So, when we take antibiotics because of a bacterial infection, billions of bacteria are suddenly attacked by antibiotics.

They struggle to repair damage, maintain their structures and continue essential functions just to stay alive.

This ultimately weakens or kills the cells.

And as you can imagine, this is pure stress for the bacteria.

One that we take advantage of.

This article series takes you on a journey through the microscopic war between bacteria and antibiotics. Across five articles, we will explore how antibiotics attack bacteria, how bacteria overcome them, become resistant and how evolution pushes bacteria to survive the antibiotic war.

In this first part of the series, we explore how different classes of antibiotics work, while focusing on the most commonly used antibiotics. Once you understand these mechanisms, you will better understand how and why bacteria fight back, evolve and develop resistance.

Antibiotics attacking bacterial cells by stopping cell division

Bacteria have a rigid cell wall made of peptidoglycan to maintain their shape and internal pressure and to protect them from the environment. Without the ability to build or repair the cell wall, bacteria become fragile and burst easily.

This vulnerability is precisely what antibiotics from the β-lactam family exploit. You have probably heard of penicillin, one of the most well-known members of this class. Other similar antibiotics are amoxicillin and cephalosporins.

How these antibiotics work is pretty simple but devastating to bacterial cells: they block the so-called penicillin-binding proteins. These enzymes sit in the cell wall where they are responsible for building and cross-linking it.

So, when a bacterium gets hit by a β-lactam antibiotic, it loses the ability to divide. Basically, every time it tries to divide, it will burst like a water balloon.

Antibiotics sabotaging bacteria’s genetic machinery

Every bacterial cell carries instructions for life in its DNA, the molecule that stores genetic information. Before dividing, bacteria copy their DNA and then share it with their daughter cells.

Bacteria also make RNA, the molecule that executes the instructions stored in DNA. RNA comes in different types with distinct roles, but it is fundamentally needed to make proteins from DNA.

Some antibiotics exploit this vulnerability by inhibiting one of the cell’s information-processing machineries. This fundamentally interferes with DNA or RNA synthesis. If a bacterium can’t produce DNA or RNA, it can’t divide or maintain its genetic integrity, leading to cell death.

The antibiotic class fluoroquinolones inhibits DNA production. For example, ciprofloxacin freezes the enzymes that help bacteria copy their DNA. When DNA replication stalls, bacteria cannot divide. They accumulate damage and eventually die.

In comparison, rifamycins inhibit RNA synthesis. These antibiotics bind to the RNA polymerase, the enzyme that produces RNA from DNA. They thereby block the first step in protein production.

It’s like cutting electricity to an entire factory; without RNA, the cell cannot produce proteins, halting metabolism and growth. This is highly stressful to bacteria and can quickly kill them.

Antibiotics blocking protein production: The ribosome hijackers

Other antibiotics directly inhibit the protein production step: To build proteins, bacteria produce a temporary working copy of those DNA instructions, the so-called messenger RNA or mRNA.

This molecule travels to the ribosome, which reads the mRNA and makes proteins from it. Since proteins are essential for metabolism, movement, growth and cell division, no cell can function without them.

Some antibiotics, like tetracycline, take advantage of this protein production vulnerability. By interfering with ribosomes, these antibiotics prevent them from producing proteins and eventually the bacterial cells from functioning.

Interestingly, not all protein-production inhibitors kill bacteria in the same way. Some antibiotics are bacteriostatic, which means they freeze growth without immediately killing the cell. The bacteria cannot make new proteins, so they can’t divide or repair themselves. Instead, the existing proteins remain active for a while, allowing the cell to survive in a weakened state.

Others, like aminoglycosides, are bactericidal. Instead of simply blocking ribosomes, they cause the ribosome to make mistakes and produce misfolded proteins. These faulty proteins build up inside the cell and damage essential structures, overwhelming the bacterium, so it eventually dies.

Antibiotics disrupting metabolic pathways

Lastly, some antibiotics target essential metabolic pathways that bacteria need to survive. For example, folate is an essential vitamin that all organisms need to grow and reproduce, and most bacteria have proteins to make their own folate. So, when antibiotics block these folate-producing proteins, the bacterium will eventually run out of folate and lose the ability to grow.

How different antibiotics kill bacteria

As we’ve seen in this post, antibiotics can impact bacteria in many different ways. But they all have the same goal: do the biggest damage possible. Antibiotics can damage a bacterium’s DNA, its protein production machinery, metabolic pathways or the cell envelope.

This damage is essentially stress for the bacterium: they must repair the damage or adapt their metabolisms to it. If they cannot cope with the damage or the stress, they’ll die. And remember, this was basically the antibiotic’s goal from the beginning.

But be aware: this stress can be both lethal and a driving force for bacterial evolution. As they learn to cope with the antibiotic and the stress, they become resistant. And in future articles, we will explore these bacterial learning processes and how they help make bacteria resistant to antibiotics.

The post How Antibiotics Kill: The Weapons We Use Against Bacteria appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And only thanks to pigments, life on Earth is possible. Pigments were the first molecules that microbes used to harvest sunlight. Microbes could then transform the light energy into chemical energy and produce oxygen.

Even the brown-reddish haemoglobin in your blood is an essential pigment as it transports oxygen within your body. Also for bacteria, pigments and their colours have life-saving functions. Here, we will look at how biopigments colour the bacterial world and what bacteria gain from producing them.

Bacterial pigments bring colour to the world of bacteria

Biopigments are molecules with complex chemical structures and at least one excited electron. Depending on the electron’s arrangement, a pigment absorbs light at a specific wavelength. It reflects the colour of the unabsorbed wavelength, which gives the pigment its colour.

As the function of pigments depends on the incoming light, sunlight plays a crucial role for bacteria with pigments. By adding certain pigments to their membrane, bacteria can adapt to environments that are directly affected by sunlight or the lack of it. This gives them an advantage over those bacteria that lack these pigments.

However, some bacteria also use pigments for other purposes, which we discuss further in this article.

Microbes harness photosynthetic power with colourful pigments

Sunlight is incredibly powerful since each light photon contains energy. Bacteria adapted to harvest energy from sunlight with special pigments.

Pigments can capture the incoming photon and transfer its energy to other molecules. This process transforms the incoming light energy into chemical energy. So-called phototrophic microbes are those that gain their energy from light.

The best-known example of a photosynthetic biopigment is chlorophyll in plants, algae and cyanobacteria. Cyanobacteria produce several complexes of bacteriochlorophylls to absorb blue and red light. As the green light is not absorbed, it is reflected, which is why chlorophyll – and thus cyanobacteria, algae and plants – are green.

Some bacteria harvest more light by producing several pigments of different types. They then arrange them in an optimal formation according to the incoming light.

For example, carotenoids capture energy in the green-blueish range and pass it on to the associated chlorophyll. Together, these photosynthetic complexes absorb light energy from almost the entire wavelength spectrum.

Halophilic bacteria and archaea are microbes that produce carotenoids to capture sunlight. You may have seen salt ponds with a reddish colour. This comes from the red and pink-coloured archaea Halobacteria, bacteria Salinibacter or algae Dunaliella. Thanks to their colourful carotenoids, these microbes adapt to salty waters that are exposed to direct sunlight.

Cyanobacteria in the deep sea, lagoons, lakes, ponds or rivers produce similar molecules to chlorophyll. These absorb the blue-green light in water, which allows these bacteria to survive in these dark environments. If you have ever seen a lagoon shining yellow or orange, this was probably due to the colourful cyanobacteria inside.

Bacterial biopigments protect from too much light

As light is full of energy, bacteria also need to protect themselves from getting burned. For this, they produce pigments that take up the excess light energy. Like this, the main photosynthetic complex does not get damaged.

Carotenoids and xanthomonadins are the colourful sun blockers of the microbial world. These molecules absorb high-energy light to protect chlorophyll from damage. Over 600 different carotenoids were described and they usually come in yellow-orange-reddish colours.

The yellow xanthomonadins absorb wavelengths within the energy-rich UV spectrum. Bacteria like Xanthomonas campestris live on plant leaves where they are exposed to direct sunlight. Hence, their yellow xanthomonadin coats are like self-made sunblocks protecting the bacteria.

Also, the pigment melanin shields the producing cell from energy-rich sunlight. Many bacteria living in the soil or bacterial spores produce these pigments. Here, melanin absorbs light from a wide range of the light spectrum to protect the inner of the cell. Hence, melanin-producing bacteria, like Vibrio cholerae and Streptomyces bacteria, are brown or black.

Bacterial pigments let electrons flow and save energy

Since bacterial pigments allow electrons to flow, they can also be energy conductors. Hence, some pigments are important components of energy complexes and synthesis machineries.

For example, yellow flavins are pigments involved in cellular metabolism. The main flavin is riboflavin, which you may know as vitamin B12. This essential molecule – produced only by bacteria – allows our bodies to work.

Phenazines are unique bacterial pigments with yellowish-green fluorescent colours. Pyocyanin, exclusively produced by Pseudomonas bacteria, shuttles electrons – and thus energy – during the respiration process. Hence, pyocyanin is essential for Pseudomonas as it keeps the bacteria healthy and alive.

Some biopigments have anti-oxidant effects

Bacterial pigments don’t just help adapt to external environmental conditions like the sunlight. They also guard the inner bacterial cell from stressful situations.

Excess or uncaptured energy or escaped light photons can react with oxygen. This process produces so-called oxygen radicals, which can damage molecules inside the bacterium. Known as oxidative stress, oxygen radicals can even become life-threatening for bacteria.

Carotenoids and xanthomonadins protect bacterial cells from oxidative stress. These pigments transform the free oxygen radicals into harmless molecules. Since carotenoids and their product vitamin A have similar functions in humans, it is only healthy for us to take up a lot of these with our diet.

In the bacterium Gemmatimonas aurantiaca, orange carotenoids also work like sunscreen and oxidative shield. These pigments both give the bacterium its bright orange colour and protect it from too much sunlight.

Bacteria combat microbial enemies with coloured pigments

As night falls, many bacterial pigments reveal their darker sides. They become important weapons for microbial warfare. Without sunlight, several pigments take on roles as virulence factors and antimicrobials as they mess up cells’ energy and oxygen household.

For example, prodigiosin is the red weapon of Serratia marcescens. As prodigiosin inhibits the growth of several bacterial, fungal and insecticidal pathogens, Serratia marcescens is an important biocontrol bacterium of plant disease.

You may have seen prodigiosin-producing Serratia bacteria on contaminated food. They develop these red, blood-like dots.

Violacein is a purple pigment with anti-viral, anti-bacterial and anti-cancer properties. For example, Chromobacterium violaceum sends membrane bubbles filled with violacein to kill bacterial enemies.

Similarly, Janthinobacterium lividum protects frogs and salamanders as it lives on their skins. Here, the bacterium throws violacein at pathogenic fungi that would otherwise infect and harm the animals.

Pyocyanin, the fluorescent electron-shuttling pigment in Pseudomonas, is also very sensitive to oxygen. It even turns Pseudomonas aeruginosa cultures in the lab blueish just by shaking and airing them.

Yet, not all bacteria have an appropriate coping mechanism for pyocyanin. Hence, these bacteria suffer oxidative stress when they come into contact with this pigment. This is why Pseudomonas uses pyocyanin also to fight bacterial and fungal enemies.

Vivid pigments colour the bacterial world

The Bacterial World is colourful – one of this blog’s taglines. You may have asked yourself what this is about and why bacteria have so many different colours.

From the dazzling pink of halophilic microorganisms to the sunny yellow of phytopathogens, bacterial pigments give their producers shiny and vibrant colours. But thanks to the colourful biopigments, bacteria also gain abilities to survive in new and challenging environments.

Some of these bacterial pigments are essential for us humans and even life on Earth. From some of these colourful biopigments, we produce vitamins that we need for our own metabolism. Also, every oxygen molecule that you just took up with your last breath, at some point, was transformed by a bacterial chlorophyll pigment.

So, I guess it is yet again time to be grateful to bacteria and their vibrant and life-enabling activities!

The post Creating the colours of the rainbow: Bacteria and the vibrant world of pigments appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

But what do bacteria and fungi use antibiotics for? Why do they produce them? And what are the advantages of microbes having antibiotics as molecular weapons?

What are antibiotics?

The father of antibiotics, Selman Waksman, first used the word antibiotics for any small molecule made by a microbe that can inhibit the growth of other microbes.

So, microbes – especially bacteria and fungi – use antibiotics to kill other microbes. These other microbes can be bacteria, fungi or bigger organisms. Not viruses though!!!

Why not viruses?

Because antibiotics bind and inhibit cellular machines in living organisms. These molecules often bind to so-called targets. Antibiotic targets can be proteins or enzymes that make for example the cell wall, other proteins or components of the respiration complex.

These proteins are generally essential. So, when antibiotics inhibit the proteins, the cells are missing these essential functions. And without them, they cannot survive and die.

Hence, like other bacterial toxins, antibiotics are lethal.

Interestingly though, bacteria and fungi make antibiotics from simple building blocks. These are present in every cell and can be amino acids, lipids or even sugars.

But instead of using these building blocks for their normal functions, microbes link them together in different ways. With this, they create new – and fancier – molecules that barely resemble the original blocks.

Then, they transport these antibiotics to the outside or send them off in outer membrane vesicles. When the antibiotic hits another microbe, there are two possibilities: either the microbe is resistant to the activity of the antibiotic or it dies from it.

But what about the microbe that produces the antibiotic? Is it resistant to the antibiotic itself?

Why are microbes that produce antibiotics not get killed?

Since antibiotics are meant to KILL other microbes, then why do producing microbes not get killed by their own antibiotics? The answer is self-protection!

Whenever bacteria or fungi produce antibiotics, they always also produce some sort of self-protective means. Just as when bacteria produce other toxins, they always need to make sure they are not killed by their own weapons.

These self-protectors usually keep the antibiotic in an inactive state. For example, they completely surround the antibiotic molecule so that it cannot bind to its usual target within the cell. Another strategy is to add a small molecule to the antibiotic – again to keep it from binding to its target.

Then, when the microbe is ready to transport the antibiotic outside of the cell, it takes the self-protection off the antibiotic. This releases only the toxic part – the antibiotic itself – into the surrounding.

Note, however, that these self-protection mechanisms are not antibiotic resistance mechanisms. Self-protection mechanisms are meant to inactive antibiotics only temporarily. Hence, these mechanisms are reversible. The antibiotic can still become active and thus toxic.

Resistance mechanisms, on the other hand, are meant to inactive antibiotics permanently. Hence, these mechanisms are irreversible. Since this usually completely destroys the antibiotic, it cannot become active anymore.

But what triggers microbes and especially bacteria to produce antibiotics? How do antibiotics help the producing cell in their daily circumstances?

Why do bacteria produce antibiotics?

To answer this question, we need to look at where the bacteria live that make antibiotics. And two-thirds of the known antibiotics are made by bacteria from the Actinobacteria family. Within this family, Streptomyces is the best-known member that produces half of all known antibiotics.

Another example is bacteria from the Myxococcus family. So, where do Streptomyces and Myxococcus bacteria live? Interestingly, these bacteria call the soil their home.

And in the soil, they often confront lots of friends and foes. And they need to constantly fight for their own survival.

Myxococcus is known as a wolf-pack predator because it kills its prey in massive attacks. Colonies of Myxococcous roll over their prey, secrete antibiotics and thus kill them and feed on them.

Streptomyces, on the other hand, uses its antibiotics a bit more civil.

To move in the environment, Streptomyces bacteria grow as long filaments throughout the soil. They build long chains and branch out into the soil as multicellular organisms. These branches are filled with Streptomyces cells but also spores so that the bacteria can extend to new places.

When the bacteria hit a period of bad weather or don’t find much food, they release their spores as a survival strategy. Plus, they start releasing nutrients for the spores. But these nutrients also attract other organisms like bacteria.

Hence, at the same time, Streptomyces produces a huge amount of antibiotics to fend off these putative food-stealers. Like this, Streptomyces makes sure their spores are safe and can survive in their new homes for a while.

How do antibiotics produced by bacteria help others?

Like Streptomyces, lots of bacteria use antibiotics to fight off predators. This assures their own survival and that of their species.

Yet, more and more research finds that bacteria not only kill other species with antibiotics so they can survive. The killing also benefits their hosts.

For example, the bacterium Janthinobacterium lividum lives on frogs where it produces the antibiotic violacein. This antibiotic kills fungi so that the bacterium protects the frog from deadly fungal infections.

Also, a bacterium that lives in our noses is the harmless Staphylococcus lugdunensis. This bacterium produces the antibiotic lugdunin. That inhibits the harmful Staphylococcus aureus from settling down in our noses. Now, scientists look into how we could use the harmless Staphylococcus lugdunensis to protect us from infections.

Another example of microbes that produce antibiotics to help others is the three-member association of ants, Streptomyces and a fungus. Several species of ants grow fungi for food. They feed their fungi with fresh plants and let them grow in special underground gardens.

To not contaminate these fungal gardens, ants carry symbiotic Streptomyces that produce antibiotics. Like this, the antibiotics kill other microbes and keep the fungal gardens free of harmful intruders. As a thank you, the ants feed the Streptomyces and give them a place to live.

About antibiotic-producing microbes

So, just as we use antibiotics to kill harmful bacteria and fungi, antibiotic-producing microbes do the same. They want to fight off predators and assure their own survival.

When you think about it: we use their own killer weapons against them. Poor microbes!

The post Bacteria use antibiotics to kill their foes and protect others appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Also, bacteria want to grow and flourish and reproduce. But they are only single cells so that their way of reproduction is unique. They reproduce asexually meaning you only need one parent bacterium to make two daughter bacteria.

When you think about it, bacterial cell division seems very easy: Start with one bacterium, divide it in the middle and you end up with two.

However, the mechanism of cell division is pretty complex and involves at least three tasks:

• the bacterium needs to decide WHERE to divide
• get all the needed machinery to the division site
• produce new cell envelope material to separate the two new daughter cells

How a bacterium starts cell division

As you can imagine, for most bacteria it makes the most sense to divide straight in the middle. Like this, they end up with two daughter cells of the same size.

This means a bacterium needs to find its middle and mark it. While it is not completely clear yet to researchers how bacteria find the exact middle, they know it involves a so-called Z-protein.

This Z-protein can bind two things: itself and the inside of the bacterial cell envelope. But it only binds the cell envelope where it is straight and not bent. And this is only the case in the middle of the bacterial cell envelope.

Hence, the Z-proteins bind themselves in a long chain linked to the straight cell envelope. Eventually, they form a ring on the inside of a bacterial cell. And this so-called Z-ring stays in the middle of the bacterium.

Also, the Z-ring is only stable when bacteria have enough nutrients and do not encounter any stress situations. This reassures that bacteria only divide when they have all the needed supplies.

How bacteria divide and produce two daughter cells

Once this Z-ring is stable, it recruits helper machineries to this now defined division site.

The Z-ring is a sign of an upcoming cell division. Now, the bacterium knows it needs to activate machineries to produce more cell envelope material and become longer. And to increase their cell envelopes, bacteria use ferries, tunnels and bridges to transport lipids into the cell envelope.

Like this, the bacterium becomes longer and can start the actual cell division. At the same time, the Z-ring becomes tighter and the cell envelope gets its natural bend again.

Now, two processes happen at the same time: Bacteria cut open their peptidoglycan envelope to separate the two daughter cells and also produce envelope material to close both cells.

After this happened, we have two daughter cells coming from the same parent. They both share the same cell envelope and genome. This is why we consider them identical twins.

But do all bacteria produce identical twins upon cell division?

Do bacteria always divide in the middle and produce identical daughter cells?

Yes, most bacteria are symmetrical. And when they divide right in the middle, they produce two identical daughter cells.

Researchers could even watch bacteria during this process thanks to amazing microscopy techniques. You can see the single stages of bacterial cell division and how bacteria produce the cell envelope in the image below.

Yet, the bacterium Caulobacter crescentus has two different cell ends. It can stick to a surface with its sticky stalk on one end and have flagella on the other.

This bacterium also starts cell division in the middle like what we discussed above. However, the new daughter cells are now different: one is still glued to the surface and the other one has flagella and can swim away.

Also, the bacterium Helicobacter pylori with its helical shape can never really find its perfect middle. Hence, the Z-ring forms somewhere inside the bacterium and its daughter cells always have different sizes.

And then there are funny bacteria that decided they don’t even need to divide in the middle. Bacteria like Gemmatimonas aurantiaca grow “budding” daughter cells out of their own parent cells. However, researchers don’t understand yet why this bacterium chooses to divide in this asymmetric way.

Another way of asymmetric cell division happens in the bacterium Bacillus subtilis when it produces spores. During the sporulation process, the spore daughter cell grows within the mother cell. In the end, the mother cell bursts to release the spore into the environment. In this case, only one daughter cell comes out of the division process.

Why and how we want to prevent bacteria from dividing

Since cell division is an essential mechanism for bacteria, nature also found ways to inhibit it. Many antibiotics or toxins inhibit the production of cell envelope material or of the Z-ring. Like this, bacteria cannot divide anymore; they cannot grow and die.

However, we also know that some bacteria can find ways around the toxicities of antibiotics or toxins and become resistant to them. Hence, by better understanding how the whole mechanism works, researchers can hopefully find new ways to interfere with bacterial growth and find new weapons in the fight against antimicrobial resistance.

The post Why bacteria divide into two and grow with the help of a strong ring appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Some microbes come to make their hosts sick. Other microbes are there to help and protect them.

This is a story of both types of microbes and an unusual host: amphibians.

Yes, also frogs and salamanders and other amphibians carry microbes on their skins.

And some of these microbes mean to kill the animals. But, luckily, the animals are protected by helpful bacteria that produce colourful antibiotics.

Read on to find out how bacteria and fungi do not get along on the skin of amphibians. We will also explore how bacteria protect amphibians from extinction.

About fungi that infect the skins of their hosts

Many frogs, salamanders and other amphibians have gone extinct because of a deadly fungal infection. And it seems that many more animals are already infected and sick from that same pathogen.

The bad guys? The two fungal species Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans. They cause a deadly skin disease on frogs and other exotic amphibians.

Similarly, the fungus Trichophyton rubrum can infect our skin and hair. This pathogen causes a disease that you may know as ringworm or athlete’s foot. Typically, you can see such a fungal infection as a red, itchy and circular rash.

But luckily there is a new weapon around to keep these fungal intruders at bay: Bacteria that get rid of the fungus to protect their hosts.

Bacteria produce colourful antibiotics…

Few microbes can grow and thrive on the gloomy skin of frogs or salamanders. One such microbe is the bacterium Janthinobacterium lividum.

This bacterium has an interesting taste for food. It eats the released skin when the amphibians shed their skin. And it also really likes the mucus on the surface of the amphibians.

As a thank you for the good meal, the bacteria help the amphibians in the fight against the deadly fungus.

How?

Generally, bacteria produce antibiotics to get rid of annoying competitors. For example, Janthinobacterium produces the antibiotic violacein, which has a dark violet colour. This antibiotic also kills the fungi that make the frogs sick.

It is still unclear to researchers, how Janthinobacterium transports the antibiotic to the fungus. We already know that the bacterium Chromobacterium violaceum produces membrane bubbles filled with violacein. And that it throws these purple bubbles at its competitors. So, one idea is that Janthinobacterium uses a similar strategy and throws violacein bubbles at the fungus.

Also, when Janthinobacterium grows on the skin of frogs, it triggers the frog to produce more anti-fungal molecules. These molecules kill the fungus and other pathogenic bacteria that are dangerous to the frog.

… and protect them from deadly fungi

Janthinobacterium is not the only bacterium that produces colourful antibiotics to protect its host.

You might have seen red dots in your shower every once in a while. These come from the bacterium Serratia marcescens which makes a red antibiotic. Interestingly, this bacterium can also live on the skins of amphibians. And here, the red antibiotic also protects from deadly fungi.

Other bacteria, like allrounder Pseudomonas, also live on the skins of some amphibians. And these bacteria produce many different antifungals to protect their hosts.

Hence, it looks as if the right skin bacteria protect frogs and salamanders from deadly fungi. And these bacteria keep throwing around colourful bubbles filled with antibiotics – sounds like a bacterial festival to celebrate their hosts?

Colourful bacterial antibiotics to save amphibians?

Now, researchers are trying to save amphibians from the deadly fungus with a process called bioaugmentation. With this strategy, researchers introduce special bacterial communities to the environment. And they hope that the bacteria will jump over to different amphibians.

Bacteria like Janthinobacterium then hopefully establish stable communities on the skins of amphibians and protect them from fungal infections. And let’s hope that these bacterial parties will save more frog species from extinction!

The post Bacteria produce colourful antibiotics to protect frogs appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

They have killer weapons to deliver lethal toxins into other microbes.

And by killing their surrounding competitors, they make space for themselves.

Like this, they conquer new places and environments wherever they go.

But some bacteria are even more sneaky than that. They don’t kill bacteria directly. Rather, they destroy the houses that bacteria live in.

This leaves the prey exposed to the harsh environment. And the attacker can claim the now available space.

Where do these kinds of battles happen? According to researchers, they might even happen in or on our bodies.

Let’s have a look at how bacteria fight by destroying each other’s houses.

Bacteria build biofilm houses

Just like us, when bacteria feel comfortable in a place, they start building houses to settle down. They grow within these houses, multiply, invite their neighbours and become social.

A happy life.

One bacterium that is a master in biofilm house building is the Escherichia coli UPEC. This pathogenic bacterium can grow in the urinary tracts of people and cause nasty bladder infections.

In bladders or on catheters, UPEC can also build biofilms. Here, it wraps itself into a thick layer of slime to protect itself from the surrounding. In this biofilm house, no molecules, like antibiotics, or other bacteria can harm UPEC.

It seems to be protected from almost any attack.

Almost.

Bacteria fight microscopic battles

Now, researchers found that even UPEC has bacterial competitors. These live in similar places like UPEC, so they already know each other.

That’s why UPEC’s opponents came up with a special strategy to make UPEC miserable. They learned to destroy UPEC’s biofilm houses. This is meant to weaken UPEC so that other antibacterial factors now have an effect.

What does that mean?

The UPEC bacterium is pretty nasty for us since we need high doses of antibiotics to get rid of it. And we know that taking antibiotics is not a good thing. So, researchers are looking for new weapons to fight this bacterium.

The idea is that if we understand how other bacteria fight UPEC, we could learn from them. Maybe we could work out similar ways to fight UPEC.

Bacteria fight by destroying biofilms

Researchers found that some bacteria produce compounds that stop UPEC from producing biofilm. One of these attackers is Salmonella enterica Typhimurium. This bacterium even developed a strategy to exclude UPEC from its own biofilm house.

Researchers showed that Salmonella produces a toxic sugar that inhibits UPEC from forming a biofilm. Like this, Salmonella directly stops UPEC from colonising new spaces.

Another bacterium, Lactobacillus acidophilus, produces a similar sugar. Researchers showed that this toxin also stops UPEC from building a biofilm.

However, it is still not clear how these sugars exactly work to inhibit biofilm production.

Bacteria fight by producing biofilm

The researchers also found that Salmonella and UPEC did not grow well together. Separated from each other, they were happy. Together, they were just fighting.

But something else was interesting: In a mixed biofilm, Salmonella managed to outgrow UPEC. It was growing faster and produced a lot more biofilm than UPEC.

This could mean that Salmonella tries to suffocate UPEC with biofilm. The researchers thought that the Salmonella bacteria grow on top of the biofilm, where they have more oxygen. Like this, the UPEC bacteria would be buried by all this biofilm slime and get less oxygen and eventually die.

Surely not a nice way to go!

What can we learn from these bacterial battles?

This study told us a lot about how bacteria live together and fight each other. Researchers are constantly looking for new ways to kill those bacteria that we cannot fight with antibiotics anymore. Based on this, we can even use bacteria as biocontrol agents to fight other pathogenic bacteria.

For example, Salmonella produces a compound that stops UPEC from forming biofilms. If we better understand how this toxin works, we might have a new method to inhibit bacteria from colonising surfaces in hospitals.

Also, UPEC and Salmonella are pathogenic bacteria and they can survive in wastewater even after cleaning. This is a major health issue. Hence, finding new ways to fight these bacteria will help us live healthier and safer.

This study was a small step in the grand fight against superbug bacteria. But those small steps are often the most important ones.

The post Bacteria fight by destroying each other’s biofilm houses appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

They don’t have eyes to see what is going on.

Neither do they have ears to hear a foe approaching.

And yet they seem to know exactly what is happening around them.

How is that possible?

In other articles, we already looked at different mechanisms of how bacteria sense their environment. And we learned about various ways bacteria use to know what is going on around them.

Here, we will look at another one of these mechanisms. A mechanism in which bacteria destroy proteins to understand the environment and adapt to it.

But before we can look at why bacteria destroy proteins, we first need to understand how bacteria produce proteins.

Bacteria need proteins to produce proteins

Every living cell, like a bacterial cell or a human cell, contains DNA. And the DNA contains many different sections, which are genes. These genes are the templates for ALL proteins that a cell can produce.

A cellular machine called the polymerase (bright blue in the figure below) recognizes the start of a gene (yellow), before it transcribes this gene into a string of mRNA (grey). Next, a ribosome reads the mRNA fragment and translates it into a protein (yellow).

This is how every living cell produces proteins from DNA.

Now, we will focus on the first step: when the polymerase recognizes the start of a gene.

Bacteria need proteins to regulate protein production

When you think about it, bacteria do not always need all genes and all proteins. Just as you don’t need an umbrella when it is sunny outside, but it is always good to keep it handy. Similarly, bacteria have heaps of genes on that long string of DNA and they need some of them only under certain circumstances.

For this, all living cells have regulators. These regulators make sure that the polymerase only produces mRNA from genes that are required at a specific time point.

And these regulators come in two forms: activators and repressors.

Activators activate genes

Sometimes, the polymerase cannot recognize a specific gene on its own. This is when the polymerase needs an activator (green). 

An activator is a protein that binds to a specific gene only when needed. This attracts the polymerase to this gene so that it produces mRNA from that gene. Like that, an activator ensures that bacteria only produce certain proteins when needed.

This means something else needs to activate the activator at a specific time point. And while some activators are activated by specific systems as explained in How bacteria sense their environment, sometimes protein-destroying systems are involved. More about that below.

Repressors deactivate genes

Repressors (dark blue) do exactly the opposite of activators. These proteins bind specific genes right at the start. This blocks the polymerase from binding the start of that gene and from producing mRNA.

But when the bacterium needs a specific protein, the polymerase has to recognize and bind that specific gene. At that point, the bacterium has to get rid of the repressor.

So, let’s have a look at how bacteria gain access to genes that need activators or are blocked by repressors.

Bacteria destroy proteins to understand the environment

The environment constantly changes for a bacterium. So, all the time, a bacterium needs to produce certain proteins to handle these new situations. Just as you take your umbrella when it is raining suddenly.

This is when the bacterium needs the polymerase to recognize a specific gene to make mRNA from it.

To get rid of a repressor or to activate an activator when needed, bacteria came up with a simple mechanism: protein destruction.

Yes, to produce proteins, sometimes bacteria destroy proteins.

Proteins that destroy proteins are called proteases and these work like molecular scissors. Proteases cut proteins in at least one specific location. This makes the protein fall apart and become kaput. 

When do bacteria destroy proteins?

Different bacteria developed various mechanisms when to destroy specific proteins. And researchers start to understand more and more about this way of regulation.

So, let’s have a look at a few cool examples of bacteria destroying proteins.

Radiation leads to protein destruction and survival

For example, the fascinating bacterium Deinococcus deserti has genes to cope with radiation and desiccation. However, the bacterium does not need to produce these proteins when there is no radiation or desiccation.

Under these circumstances, the repressor D (dark blue in the figure below) blocks these genes and makes sure the polymerase cannot recognize them.

But as soon as the bacterium is hit with radiation (lightning), the radiation activates the protease M (red). This protease can now bind the repressor D and destroy it. Now, that the repressor does not block the radiation genes anymore, the polymerase can recognize the genes and produce mRNA from them. Now, the ribosome produces proteins (yellow) that cope with the radiation. 

And this is how the bacterium Deinococcus deserti destroys proteins to survive. And yes, this bacterium has the superpowers to withstand radiation and desiccation like no other bacterium.

Antibiotics lead to protein destruction and resistance

In another example, Staphylococcus aureus has a similar mechanism to cope with antibiotics and become resistant. 

In the membrane of this bacterium sits the protease R (red) that is generally inactive. However, when the bacterium meets antibiotics (green molecules), the antibiotics change R. 

Now, the protease falls into the inside of the bacterium and destroys its target protein. This is the repressor I (dark blue), which sits and blocks a certain gene. After protease R destroyed repressor I, this gene is unblocked and the bacterium produces a protein (yellow) that cleaves the antibiotic. 

And this is how Staphylococcus aureus becomes resistant to antibiotics by destroying proteins.

Heat leads to protein destruction and survival

But bacteria do not only destroy repressors. They also use a similar mechanism to activate their activators. 

Generally, to keep an activator inactive, another protein is involved. This is the so-called anti-activator since it captures the activator and inhibits it from functioning. So, for the activator to become active and to bind its specific gene, the anti-activator needs to go. And this is exactly what bacteria do.

For example, in the soil bacterium Bacillus subtilis, the anti-activator Y (dark blue) captures the activator S (green). Plus, Y brings S to the cellular garbage machine (purple) to destroy this protein.

However, as soon as it is getting too hot for the bacterium, Y becomes unstable. So unstable, that it cannot hold S anymore. This means S gets freed, binds its favorite genes and leads the polymerase to them. Now, the bacterium produces proteins (yellow) that help the bacterium to cope with the damage from the heat.

And this is how Bacillus subtilis destroys proteins to cope with heat.

Destroying proteins means bacteria can survive

Here we explored three different ways of how bacteria destroy proteins for their own benefit. Interestingly, the benefit always handles the incoming signal which is often a sign of stress.

Like in Deinococcus deserti, radiation activates protein destruction that leads to protein production. And these new proteins now handle the damage after the radiation attack.

Or in Staphylococcus aureus; antibiotics activate a specific protease that destroys a repressor. Now, the produced proteins are meant to destroy the harmful antibiotics.

So by closing these circles, bacteria found efficient ways of how to read their environment and adapt to it.

Interestingly, most bacteria seem to use similar mechanisms. This means, the better we understand the way most bacteria work, the better chances we have to fight the nasty ones. So we need to keep researching the good bacteria, to understand the bad guys too!

The post Bacteria destroy proteins to understand the environment appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Phages are basically genomic information – DNA or RNA – within a lipid-protein shell. Distributing their DNA or RNA into as many hosts as possible allows the phages to survive. They then reprogram the host to produce more phages packed with more phage DNA or RNA.

These newly produced phages then trigger the host to release themselves which can even kill the bacterium. With the release, the phages are spread further into the surrounding until they encounter another host and the cycle begins again.

Of phages and bacteria

Many different bacteriophages exist that specifically infect certain bacteria. So, just as their hosts differ, the phages differ as well. They come in different shapes, sizes and reproductive mechanisms.

Some phages have very simple shapes as in the picture below. Here, we will focus on the filamentous phages that can be even longer than the host bacterium itself.

Filamentous phages are very common in bacteria and they also have a special ability: They program the bacteria in a way that bacteria do not always produce the phage. They control the bacterium and wait until the right moment comes for them to be produced.

This means that these bacteria have DNA of the phages inside their own DNA. And only when the phage DNA is activated, the bacteria actually produce the phages. Until then, the phage is a so-called silent phage within the bacterium.

Let me be your phage

One bacterium that is infected with a silent phage is the pathogenic bacterium Pseudomonas aeruginosa. Within its genome, Pseudomonas aeruginosa contains the DNA for the filamentous Pf4 phage. However, it only produces this phage when the bacteria live in a biofilm community.

So, it seemed that the phages must somehow help the bacteria in the biofilm. As a new study found these phages actually help the bacterium become more resistant to antibiotics and chemical and toxic substances inside the biofilm.

But the way the phages achieve that is a fantastic antibiotic resistance mechanism that was not known before. To learn about the strategy, researchers took images with the microscope of the Pf4 filamentous phage. And they found these long phage filaments.

I wrap around you

While these structures were pretty impressive, they didn’t explain how the phages would actually behave within the biofilm together with Pseudomonas aeruginosa.

So, the researchers added some artificial biofilm from the bacterium to the phages. They then looked at the phages again in the microscope and they saw that the phage assembled and formed ordered filaments. These looked like highly organised nets of phages.

I protect you

The researchers then wanted to see how the bacteria could fit into these nets. So, they took images of the phages together with the bacteria. And they saw that the phages form their nets close to the bacterial cells just as in the picture below.

It seemed that the phage nets wrapped closely around the bacterial cells. Like this, the phages would form a droplet shape around the bacterial cell and separate it from the surrounding.

And these droplets are the foundation for the resistance to antibiotics of the bacteria. When researchers added different antibiotics to the phage-bacteria-droplets, the bacteria survived.

On the contrary, the bacteria on their own were dying from the antibiotic attack.

This means, that the phage net works as a wall to protect the encapsulated bacterium from toxic molecules in the surrounding. This is a completely new and remarkable mechanism of bacteria to protect themselves from environmental dangers. And they use their very own phages to do that!

It seems that another race against antimicrobial resistance just started…

And then I start again

Let’s put it all together and have a look at the life cycle of these phages:

Pseudomonas aeruginosa carries genes for the Pf4 phage in its genome and only activates them when it grows within a biofilm. At this moment, Pseudomonas produces both biofilm material and the Pf4 phage. These released phages then form nets around the bacterial cells. With this net, the phages protect bacteria from antibiotics and other toxic substances.

So, it seems that phages protect their own hosts from environmental dangers. After having hijacked the bacteria’s cell for their own production, it’s actually a pretty nice thing to do.

The post Love thy host: Phages protect bacteria from antibiotics appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Yes, bubbles!

No, bacteria don’t just produce bubbles and try to hit another microbe with them. They are more sneaky. Bacteria fill these bubbles with antibiotics. And antibiotics are toxic and kill microbes.

So, when these toxic bubbles hit other bacteria, they will suffer.

Let’s look at where these bubbles come from and why bacteria decide to fill them with antibiotics.

Bacteria and their membrane(s)

Bacteria come in one of two kinds. They can have one or two cell membranes.

If a bacterium has one cell membrane, it is called Gram-positive. If it has two cell membranes, an inner and an outer membrane, it belongs to the Gram-negative bacteria. 

The outer and inner membranes of Gram-negative bacteria are slightly different. Interestingly, the inner membrane of Gram-negative bacteria is the same as the cell membrane of Gram-positive bacteria. But in Gram-positive bacteria, that membrane has a lot of additional stuff to make it thicker.

Because Gram-negative bacteria have two membranes, their outer membranes can form “blebs”. These blebs, also called vesicles, eventually form round spheres – or bubbles – and detach from the membrane which is how they are released into the environment.

Bacteria and their outer membrane bubbles

As you can see, these bubbles are made from the outer membrane of Gram-negative bacteria. This is why they are called outer membrane vesicles. These are basically a double layer of lipids in the form of a sphere with stuff inside. 

Within these bubbles, bacteria pack anything that they want to get rid of. This can be cell junk and can come from cell machines that don’t work anymore. Bacteria can get rid of that stuff by throwing it out.

About Chromobacterium violaceum

One bacterium that produces these outer membrane vesicles is Chromobacterium violaceum. And this one has a special reason to produce bubbles: it uses them to kill other bacteria.

Chromobacterium violaceum produces the antibiotic violacein. Violacein is a purple molecule and turns Chromobacterium colonies into purple dots. 

Since violacein is an antibiotic, it kills other bacteria. However, this antibiotic only kills Gram-positive bacteria, those with only one cell membrane.

The problem with violacein is, that it is a very hydrophobic molecule. This means that it is insoluble in water. Hence, researchers were interested to find out how Chromobacterium transports violacein through water to other bacteria. 

Chromobacterium violaceum bacteria produce toxic bubbles

So, researchers had a look at Chromobacterium cells. They saw that these bacteria produce bubbles from their outer membrane. And they do indeed look like spikey bubbles as in the picture below.

The researchers then purified the vesicles and added them to Staphylococcus aureus, a Gram-positive bacterium. The vesicles killed Staphylococcus aureus, hence the researchers thought that the violacein would be inside these vesicles.

Then they grew a Chromobacterium mutant that did not produce any violacein. But this mutant still produced outer membrane vesicles. Surprisingly, the vesicles from this mutant did not kill Staphylococcus aureus. 

From this, the researchers concluded that Chromobacterium transports the violacein within the bubbles.

This meant that the researchers found new functions for outer membrane vesicles. Hence, bacteria use them

a) to solubilise a hydrophobic molecule

b) to transport a hydrophobic and toxic molecule towards other bacteria

c) as bacterial weapons

Now, this concept gives researchers interesting possibilities to apply outer membrane vesicles.

Maybe, one day we will find a way to fill these bubbles with therapeutic molecules and send them towards tumour cells or we just found a new way to deliver antimicrobial substances in general.

For sure, scientists will come up with some cool new ideas to use outer membrane vesicles in the clinic, but as always, that requires a lot more research ?

The post Bacteria firing toxic bubbles appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Yes, the bacteria in your gut have certain superpowers that we benefit from. They help us digest food, keep us mentally and physically healthy, activate our immune system and keep out harmful pathogens.

Here, we will explore some of these fascinating aspects of a healthy gut microbiome, what it is, what it does and how you can keep its superpowers. Learn more about what a healthy gut microbiome actually means and does for you.

What is the gut microbiome?

The gut microbiome consists of all microbial communities that live in your gastrointestinal tract. In there, you can find many diverse players, like bacteria, viruses, fungi and archaebacteria. Here, we will focus on the bacterial members of our gut microbiome, but don’t forget that they all work together to achieve their goals.

Every person has their own unique gut microbiome. So, everyone – depending on their socio-economic state, diet, age, geography, drugs, sleep and other environmental substances – has their own special microbial friends. And studies showed that each person’s gut microbiome is stable over time, even after antibiotic treatment, acute intestinal infections and modified diets.

When you think about it, your gut is a very welcoming environment for most bacteria. It is always about 37 C, a lot of food from your meals and many other microbial friends to party with.

Surprisingly, many bacteria are unable to grow in the lab, so researchers still don’t know much about them. That’s because we don’t know what these gut bacteria need to grow outside of the gut. Yet, researchers found their bacterial DNA in human guts, so they must be living there, somewhere…

Our gut microbiome plays many roles in our wellbeing

In comparison to other microbial niches within our bodies, the gut microbiome is probably best characterized. However, many studies also try to characterise the microbiomes of other parts of our body, as different skin areas. Imagine different organisms living on your feet than on your hand or under your armpits, ears or even eyes.

The reason why researchers mainly study the gut microbiome is due to the accessibility of samples. The sample comes out of your body, so you can directly use it without swapping a person.

Second, the gut microbiome plays important roles in many diseases. So, a lot of research focuses on understanding the interplays between these diseases and the gut microbiome. The aim here would be to find cures or intervention therapies.

How do gut bacteria support our health?

While researchers are still trying to unravel the full impact of our gut microbiome on our health, we are understanding it better and better now. By now we know that a few important players in our gut microbiome are a sign of good health. These are Faecalibacterium, Roseburia, Lachnospiraceae, Eubacterium and Akkermansia muciniphila.

For example, our friendly gut bacteria help us in food digestion. Some of the foods that we eat, we can’t fully digest ourselves, like many complex sugars. In this case, the bacteria in our gut break down these indigestible molecules and produce compounds that we otherwise would not have.

For example, they produce gasses and certain molecules called short-chained fatty acids. While the gasses eventually make their way out of our gut, the short-chain fatty acids play important roles in our overall well being.

These molecules have a positive impact on our mental health, while they also strengthen the gut wall to keep our gut intact. Short-chain fatty acids also strengthen our immune system and help our friendly gut bacteria to grow better. On the other hand, pathogenic bacteria do not like short-chain fatty acids and have thus a harder time settling down in our guts.

Yet, our friendly gut bacteria protect us actively from harmful pathogens that can cause diseases. For example, they fight pathogenic bacteria with harmful killer weapons or produce compounds that are toxic to them.

Also, don’t forget that after a single pathogenic bacterial cell somehow made its way to our gut, it encounters billions and trillions of bacteria that already live there. So, altogether, our microbiota developed many strategies to ensure that any invading pathogenic bacterium feels unwelcome in this environment.

What does an unhealthy gut microbiome look like?

However, once in a while, our gut microbiome seems to be “out of balance”. This can often lead to disease or irritation.

While researchers still don’t know exactly, what the “normal” gut microbiome actually looks like, they are analysing the microbiomes of people with specific diseases. For this, they compare the gut bacteria from people with a disease with the gut bacteria from people that do not have that disease.

And very often, they find that healthy people have a broader variety of bacteria living in their guts. So, somehow all these different bacteria grow together and work as a team to keep us healthy.

This means, one or two bacterial species are often more present in the microbiomes of people with diseases. For example, the bacterium Faecalibacterium prausnatzi likely has beneficial effects on our gut health. However, unhealthy people often have less of this bacterium.

This shift in our microbial gut flora is what researchers call gut dysbiosis. However, whether this shift is the cause or the result of the disease is still not always clear.

Generally, people with gut dysbiosis have fewer bacteria that produce short-chain fatty acids. At the same time, they have more bacteria that degrade the mucus layer of the gut. And the mucus layer is what keeps our gut healthy and intact, so its degradation is usually not a good sign.

Many chronic diseases seem to be associated with gut dysbiosis. For example, type 2 diabetes, obesity, inflammatory diseases or Crohn’s disease, but also mental disorders like depression. However, the exact links are not clear yet.

How can I keep a healthy gut microbiome?

Researchers agree here: You are what you eat!

Diversity is key when it comes to our gut microbiome. This means that you want to make sure ALL of your bacteria stay happy within your gut. So, to keep your diverse bacteria with you, it is vital to eat everything.

Your aim should be to grow those bacteria within you that produce short-chain fatty acids from your food. And for that to happen, you should feed them foods that are high in complex sugars, like fibres.

Also, some studies suggest that certain food additives impact your gut bacteria negatively. These include for example emulsifiers, which work like soaps and kill certain bacteria. Also, stabilisers were shown to induce colitis in animals and artificial sweeteners led to changes in the microbial composition and glucose intolerance in mice.

Most importantly, antibiotics have drastic effects on our gut microbiota. Researchers actually think this is one of the main causes of our modern chronic diseases.

What are probiotics and prebiotics?

The FAO/WHO considers “live microorganisms which when administered in adequate amounts confer a health benefit on the host” as probiotics. These are mainly bacteria that usually live in our guts and that have been well characterised by researchers before.

Interestingly, probiotics do not stay in your gut for a long time. This means to have a long-lasting effect, you should keep eating them regularly.

For example, a probiotic strain of Escherichia coli can slow down the growth of a pathogenic Salmonella strain. Escherichia coli has transporters that specifically bind iron and uptake iron into the cell. With this mechanism, the Escherichia strain uses the iron of the environment, so that there is none left for Salmonella. Because Salmonella and all other bacteria need iron for growth, Salmonella has trouble growing and colonising the gut environment.

Foods with probiotics are for example fermented foods, like yoghurt, kefir, kimchi, kombucha or fermented vegetables. But beware here, as not all of this food actually contains approved probiotic strains.

And to feed your gut bacteria the right food, make sure to eat enough prebiotics as well. They are basically the food for your gut microbiome party.

These include foods that your body cannot digest, which is why your gut bacteria take care of them. Like this, prebiotics promote the growth of probiotic bacteria in your gut. You can mostly find prebiotics in fibres as complex sugars in many vegetables, especially in asparagus, onions or garlic.

Lastly, synbiotics are combinations of probiotic bacterial strains and prebiotics. This basically means that the right bacteria come and bring their own food to your gut party.

Help your gut microbiome help you

So, by eating the right food, you can make sure the right, helpful bacteria grow and live in your gastrointestinal tract. And as a thank you for feeding them, they make sure to protect you and keep you healthy. Great bacteria and their superpowers.

The post How a healthy gut microbiome protects you and how to keep its superpower appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world