of the American Chemical Society


Carmen Leitch

Microbiology

Microbes can easily share genes. Not only can different types of bacteria do this, there is also evidence …

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Microbes can easily share genes. Not only can different types of bacteria do this, there is also evidence that entirely different branches of life – archaea and bacteria can also share genes. Some microbial genes can be found on small bits of DNA called mobile genetic elements, which are not a part of a microbe’s genome, but can still be expressed when they’re a microbial cell. These mobile genetic elements can move from one cell to another in a process known as horizontal gene transfer. Researchers have now found that bacteria in the maternal microbiome can share genes with bacteria in the infant microbiome, in the period just before birth until a few weeks after delivery – the perinatal period. Horizontal gene transfer enables maternal microbes to influence how bacteria in the infant microbiome are functioning, without actually moving the maternal microbes themselves. These findings have been reported in Cell.

Image credit: Pixabay

“This is the first study to describe the transfer of mobile genetic elements between maternal and infant microbiomes,” said senior study author Ramnik Xavier of the Broad Institute of MIT and Harvard. “Our study also, for the first time, integrated gut microbiome and metabolomic profiles from both mothers and infants and discovered links between gut metabolites, bacteria and breastmilk substrates. This investigation represents a unique perspective into the codevelopment of infant gut microbiomes and metabolomes under the influence of known maternal and dietary factors.”

The gut microbiome produces metabolites that can affect various aspects of infant development, such as immune system maturation and cognitive development during the perinatal period, a critical window. At birth, microbes move from the maternal microbiome to the infant microbiome, but we still have a lot to learn about how microbes are affecting development, and how they are developing into a microbiome themselves.

In this study, the researchers tracked the microbiomes and metabolites of 70 infant-mother pairs, from late pregnancy until the babies were one year old. This research showed that mobile genetic elements moved from microbes carried by moms and into microbes carried by infants. The mobile genetic elements that were transferred were often related to diet.

Infants were also found to have less diversity in their metabolomes compared to moms, however, there were metabolites, and links between microbes and metabolites that were identified exclusively by infants. Infants that got regular formula (that was not excessively hydrolyzed) also had metabolomes and cytokine signatures that were different from infants that were exclusively breastfed.

“The infant gut harbored thousands of unique metabolites, many of which were likely modified from breastmilk substrates by gut bacteria,” noted co-first study author Tommi Vatanen of the Broad Institute of MIT and Harvard. “Many of these metabolites likely impact immune system and cognitive development.”

This process seems to be a way for the maternal microbiome to exert an influence on the infant microbiome withouth transmitting specific species of bacteria.

Prophages, which are dormant bacteriophages, also seem to be involved in the movement of mobile genetic elements between the maternal and infant microbiomes, added Xavier.

Sources: Cell Press, Cell


Carmen Leitch

Microbiology

The microbes in our guts are closely connected to our brains, in a link known as the gut-brain …

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The microbes in our guts are closely connected to our brains, in a link known as the gut-brain axis. Scientists have now found that a bacterium called HA-114 Lacticaseibacillus rhamnosus could help prevent amyotrophic lateral sclerosis (ALS). In a roundworm model of ALS, neurodegeneration was prevented by the microbe. The findings have been reported in Communications Biology.

Image credit: Pixabay

In ALS, the nerve cells that control movement, called motor neurons, gradually die off, causing a loss of movement and function. While the cause of ALS is still under investigation, this study has suggested that lipid metabolism disruptions are contributing to neurodegeneration, and HA-114 can provide protection against that deleterious influence.

Other research has also indicated that dysfunction in the gut microbiome may be involved in the development of ALS and other neurodegenerative disorders, noted lead study author Alex Parker, a Université de Montréal neuroscience professor.

When the researchers added the HA-114 microbe to the diet of the roundworm ALS model, motor neuron degeneration was suppressed, noted Parker. “The particularity of HA-114 resides in its fatty acid content.”

Roundworms called Caenorhabditis elegans have about 60 percent of their genome in common with humans and serve as common animal models. They carry some genes that have been linked to ALS.

Thirteen bacterial strains and three combinations of strains were tested on the worms. HA-114 had a significant impact, and reduced the motor disruption that occurs in models of both ALS and Huntington’s disease.

Additional work indicated that two genes, called acdh-1 and acs-20,  are involved in the neuroprotection provided by the bacteria. These genes are involved in the metabolism of fats, or lipids, and the breakdown of fatty acids for energy, a process called beta oxidation, which occurs in mitochondria.

Parker suggested that HA-114 is supplying fatty acids that enter mitochondria through a non-traditional pathway, which restores a balance in energy metabolism that becomes disrupted in ALS, and that decreases neurodegeneration.

The researchers are working on validating these findings in a mouse model of ALS, and are now planning to start a small clinical trial with ALS patients.

Sources: University of Montreal Hospital Research Centre, Communications Biology


Carmen Leitch

Microbiology

One of the most significant consequences of climate change is the greenhouse gases generated from the microbial decomposition …

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One of the most significant consequences of climate change is the greenhouse gases generated from the microbial decomposition of organic matter in thawing permafrost soil. Permafrost refers to ground soil frozen at 0℃ or lower, year after year. Permafrost regions of the Earth are mostly found in the north and south poles. During summer, some thawing of the permafrost landscape is considered normal, but with climate change, thawing has increased annually.

Studies of permafrost soil have previously identified ancient bacteria, viruses, fungi, and even protozoans that can potentially become infectious after several years of being frozen. Apart from identification, the global impact of the microbial composition of permafrost on human health remains largely undetermined. 

More recently, DNA was isolated from soil samples in the carbon-rich Yedoma permafrost of Siberia. The Yedoma permafrost is known to have preserved animal remains like mammoths and ancient microbial content. An international team of scientists from Russia and Germany conducted a ‘metagenomic’ analysis of various soil samples from the Yedoma permafrost, which involves the detailed characterization of all DNA extracted from multiple soil samples. Their studies from the Yedoma soils have identified bacterial genes from several bacterial species with no specific correlation to the age of the permafrost. Interestingly, a high frequency of the beta-lactamase gene was detected within the identified bacterial genomes. What does this mean? The DNA samples belong to diverse bacterial species, and all carry the gene for the enzyme beta-lactamase. Beta-lactamases are enzymes that cause the inactivation of penicillin-derived antibiotics, thereby conferring antibiotic resistance to the bacteria carrying them (in their genome or plasmids). 

Active microbial life has been discovered in the arctic before. But the discovery of bacterial DNA, a large proportion of which carries antibiotic resistance, is unexpected. This finding is even more perplexing to scientists because these soils have remained far removed from human civilization that have heavy antibiotic usage. The acquisition of antibiotic resistance is technically possible outside a clinical setting. Bacteria acquire genes from their environment all the time. However, the potential danger of thawing permafrost and the release of bacterial DNA offering antibiotic resistance is concerning.

Antimicrobial resistance (AMR) is a global health issue that severely challenges our ability to treat bacterial infections effectively. Tracking and early identification of AMR in clinical settings is key to reducing its spread. The discovery of antibiotic resistance in permafrost does not directly affect clinical care today but has implications for the future of AMR, especially with a rising concern about climate change. 


Anusha Naganathan

Microbiology

The microorganisms of the world are in constant conflict, battling for resources and space in a microbial arms …

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The microorganisms of the world are in constant conflict, battling for resources and space in a microbial arms race. Some viruses can infect amoeba, while others might infect archaea or bacteria. There are even bacteria that can prey on other bacteria. Scientists have now discovered a bacterium that stalks cyanobacteria in the earth’s biocrusts. These newly identified predators, called Candidatus Cyanoraptor togatus (C. togatus), or Cyanoraptor, can attack cyanobacteria living in desert soil.

After infecting its prey, Cyanoraptor begins to replicate until it kills the prey, releasing a new army of attackers. / Credit: Photo courtesy of Julie Bethany Rakes

Cyanobacteria are photosynthetic, and play a role in the production of oxygen and nitrogen fixing in the environment, processes that many other organisms rely on. Cyanobacteria also form biocrusts, which are beneficial communities of cells that live on the surface of soil. They help prevent erosion, trap dust, and increase nutrient and water levels in the soil. Though they are important to the desert ecosystem, they are also targeted.

“There was something killing the biocrusts. It was not a virus, and it was not a small animal. It could only be another bacterium,” said Professor Ferran Garcia-Pichel of Arizona State University.

Biocrusts usually look like soil. But after a Cyanoraptor attack, circular rings appear in which the cyanobacteria have been eliminated. Researchers identified them in the field, then assessed them in the lab, revealing more about Cyanoraptor. The findings have been reported in Nature Communications.

Julie Bethany Rakes noticed something amiss in plaques, where cyanobacteria had disappeared. She continued investigating. / Credit: Photo courtesy of Julie Bethany Rakes

In their early stages, Cyanoraptor cells are small and spherical; these so-called propagules just wait for their prey, not growing or dividing. If a cyanobacterium gets close, the Cyanoraptor attacks by binding to its prey with a docking structure. The cell wall of the prey cyanobacterium dissolves, and the predator Cyanoraptor enters the cyanobacterial cell and starts consuming it. Cyanoraptor continues to grow larger, then divides into many new cells once it reaches a certain size. The prey cell dies, and Cyanoraptor transforms into propagules once more until another victim comes along.

The desert ecosystem loses the benefits provided by cyanobacterium as more get consumed by Cyanoraptor. “In general, this means that there could be serious consequences for desert health, fewer nutrients, less stable soil and water retention so a reduction in time plants and other organisms can be active. With the loss of these functions, organisms that rely on these services, such as plants may suffer, which could then have further consequences up the food chain,” explained first study author Julie Bethany Rakes, PhD.

Sources: Arizona State University, Nature Communications


Carmen Leitch