Consider the scent of a ripe cheese or a glass of wine—these aromas come from bacteria and other microbes. Even less pleasant odours, like old sweat, smelly feet or a mouldy apple, are thanks to molecules produced by microbes.

Let’s explore the fascinating world of bacterial smells, their origins and what we can learn from them.

Microbial smells come from volatile organic compounds

All microbes produce volatile organic compounds as part of their metabolism. These molecules are generally gaseous and vaporous, allowing us, animals and even plants to smell and react to them.

Depending on their environment, the substrate they use, pH, salt concentration and temperature, microbes produce various volatile organic compounds. These can range from simple gases like carbon dioxide or ammonia to organic acids such as isovaleric acid or large and complex steroid derivatives.

For both microbes and us, volatile organic compounds serve as a means of communication and information. As we’ll see, these small compounds play crucial roles in microbial communities and their survival. On the other hand, for us, certain volatile organic compounds signal to our brains that bacteria are present, indicating that something may not be safe to eat or drink.

Some bacterial odorous molecules have a dual nature: indole, produced by gut bacteria from food, gives faeces its characteristic odour. Yet, at low concentrations, indole has a flowery scent and is even used in perfumes.

Bacteria attract animals with earthy smells

Do you recall the scent of fresh rain? That earthy, musty smell comes from a molecule called geosmin, produced by bacteria of the Streptomyces family.

Streptomyces live in the soil, where they produce soil material and form long thread-like filaments. To survive and spread, they use the volatile organic compound geosmin.

When these bacteria release their spores into the soil, they cover them with both antibiotics and geosmin. While the antibiotics protect the spores from other microbes, geosmin attracts small insect-like animals. These creatures eat the spores and distribute them in the environment.

In this case, geosmin signals a food source to the animals as the spores nourish the animals. At the same time, the spores use the animals for transport to new areas. Once conditions improve, the spores develop into bacteria and start forming their filaments in the soil.

Also mosquitoes are attracted to the smell of geosmin in ponds and waters. Here, cyanobacteria produce the molecule, so the mosquitoes decide to lay their eggs here as the bacteria are food sources for the larvae.

Bacteria produce characteristic food smells

Other pleasant and unique bacterial smells come from the fermentation of fruit, vegetables or milk. During this process, bacteria produce compounds that give food not only their characteristic tastes but also aromas.

As an ancient fermentation product, vinegar has a very characteristic sour smell due to volatile organic compounds produced by microbes. Mainly bacteria from the Lactobacillus and Leuconostoc families and some yeasts degrade the sugars of cereals or fruits to produce acids and alcohols.

Also, the fine aromas of wine and cheese come from the many volatile organic compounds bacteria and yeasts produce during fermentation. They include alcohols, aldehydes, ketones, lactones, esters as well as many other classes of chemicals. As you probably know, depending on the origin of the grapes or milk, the ripening temperature and the microbes added, the resulting product can taste and smell entirely different.

However, the unpleasant smell of rotten foods is also due to bacterial metabolic activity. Meat, fish and eggs contain molecules like choline and trimethylamine oxide. Over time, bacteria break these down into trimethylamine. Your brain likely recognises this off-flavour as a sign of food decay, triggering you to reject rotten foods to protect your health.

Bacteria create your unique body odour

Interestingly, your body odour changes based on what you eat and which microbes and bacteria you introduce into and onto your body. Depending on your diet and health, your body secretes different mixes of sweat—generally a watery mixture of minerals, amino acids, fats, urea and antimicrobial substances.

Although your skin produces odourless sweat all over the body, some areas are more hospitable for bacteria and microbes than others. Consider your armpits, where your main body odour originates: They contain more sweat glands and slightly different hair follicles, making them moister and more enclosed. With more water and nutrients available, your armpits are very microbe-friendly.

Consequently, the microbial communities in your armpits can differ completely from the rest of your body. Here, three bacteria—Corynebacterium striatum, Corynebacterium jeikeium and Staphylococcus haemolyticus—have special strategies to survive the high salt content of sweat and even use the urea in sweat as food.

They break down the molecules in sweat into volatile organic compounds that together give each person their unique body odour. For example, sulphur-containing compounds, often with strong onion-like smells, are produced by Corynebacteria.

Our sweat also contains lactic acid and glycerol, from which Staphylococcus and Propionibacteria produce acetic and propionic acid. These molecules directly impact your body odour as they evaporate leaving a pungent smell or supporting the growth of other bacteria. But our smelly sweat has advantages too: After eating citrus fruits, people’s sweat contains limonene, a mosquito-repellent possibly generated by skin bacteria.

Bacteria are responsible for smelly feet

Another significant area of your body directly impacted by bacteria and their smell-creating superpowers is your feet.

Our feet actually contain the highest variety of microbial communities, with Staphylococcus, Corynebacterium and Brevibacterium being the most common. These bacteria feed on skin particles, urea and the amino acids in sweat.

For example, Staphylococcus epidermidis, a normal resident of human skin, degrades the amino acid leucine into isovaleric acid. Unfortunately, this molecule has a powerful, rancid cheese-like odour—the reason for smelly feet.

Fortunately, other bacteria, like Brevibacterium, Micrococcus and Kytococcus, can completely degrade both leucine and isovaleric acid, thus preventing the unpleasant smell. As usual, it comes down to having the friendly bacteria around.

Bacterial smells in your life

As we’ve seen, the world of bacterial smells is fascinating and complex. From the earthy smell of rain to the rancid odour of sweaty feet, bacteria play crucial roles in creating the smells that surround us.

These microbial odours are not just curiosities; they have important functions in nature and human biology. They can act as communication signals between microbes, influence animal behaviour, make our food smell delicious and even impact our unique body odour. So, embrace the microbial world with all its facets, colours and smells!

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Those bacteria that call your gut their home are the so-called commensal bacteria. Luckily, they have a special superpower: They can protect us from bacteria that cause infections and make us sick. For this, our commensal gut bacteria developed some extraordinary strategies to defend these pathogens.

So, by nurturing our friendly gut bacteria, you are also strengthening your protection against diseases. Here, we will look at what kind of bacterial wars are going on in your gut and how your gut bacteria defend pathogens and keep you healthy.

Your gut bacteria defend pathogens with toxic molecules

Bacteria have many different means to kill other microbes, competitors or even their own siblings. Often, these bacteria produce molecules that are toxic to their prey, which means they inhibit cellular proteins or machineries. Without these machineries, the prey is then lacking an essential cell function to grow or survive, so that it eventually dies.

Interestingly, gut bacteria produce and deliver many different toxic molecules of various shapes and sizes, functions and even origins.

Gut bacteria produce bacteriocins

Many bacteria produce molecules that are like antibiotics specifically to kill bacteria. These are called bacteriocins.

Some bacteriocins are simple and small molecules, while others can be big and fancy. However, they all have a similar goal: they bind to a specific target in the prey bacterium and prevent that target from working properly.

So, no wonder that many bacteria in our gut microbiome produce bacteriocins that are toxic to pathogenic intruders. Also, we carry a lot of different bacteria in our guts and they all produce different bacteriocins. Hence, incoming pathogens face this huge load of toxic molecules making it really difficult to establish themselves in our intestines.

For example, one bacterium that loves the warmth and lack of oxygen in our gut is the bacterium Ruminococcus gnavus. And this one produces at least two bacteriocins, Ruminococcin A and C, that are toxic against human gut pathogens like Clostridium perfringens.

Other friendly gut bacteria, like Escherichia coli or Blautia producta, also produce bacteriocins that are toxic to pathogens, like Enterococcus faecalis. And some of their bacteriocins can even impact our gut cells by activating and strengthening our immune response.

Gut bacteria produce short chain fatty acids from fibres

Another way to protect against pathogenic gut bacteria is directly related to your diet. When we eat a lot of fibres, which are non-digestible carbohydrates, our friendly gut bacteria break these up. From these fibres, they produce small molecules that are called short-chain fatty acids, which have many positive health benefits for our overall wellbeing.

Interestingly, when we have a lot of these short-chain fatty acids in our intestine, the pH drops. This is already pretty difficult for most pathogenic bacteria, as not many can handle this acidic environment.

Plus, short-chain fatty acids diffuse into pathogenic gut bacteria where the pH drops as well. This can disturb many cellular machineries from functioning properly and not many bacteria have the right tools to defend against this attack, so they’ll die.

Gut bacteria convert bile acids into toxic compounds

To better digest the fats in food, our liver produces bile acids. These molecules bind fatty acids and lipids so that we can take them up better into our bodies.

But some of our friendly gut bacteria can convert these primary bile acids from our liver. For example, one of these bacteria, Clostridium scindens, transforms them into secondary bile acids that can bind the lipids of bacterial membranes.

Like this, secondary bile acids open the membranes of some pathogenic gut bacteria, like Staphylococcus aureus, Bacteroides thetaiotaomicron or Clostridoides difficile. This eventually kills the intruders and keeps our guts pathogen-free.

Killing pathogens with bow and arrow

Yes, also direct bacterial wars are happening in our guts! And they are nasty!

Some bacteria use tiny little bows to shoot deadly arrows into other bacteria. And these arrows can be incredibly toxic so the shot bacterium has barely any chance to survive the attack.

Luckily, our gut bacteria use their bows and arrows to defend against gut pathogens. For example, commensal bacterium Bacteroides fragilis has three different bows and can shoot various arrows. And research showed that this bacterial friend can protect us from bacteria that otherwise cause intestinal diseases.

Interestingly, Bacteroides fragilis is not opposed to hit’n’kill its own toxic bacterial siblings since some members of his family can indeed make us sick. But our friendly Bacteroides fragilis collected many different immunity proteins against its evil siblings so that their toxic arrows cannot harm it. Instead, Bacteroides fragilis keeps shooting and killing until we are safe from the pathogenic sibling.

Keeping nutrients from pathogenic gut bacteria

Another important way how gut bacteria defend pathogens is by keeping nutrients away from them. In all mixed microbial communities, bacteria fight for nutrients, especially for metals like iron, zinc but also sulphur sources.

Luckily, our gut bacteria developed some sneaky ways to steal these metals from gut pathogenic bacteria. By sending out special proteins that bind these metals very tightly, the commensals make sure to keep these metals from the pathogens. And if the pathogenic bacteria don’t have enough of these essential metals, they won’t survive and will eventually die.

Strengthening the mucus layer to block pathogenic gut bacteria

When you think about it, your gut is not part of your body – even though it is inside of you. All the food that we eat, stays within this digestion tube (mouth, oesophagus, stomach, intestines) until it comes out on the other side.

And to protect us from harmful microbes and molecules, we need to have a clear physical barrier from the content of the tube. This barrier is the so-called epithelial layer, which is covered by a slimy mucus on the outside. And this sticky slime helps keep off intruding microbes so that they cannot breach through the epithelial wall and get into our bodies.

Luckily, our helpful gut bacteria help us maintain this slimy defence wall. Because just by being close to this mucus layer, the epithelial wall produces more slime. And if the slime gets thicker, gut pathogenic bacteria have more difficulties getting into our bodies.

To help the slime grow, some bacteria adapted very well to the conditions within the gut. For example, our friendly gut bacterium Ruminococcus gnavus cuts off the very end of the mucus layer and feeds itself with it. This does not harm the mucus itself, but it keeps the bacterium close by. And this in turn triggers the epithelial wall to produce more mucus. So, everyone wins.

How to help your gut bacteria defend pathogens

Now, that you better understand how your gut microbiome defends pathogenic gut bacteria, make sure you support them keeping you healthy. By feeding your gut bacteria the right foods, you will help them be comfortable and happy in your gut. And when the right bacteria grow within you, they will gratefully protect you from nasty intruders!

Another idea for researchers is to use what they have learned to keep you healthy. The idea is to develop probiotics or prebiotics that help us defend against nasty pathogens. For example, you might take pills containing toxins against pathogenic gut bacteria or probiotics with bacteria that can fight off pathogens.

Whatever it may be, you can always help your gut bacteria be happy in your intestines by eating the right things. That means lots of fibre and veggies! ?

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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

So, they talked of cocci and bacilli based on the spheres and rods that they saw under the microscope.

And they classified microbes and bacteria based on these shapes.

It came only with later, modern technologies that scientists learned that there was more to bacteria than their shapes. Even though bacteria looked similar, they had different superpowers.

Yet, some of these bacterial superpowers are indeed influenced by their cell shapes.

So, what is it about bacterial shapes? Why do bacteria look differently? And how do the different shapes of bacteria help them survive and thrive?

What gives bacteria their shapes?

To protect themselves from the environment, bacteria as well as all other organisms have cell envelopes. These keep the cellular machines and internal parts together so that a bacterium can function within this envelope.

And this envelope also gives bacteria their shape.

Both Gram-positive and Gram-negative bacteria have a layer of so-called peptidoglycan within their envelope. This peptidoglycan layer is made of sugars that are linked together by very strong bonds. This is why the peptidoglycan layer is pretty rigid and stiff and has a specific shape in each bacterium.

Either on the inside or on the outside, the peptidoglycan layer is linked to the cellular membranes. Together, these make up the bacterial envelope with a specific cell shape.

What different shapes do bacteria have?

Microbiologists have different ways to classify known bacterial shapes. Here, I will introduce you to the bacterial shapes according to what makes the most sense to me.

Rod-shaped bacteria

As the name suggests, these bacteria have a rod or cylindrical shape. Examples of rod-shaped bacteria are Escherichia coli and Bacillus subtilis.

Scientists are also convinced that rod-shaped bacteria are the evolutionary ancestors of all other bacterial shapes.

The shape comes from proteins that form long cables within the bacterial cell. These span out the whole bacterium from one end to the other.

Rod-shaped bacteria grow by two modes that we talk about in Why bacteria divide into two and grow with the help of a strong ring: First, they extend their cell size by growing the peptidoglycan, the cable proteins and the membrane.

Second, the cable proteins determine the middle of the cell, where the bacterium produces a special ring. Eventually, this ring narrows so that the bacterium divides and two bacterial cells form.

Spherical bacteria

The spherical bacteria – or so-called cocci – include many pathogenic bacteria like Staphylococcus aureus, Streptococcus pneumoniae and Neisseria gonorrhoeae.

Microbiologists think that spherical bacteria were once rod-shaped as well. However, spherical bacteria do not have these long cable proteins that extend their cell bodies. Thus, they stay spherical and grow by dividing their spherical cells right in the middle.

However, sometimes the two daughter cells do not completely divide and they stay attached to each other. This is why some spherical bacteria live as so-called diplococci.

Curved bacteria

Curved bacteria have the shape of a comma or banana and are sometimes also slightly twisted. Examples of curved or banana-shaped bacteria are Caulobacter crescentus and Vibrio cholerae.

These curved bacteria usually live in watery environments where there are flows. Here, the curved shape helps the bacteria to align with the flow while staying attached to a surface.

In the case of Caulobacter crescentus, one end of the bacterium is glued to a surface with a strong super glue. When this bacterium divides in the middle, one daughter cell remains attached to the surface, while the other one can swim away and find a new location to settle down.

Spiral bacteria

Spiral bacteria are a mix of rods and curves which give them a helical twist. Hence, these bacteria have a corkscrew shape.

Many pathogenic bacteria use their corkscrew shape to swim through gel-like solutions. This includes Helicobacter pylori and Campylobacter jejuni.

Since spiral – or helical – bacteria are also thinner, they can reach locations that are too narrow for other bacteria to reach. They also use their flagella to push themselves forward and “wriggle” through narrow pores.

Star-shaped bacteria

Some bacteria look even fancier than others: They are real stars – yes, bacteria with a star shape.

While we don’t know much yet about star-shaped bacteria, they belong to the so-called Stella species or are Methylomirabilis oxyfera. These usually grow in freshwater, soil and sewage.

The star shape comes from six little arms that extend out of the bacterial cell. These push and grow to the outside giving these bacteria a shiny star shape.

Why do bacteria have different shapes?

Now that we have seen the different shapes of bacteria, you might ask yourself, why do bacteria have these different shapes? How do they help them?

As always in biology, it comes down to how a property helps a bacterium survive in a certain location. Often, the cell shape gives a bacterium advantages over other bacteria and it is easier for them to settle down and face harsh environments.

For example, spherical cells have the lowest surface-to-volume ratio. This means they have a large envelope surface through which they can take up a lot of nutrients. All this while their cell volume is relatively small. So they don’t actually need that many nutrients. This helps cocci to grow in locations where there are little amounts of nutrients.

On the other hand, rod-shaped bacteria often have flagella. And thanks to their shapes, they are efficient swimmers. This allows them to swim to new places in cases of danger or the lack of nutrients.

Bacterial cell shapes help face harsh environments

Also, straight rod cells can pack into biofilms more efficiently and build organised structures. This helps them colonise different locations and resist dangerous environments.

Many rod-shaped bacteria also form longer filamentous organisms. These stronger and larger structures protect bacteria from being eaten by other organisms. Another advantage of these multicellular organisms is that they allow more cells to attach to surfaces and colonise hosts.

Lastly, both curved and helical bacteria use their shapes to get better around their environments. Curved bacteria grow in watery environments but also in our guts. Here, their shapes help them align with the flow of water or our gut content while they stay attached to a surface or the gut wall. This keeps them at their preferred location and protects them from being flushed away.

Spiral bacteria use a fascinating helical movement to screw through gel-like or viscous fluids. This for example helps pathogens swim through the mucus of our stomach and guts and colonise us and make us sick.

Bacteria and their shapes

Here, we looked at the different shapes that bacteria have and how these help them survive. Bacteria always face harsh and new environments and conditions and only survive if they have the right tools or means.

So, by adapting their shapes, bacteria often have advantages over other bacteria. Plus, they look cool and fabulous!

The post Looking fabulous: Why bacteria need to stay in shape too 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!

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

We are completely surrounded by them and we surely would not be the same if it was not for our microbial friends.

Unfortunately, every once in a while, we read and hear negative news articles about certain players of the microbial world. And then we forget that many other microbes and bacteria are actually very helpful to us, our health, the environment and food production.

But the goal of the BacterialWorld blog is to remind you how colorful and interesting the microbial world is.

20 interesting microbes everyone should have heard about

The microbial world consists of many interesting players: bacteria, viruses, phages, fungi, protozoa, unicellular eukaryotes and microscopic animals. And together, they all make the microbial world such a diverse and fascinating environment.

So, here, we assembled a list of common and interesting microbes. Some of them you might find delightful, others you rather want to avoid and that is okay.

We want you to be aware that there are many more cool microbes and bacteria out there than what you hear in the news.

And that thanks so research, we know a lot about how to use these microbes or how to avoid them if they are dangerous.

For this list, I got help from microbe lover Rachel and her GIANTmicrobes which she introduced during the #MicrobesinMay challenge on Twitter.

Ready to learn about the microbial world and interesting bacteria and microbes?

1. The bacterium Escherichia coli

Escherichia coli is rod-shaped and can have flagella all around its cell. 

Most people have heard of Escherichia coli because of contaminated food or lakes. However, most strains are harmless and this bacterium is actually super important for your digestive health.

This is also why Escherichia coli is by far the most intensively studied and best-understood organism on the planet.

Escherichia coli serves as a model organism for microbiology and biotechnology. It is helping scientists to learn about everything DNA-related, as well as protein production and cell growth. In most research labs of biological or life sciences, scientists use this organism every day to produce proteins, produce gene fragments or use it as a vehicle for plasmids and vectors.

2. The Influenza virus

The influenza virus is an RNA orthomyxovirus that causes respiratory infections, which you may know as the ‘seasonal flu’. Luckily, there is a vaccine against the flu that you should get every year if you are able to.

Influenza is an RNA virus that contains 8 genetic segments. Generally, RNA viruses are prone to mutate a lot; this happens during so-called antigenic drift and antigenic shift events. These “shifts and drifts” can change the structure of the virus’s surface proteins. Unfortunately, this change makes it harder for our immune system to recognize and respond to the virus.

Because the flu virus is ever-changing, you should help your immune system to recognize the new antigens. You can do this best by getting the new FluShot every season. But be aware that each virus is different and a FluShot will not protect you against other viruses.

3. The fungus Saccharomyces cerevisiae

You may encounter this fungus – almost on a daily basis. Saccharomyces cerevisiae is also known as the common yeast.

We use this yeast to make beer and bread. Like many other microorganisms, Saccharomyces cerevisiae performs microbial fermentation. This means it eats sugar and turns it into alcohol in beer and CO2 for bubbles in beer and bread.

We cannot state enough that the yeast Saccharomyces cerevisiae is a fungus and not a bacterium. It produces rounded cells and researchers use it as a model organism for eukaryotes. This means its DNA is enclosed in a membrane and not swimming around freely as in bacteria. Humans are also eukaryotes, so lots of knowledge of human cellular and molecular biology comes from yeast research.

Saccharomyces cerevisiae also plays a role in biotechnology. Some strains produce biofuels while others produce recombinant proteins that we use as therapeutics.

4. The bacterium Lactobacillus acidophilus

Lactobacillus acidophilus gets its name because it produces lactic acids from sugars, which usually makes its surrounding very acidic.

Lactobacillus acidophilus cells are rod-shaped and usually grow in pairs or chains. This bacterium lives in our mouths and guts where it prevents the growth of other bacteria by maintaining a healthy microbiota.

This bacterium also helps make yogurt, since it breaks apart milk sugars to make acids and other healthy molecules. This is why Lactobacillus acidophilus is also a probiotic, meaning a microbe that promotes health. There are many claims out there promoting its use to increase health, but more research is needed.

5. The Rhinovirus

The Rhinovirus may look cute but it is one of those nasty viruses that you may not like. It causes the common cold and we all know how we feel not cute with a cold. There are more than 100 different varieties of rhinoviruses and together they cause almost half of all colds.

Rhinovirus is an RNA virus in a 20-sided capsid. They are some of the smallest viruses and can spread by aerosol or direct contact. The virus replicates best in temperatures slightly cooler than body temperature, like in the nose. In fact, “rhino” means nose in Greek.

Currently, there is no vaccine against Rhinovirus. And since it’s a virus, antibiotics won’t work against it.

The best way to protect yourself is good hand hygiene and physical distance from people with a cold.

6. The microscopic water bear

One of the most interesting and cutest microbes is definitely the water bear.

But what exactly are water bears?

Hypsibius dujardini are microscopic creatures, classified as the Tardigrada phylum.

As the name suggests water bears resemble bears and walk on eight tiny legs. Tardigrade means “slow walker”. So if you imagine a slow-walking bear through water, this is kind of what water bears are!

Besides being adorable, water bears can survive extreme conditions and they are found worldwide in diverse environments. Many species live in water or around moss. To survive in any habitat, water bears enter a state of cryptobiosis where it dries out and stops its metabolism. In this state, they can last several decades.

Water bears can live in hot springs, polar ice, mountains and deep in the ocean. In fact, researchers found that water bears can even survive the vacuum of space! That’s good since a capsule containing some crashed on the moon in 2019.

Learn more about what tardigrades look like under the microscope.

7. The microscopic rotifers

To us, Rotifers are certainly one of the most interesting and cutest microbes. These microscopic animals are almost all female and can reproduce without the involvement of males.

Rotifers are tiny free-living creatures found mostly in freshwater. Rotifers have a cylindrical body and a ring of cilia around their heads. When the cilia move, it appears as a wheel (rotifer means “wheel bearer”). This movement pushes food into the animal and helps them move through the water.

Rotifers are sexually dimorphic and the males are much smaller and usually do not live long.

Reproduction of this microbe is rather interesting: Unfertilized eggs grow as clones within their mother. But studies have found genetic differences without sexual reproduction. It is now just a question of how?

8. The bacterium Porphyromonas gingivalis

The bacterium Porphyromonas gingivalis causes bad breath and gum disease, so make sure to brush and floss regularly to keep it in check.

Porphyromonas gingivalis cells are rod-shaped and live in our mouths. They are anaerobic, so they don’t need oxygen to grow. This may seem odd since we should have oxygen in our mouths all the time. However, many different microbes grow in our mouths where they form biofilms. These are layers of almost no oxygen, in which the bacteria settle.

In the oral biofilm, the dental plaque, Porphyromonas gingivalis lives close to the gum line where oxygen is depleted. Here, the bacteria can infect the gum and cause erosion called periodontitis.

9. The Rubellavirus

The “little red” Rubellavirus is known to produce red rashes on children’s arms and faces. Luckily, there is a vaccine to prevent infection.

Rubella is an RNA virus in a 20-sided capsid wrapped by a lipid membrane. Also called German measles because it was first identified in Germany, rubella was once a common childhood disease causing rash, fever and sore throat. While it posed minor risks to children, rubella could be deadly for the unborn in the womb.

Today rubella is very rare because of the MMR vaccine, which protects against mumps, measles, and rubella. Thanks to scientific research and vaccination, many countries could be declared “free of endemic transmission of rubella”.

10. The morbillivirus

Separately, the virus that causes the measles. This virus leads to red spots all over the body and can be deadly. Fortunately, the MMR vaccine prevents infection.

Morbillivirus is a spherical RNA virus. Measles is very contagious and spreads by personal contact and contaminated surfaces. It infects the respiratory system and causes rash, fever, cough, running nose and red eyes. Measles can cause serious complications and be deadly for kids.

Today, morbillivirus is still responsible for more than 100 000 deaths yearly, down from more than 2 million deaths annually. This is due to the introduction and widespread use of the MMR vaccine.

11. The bacterium Shigella dysenteriae

If you’ve ever experienced Shigella dysenteriae, you would remember! This bacterium infects the intestines and causes shigellosis, which is incredibly painful and uncomfortable. Antibiotics treat this disease, but hygiene is the best prevention.

Shigella dysenteriae are rod-shaped bacteria. They have a biological needle with which they fire the so-called ‘Shiga toxin’ into our gut cells. This leads to stomach pain and watery diarrhea.

This bacterium travels through the fecal-oral route, from contaminated food or hands. It is very contagious because it needs only a few cells to make someone sick.

What’s the best way to protect yourself? Always cook food thoroughly to kill all bacteria. And wash your hands to prevent spread!

12. The human papillomavirus

This virus may look cute, but human papillomavirus has been linked to certain cancers! The human papillomavirus is a common virus that infects many. Thankfully, there is a new vaccine to prevent high-risk infections.

The human papillomavirus is a DNA virus surrounded by a circular capsid. This virus is very common and in most cases, one may not have any symptoms while the body clears the virus.

Sometimes, the virus causes small tumors called papillomas that appear as warts. If left untreated, those tumors can become cancerous.

The human papillomavirus spreads by direct contact and is one of the most common sexually transmitted diseases worldwide. A vaccine is available to prevent infection from the major cancer-associated human papillomavirus types.

13. The bacterium Anabaena

Anabaena, known as cyanobacteria, are photosynthetic bacteria, even though they resemble eukaryotic algae. These helpful bacteria contain pigments that give Anabaena the blue-green colour.

Commonly found in aquatic environments, cyanobacteria use their pigments to convert light into energy. Using that light along with CO2 and water, they convert it to sugar and oxygen. In fact, cyanobacteria are a major source of oxygen in our atmosphere today!

The bacteria are even more interesting since some of their cells have special superpowers. These so-called heterocysts can “fix” nitrogen.

Heterocysts have extra thick- cell walls to exclude oxygen that otherwise harms nitrogen-fixing enzymes. The heterocysts then share the fixed nitrogen with surrounding cells.

14. The bacterium Clostridium botulinum

Clostridium botulinum produces a neurotoxin known for causing botulism. But that same toxin is also a component of Botox. Just another way we use microbes for good.

Clostridium botulinum is a rod-shaped, spore-forming, anaerobic bacterium. Found in soils, it can enter the food supply as spores. Under correct conditions, like in canning, spores germinate and produce the toxin. Thus, food should be processed with high heat and pressure to kill spores.

The botulinum toxin is the most toxic substance known and causes paralysis. While botulism is serious and can be deadly, scientists found ways to use the muscle-paralyzing function of this toxin. In small doses, the toxin treats muscle disorders such as spasms. Also found in Botox, the toxin paralyzes muscles that lead to wrinkles.

15. The varicella-zoster virus

Remember those itchy spots caused by chickenpox? I do! But now many children don’t have to experience the results of the varicella-zoster virus because of the chickenpox vaccine (lucky them!).

The varicella-zoster virus is a highly contagious DNA herpesvirus. As a primary infection, the virus causes so-called varicella. You might remember this as body rash and itchy blisters that last a few days.

Yet, the varicella-zoster virus actually can remain dormant in our nervous system (called latency) and reactivate later in life. This secondary infection can then lead to herpes zoster, also called shingles.

While chickenpox is usually a non-serious childhood disease, shingles affect adults and can have serious complications and pain. That’s why there is a separate shingles vaccine, too. No one wants to be itchy or in pain, so make sure to get the vaccine!

16. The bacterium Borrelia burgdorferi

Borrelia burgdorferi is a spirochete bacterium shaped like a corkscrew with flagella at both ends. These bacteria live in ticks and can infect humans when bitten by an infected tick.

These bacteria cause Lyme disease, a zoonotic disease where the pathogen jumps from an animal to a human.

Lyme disease is best known for causing a bull’s eye rash. But it also causes fever, headaches and fatigue. Some cases of Lyme disease are asymptomatic and if left untreated can lead to serious neurological or heart issues. Make sure to protect yourself when going hiking and camping.

17. The bacterium Listeria monocytogenes

This bacterium has made headlines, but not for anything fun. Listeria monocytogenes has led to many food recalls because of contamination concerns. It can grow at 0°C, so even refrigerated food can be infected.

Listeria monocytogenes cells are rod-shaped and covered with flagella. This food-borne pathogen causes listeriosis that may result in sepsis, meningitis, or death. It’s especially dangerous for immunocompromised and unborn, which is why pregnant women shouldn’t eat soft cheese or uncooked meat.

Listeria monocytogenes is found in environments where food grows. Contamination can occur during food harvesting and processing. Once inside a human cell, they manipulate it so that the cell propels the bacteria into the next cell.

18. The Epstein-Barr virus

Did you know that the Epstein-Barr virus is one of the most common human viruses? It causes the commonly called kissing disease because we transfer the virus by saliva and bodily fluids.

The Epstein-Barr virus is a DNA herpesvirus with a lipid envelope. Most infections occur in childhood and are asymptomatic or with only mild symptoms. Roughly 90% of adults have antibodies against Epstein-Barr, which means they were once infected with this virus.

When infecting adults for the first time, the Epstein-Barr virus can cause mononucleosis. Symptoms include fever, sore throat and extreme fatigue, lasting weeks to months. You can prevent the spread by not sharing utensils or drinking cups.

19. The bacterium Staphylococcus aureus

One of the best-known bacterial warriors is Staphylococcus aureus and its methicillin-resistant super brother MRSA. These two can infect almost all parts of the human body with their arsenal of virulence factors.

Staphylococcus aureus cells are round-shaped and form grape-like clusters. Most people have this Gram-positive bacterium in their nose or on their skin.

Unfortunately, with certain triggers, this harmless bacterium can become a pathogen. Then, Staphylococcus aureus produces virulence factors, such as toxins, enzymes, and antibody-inactivating proteins. These bacteria can also form biofilms on medical implants.

What about MRSA? Those are strains of Staphylococcus aureus that are resistant to the antibiotic methicillin (Methicillin-resistant Staphylococcus aureus). Antibiotic resistance occurs when bacteria acquire ways to inactive antibiotics and has become a worldwide health crisis.

20. The protozoan Toxoplasma gondii

Love cats? Well, those cats might have a ‘friend’: Toxoplasma gondii. This parasite can be carried by cats and is one of the most common parasites in the world. The infection causes toxoplasmosis which is an important zoonosis.

Toxoplasma gondii is an obligate intracellular parasite. It can reproduce sexually only in cats (called the definitive host) or asexually in any warm-blooded host (such as mice or humans). A cat can become infected by eating an infected mouse, then pass the infection to humans via litter.

Toxoplasmosis infections can occur from eating contaminated food or from infected cat droppings. In most cases, the infection is asymptomatic. However, immunocompromised and pregnant people are at risk for complications.

Which one is your favorite among the interesting microbes?

We hope we could give you a broad overview of interesting microbes and bacteria common in the environment and on the human body. This list of common microbes is meant to raise awareness of how multifaceted the microbial world is.

Yes, some of these microbes cause diseases. But thanks to research, we now have ways to boost our immune systems to clear diseases caused by pathogens or to prevent microbial diseases in the first place with vaccines.

And don’t forget that so many microbes are actually super helpful and fun to look at! Just look at this cute water bear dancing around!

If you have questions about any of these microbes or want to learn more about any player in the microbial world, comment below or send us an email.

And if you want to know more about Rachel and interesting bacteria, follow her on Twitter, or connect with her on LinkedIn.

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