Whatever you do throughout your day, you are constantly bringing microbes onto and into your body. Especially when eating, you introduce a mix of microbes into your gastrointestinal tract.

In this dark, airless place, microbes flourish, working tirelessly to keep you in good shape. They improve your body’s health starting from the gut and strengthen your gut’s defences by fighting off unwelcome intruders.

Gut bacteria break down the food you eat from which they produce all sorts of molecules. The most important ones are called short-chain fatty acids. These small molecules impact the health of your gut and your overall body.

Here, we’re looking at gut bacteria that produce short-chain fatty acids and how they maintain the health of your gut. We’ll also explore ways to help bacteria make even more of these beneficial molecules.

Let’s start by understanding how your gut protects your body.

The mucus layer of the gut as a first line of defence

The food you eat passes through your body, yet it is always in contact with your body’s outer layer of cells. Only in the gastrointestinal tract do your gut cells absorb molecules from food and transport them into the body.

This means the outer layer of your gut, the so-called epithelium, faces away from the body and is in constant contact with the outside. One of its main jobs is to prevent harmful components from getting too close or even entering the body.

That is why goblet cells, which are special gut epithelial cells, produce a thick, slimy mucus. As they constantly secrete mucus, the cells actively push everything away from the epithelium, while the ever-growing mucus layer sits like a protective shield on top of the the intestinal epithelium.

When the mucus layer is too thin or broken, harmful microbes and bacteria can come into contact with the gut. This can trigger inflammatory immune responses, resulting in chronic diseases such as inflammatory bowel diseases.

Commensal gut bacteria produce short-chain fatty acids

While this slimy physical barrier is already a strong first line of defence for your gut, you can also rely on your gut microbes. Those that reside in and on your body over a long time are called commensal microbes.

One way to make them stay with you is by feeding them their favourite foods. Gut bacteria eat what you eat, while some commensals like Ruminococcus gnavus and Akkermansia muciniphila also eat the mucus in your gut.

And from your food, the majority of gut commensals prefer the dietary fibre. That is the indigestible part of plant-based foods as it passes through your small intestine unchanged. Once it reaches the large intestine, your gut bacteria get to work.

They break down the fibre, ferment it and produce all sorts of molecules from it. The most important group of molecules are the short-chain fatty acids, including acetate, propionate and butyrate.

The commensals Bacteroides thetaiotaomicron, Bifidobacterium longum, Eubacterium and Blautia coccoides are actually some of the best-known producers of short-chain fatty acids. Just by eating a lot of dietary fibre, you increase both the different microbial strains growing in your gut and the amount of short-chain fatty acids they make.

How short-chain fatty acids improve gut health

From the gut, short-chain fatty acids diffuse through the mucus and reach the epithelial layer. Here, they bind to receptors on the goblet cells and activate certain pathways.

They trigger goblet cells to grow and produce more mucus. This increasing mucus layer, in turn, protects more effectively against harmful bacteria while providing more food for your commensals.

For example, two gut bacteria, Akkermansia muciniphila and Blautia coccoides, produce the short-chain fatty acids acetate and propionate. Both molecules trigger gut cells to make more mucus, improving gut health and feeding commensal bacteria while fighting off intruders. In mice, Bifidobacterium longum induces the growth of mucus, likely by producing acetate.

The diet-microbiome-gut health connection

Now, let’s tie all these pieces together: By eating plant-based fibres, you feed your beneficial gut bacteria. These digest and ferment the fibre and produce short-chain fatty acids, which bind to your gut cells and trigger them to produce more mucus. This increasing mucus layer shields off your gut while feeding your gut bacteria.

Generally, the more fibre we eat, the more beneficial bacteria live in our guts. They become more active at digesting fibre since they lose their appetite for the mucus.

Beneficial bacteria like Blautia can even be found in human stool after 12 weeks of eating high-fibre diets. Hence, it seems that the commensal Blautia decides to settle down in your gut depending on what you eat. So, by eating food full of fibre, you can attract helpful bacteria to you.

On the other hand, when you eat little fibre, your gut bacteria start eating your mucus layer, since their preferred substrate is not available. This can lead to inflammation and other gut health issues.

You are what you and your bacteria eat

When considering the role of your gut bacteria for your health, the saying “you are what you eat” may take on a new meaning.

By eating a lot of different plant fibres, you’re not just feeding yourself — you’re also feeding the bacteria in your gut. Your food gives them the right fuel to produce short-chain fatty acids that strengthen your gut’s protective layer and gut health. This, in turn, impacts the health of your body, mind and cardiovascular system and even your emotional and mental wellbeing.

Hence, by eating more veggies, fruits and seeds with lots of fibre, you influence which types of bacteria live close to and inside of you. So, what you eat affects how you feel, quite literally from the inside out.

Your gut bacteria will thank you for that extra serving of vegetables. To show their gratitude, they’ll provide you with all the good stuff to keep you healthy.

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

Whatever it was, chances are high that part of your food was fermented by microbes. As exceptionally healthy and tasty as fermented foods are, these would not exist if it weren’t for microbes and their fermentation superpowers.

Yet, microbial fermentation is a lot more than processing food and giving it a new taste or aroma. Indeed, depending on who you ask, microbial fermentation means slightly different concepts.

For once, fermentation is a metabolic pathway in some microbes and organisms. It is an energy-saving way to degrade and metabolise substrates and produce complex and energy-rich fermentation products.

Secondly, microbial fermentation describes the process of preserving food based on the fermentation pathway. For this, we let microbes break apart and ferment food in a controlled manner, eventually producing well-known fermented foods, like yoghurt, beer and chocolate.

Lastly, the industrial process of growing microbes in big cultures is often called microbial fermentation. The goal of this process is for microbes to produce a specific product – and often they do so through the fermentation pathway.

As you can see, the different definitions for microbial fermentation are grounded on the same principle: microbes degrading substrates and making fermentation products from them. Here, we will look closer at the biochemistry of microbial fermentation and explore some examples of where this microbial superpower naturally occurs and how we make use of it.

The biochemistry of microbial fermentation

From the view of a biochemist, fermentation is first of all a metabolic pathway to conserve energy. Most organisms gain energy from opening chemical bonds of molecules. This releases the energy-rich electrons that are bound within the bond. They then save these electrons in other molecules or fuel cellular machineries.

Most microbes have one preferred substrate for their metabolism. For many, this is glucose, the same sugar that our cells preferably burn and degrade. By degrading glucose, they (and us) produce several intermediary products, the most important one being pyruvate. This degradation process sets free several electrons, which microbes save in a molecule called ATP. ATP is the main fuel for microbial growth machines, swimming motors or transporters.

Sometimes microbes find themselves in environments with an excess of their preferred substrate. In this case, setting free all the energy would produce a lot of heat, damaging or even burning the cell. Hence, as an alternative, energy-conserving pathway, they switch to fermentation metabolism.

During this pathway, they degrade the substrate only partly, thus not extracting all available electrons from it. Instead, they use one of the intermediary products and bind it to another molecule in an energy-neutral reaction. This conserves the electrons and energy within the fermentation product.

What makes fermentation so fascinating: Many species have unique fermentation pathways. Depending on their genes, they branch off the fermentation pathway at any intermediate and produce different molecules.

For example, from pyruvate, some microbes produce ethanol, which we use for beer or wine production, and others produce lactic acid, like for yoghurt production. Other microbes ferment substrates like citrate or succinate and produce complex molecules like caffeine or colourful biopigments.

By conserving the high-energy electrons in the fermentation products, microbes produce fewer ATP molecules. Hence, they have less energy available at that moment. But if they need energy later, they can break down the fermentation product to extract the electrons. Often though, their energy levels are so high, that they even export the product to get rid of it.

Fermentation is thus a way for microbes to process molecules and conserve energy. Gladly, we learned to make use of this pathway as microbes help us convert energy-rich substrates into beneficial products.

Microbial fermentation for food preservation

One source of energy-rich substrates are carbohydrate and fibre-rich foods, which is why these are some preferred environments for microbes. By fermenting fruits, vegetables, milk and grains, microbes can grow and spread on seemingly any plant-based substrate.

Gladly, we learned to grow microbes and ferment food in controlled environments, making food fermentation one of the oldest human technologies. Throughout history, many cultures have optimised different fermentation processes and created all kinds of products.

Food fermentation can include adding so-called starter microbes to the food or using those microbes that naturally live in the foodstuff. These microbes break apart the carbohydrate component of the foodstuff to fuel their fermentation pathways.

The resulting fermentation products can be beneficial vitamins, antioxidants or molecules that change the aroma, taste, texture or stability of the foodstuff. The degradation and modification of the food itself and the accumulation of fermentation products, over time, make our well-loved cheeses, coffee, bread, chocolate, beer, wine, kombucha, yoghurt or kimchi.

For example, thanks to microbes, cheese and yoghurt taste and smell differently than the original milk. Coffee and chocolate get their complex and unique aromas only thanks to the microbial fermentation of coffee and cocoa beans.

During fermentation, many bacteria produce strong acids from the original substrate. Thus, the resulting food becomes acidic and sour, which prevents other microbes from growing and spoiling the food. That’s why food fermentation became an efficient way to conserve food. Many vegetables, like cabbages, pickles or olives, are thus preserved into sauerkraut or kimchi, sour pickles and olives, and the like. Also making kombucha, kefir or cheese are ways to preserve the original tea or milk.

When fermenting cereals, yeasts mainly produce carbon dioxide or ethanol. Carbon dioxide, for example, in sourdough bread makes the bread rise. In the beer-brewing and wine-making processes, yeast produces ethanol as well as several beneficial and aromatic molecules that give beers and wines their tasteful and diverse aromas.

About the microbes involved in food processing

Each fermented food has a unique community of microbes that changes with the fermentation process over time. With the rise of one microbial species, the pH of the food might change or a certain substrate becomes available, which might kill one species or feed and thus help another one grow.

In many vegetable-based fermentation products, lactic acid bacteria, such as Leuconostoc, Lactobacillus and Weissella, are the primary microbes. They produce acids which prevent food-spoiling microbes from growing. The acids also give the resulting kimchi and sauerkraut their sour and acidic tastes. On the contrary, in alkaline-fermented foods of Asia and Africa and in bean-fermented foods, such as tempeh, miso or natto, Bacillus bacteria are usually responsible for the fermentation process.

In milk fermentation, bacterial cultures are of two types: Lactococcus, Lactobacillus, Leuconostoc and Streptococcus bacteria that acidify the milk. This denatures the milk and produces yoghurt-type products, such as yoghurt, buttermilk and kefir.

As a second step during the cheese-making process, Brevibacterium, Propionibacterium, Debaryomyces, Geotrichum and Penicillium are added. These bacteria and fungi produce more complex molecules and give the ripening cheese its unique flavour, texture and aroma.

For cereal fermentation, yeasts are the most widely used microorganisms, producing beer, sourdough bread, sake and whiskey. For bread-making, the principal yeast is Saccharomyces cerevisiae. Other Saccharomyces species, as well as Torulaspora, Hanseniaspora and Pichia are responsible for fermenting most cereal-based drinks.

How the human body benefits from fermentation

As we’ve learned above, many fermented foods are full of microbes – as long as the food was not heated or pasteurized. Hence, when eating fermented foods, you also take in the microbes in and on the food. And these are ready to settle in your body, feed off your food and do some more fermentation.

After arriving in your gastrointestinal tract, the microbes start digesting part of your food too. They degrade the plant cell structures of vegetables, fruits, cereals, seeds and nuts as well as non-digestible fibres. This releases sugars which gut microbes ferment to short-chain fatty acids and gases, like methane. These fermentation products have beneficial effects on your digestion, mental and gut health as well as your immune system.

Hence, by eating fermented foods you gain beneficial microbes – some of them are the so-called probiotics. And by eating plant-based foods you give your gut microbes the appropriate food to ferment, which is what makes some of them prebiotics.

But this is not the only place where microbial fermentation takes place in your body. For example, Lactobacillus bacteria are the key players within the vaginal microbiome and their fermentation activities influence the health of women.

Within the vaginal tract, host cells provide Lactobacillus with glycogen. From this, the bacterium sets free glucose and ferments it to produce lactic acid and hydrogen peroxide. These molecules decrease the pH creating an acidic environment within the vagina. This acidity kills some pathogenic microorganisms directly and prevents others from growing. Hence, by feeding residential Lactobacillus bacteria, the body helps them grow and in return they protect it.

Microbial fermentation as a pillar of industrial production

The more we learn about microbes, bacteria and their fermentation pathways, the better we can use their metabolic superpowers for our own good. Especially the biotechnology and food industry are making great use of microbial fermentation.

We now grow microbes in big batches and harvest fermentation products, like bioethanol, lactic acid or vitamin B12. In many cases, microbes grow on plant-based products or even ferment waste into usable and, thus, green products. As you can guess, food fermentation based on appropriate starter cultures is taking place on large scales to produce many of our beloved foods.

As such, microbial fermentation is an essential part of our lives. Not only as a fundamental process in cellular metabolism and thus human health, microbial fermentation has become a key pillar in food production and preservation as well as industrial production.

As a sustainable tool to produce plant-based foodstuffs, pharmaceuticals and fuels, microbial fermentation may even play a crucial role in our journey towards a greener and more resilient future. Just another reason to be grateful to microbes and their fascinating superpowers.

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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. As bacteria produce SCFAs close to the 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, the friendly gut bacteria Akkermansia muciniphila and Ruminococcus gnavus cut off the very end of the mucus layer and feed themselves with them. This does not harm the mucus itself, but it keeps these bacteria 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 have you ever asked yourself where yogurt comes from and how it is made from milk? Do you know why yogurt tastes so sour and yet delicious?

What if I told you that yogurt only tastes like this thanks to bacteria and their superpowers?

Yes, bacteria not only produce delicious chocolate, wine, beer or bread. But it is also bacteria that make yogurt from milk.

Here, we will look at which bacteria produce yogurt and what makes it so creamy, sour but also healthy.

What’s in your yogurt?

Yogurt would not exist if it wasn’t for our bacterial friends. Interestingly, it only takes two bacterial species to create this white creamy dream that we call yogurt. These two bacteria are Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus.

Within milk, these two bacteria live in a symbiotic relationship. This means they help each other grow and survive. And together, they produce delicious yogurt.

These two bacteria make many molecules that give yogurt its characteristic flavor. These include lactic acid and other acids like acetoin, acetate, acetaldehyde. Because of all these acids, yogurt tastes quite sour.

Also, our two bacteria produce exopolysaccharides. Generally, bacteria use these to make biofilms. But in this case, the exopolysaccharides with their long sugar chains make the yogurt creamy and viscous.

Thanks to bacteria and the milk content, there are also a lot of healthy molecules in yogurt: proteins that are rich in energy, calcium, and vitamins B2, B6 and B12.

How is yogurt made?

It seems that all we need to make delicious yogurt are milk, our two bacterial species Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus and the right temperature. We call these two bacterial species the yogurt starter cultures.

But before their superpowers produce yogurt from milk, the milk needs to be prepared. This is basically to get rid of all the other stuff that we don’t need.

So, to kill all other microbes that might spoil our yogurt, the milk is heated to 95 °C. You might know this process as pasteurization.

After the milk cooled down to about 40 °C, our two starter bacteria are added. Next, the mix is filled into cups and sealed. The cups are then stored in a warm room – something researchers call incubation. During this incubation time, the bacteria can get to work and use their superpowers.

This means that our two bacteria start a process called microbial fermentation. They break down the milk sugar lactose and produce lactic acid and other acids.

Due to all the acids, the pH of the milk drops and it becomes sour. Now, the acids denature the milk proteins – this is the same process that you see when you heat an egg: it becomes harder and loses its fluidity. The milk becomes more viscous and gets a gel-like texture and creaminess.

Why is yogurt good for you?

We already saw that yogurt has a lot of good stuff and some studies showed that it is healthy for us because of all these molecules. But how do these vitamins, proteins and short-chain fatty acids impact our health?

For example, yogurt stimulates the immune cells that are in our guts. This improves our immune system so that it can better fight bad intruders.

Our two starter bacteria also break down some of the milk proteins and produce so-called bioactive peptides. Our guts like these peptides a lot. Hence, it transports them into our bodies where they have health benefits.

Also, the sugars in yogurt are prebiotics. This means they are the right food for other bacteria that live in our guts and that keep us healthy.

Plus, yogurt is full of protein that our bodies need to grow muscles and stay strong. Interestingly, yogurt protein has two important fractions: whey and casein protein.

The whey protein is considered a “fast protein”. This means, our body digests this type of protein faster which gives us energy immediately after eating yogurt.

The other fraction is casein or the “slow protein”. This type of protein clots in our stomach because of the acids. But our body can digest this protein clot only slowly. Hence, the casein protein gives us energy even up to 7h after eating yogurt. Like this, yogurt helps with satiety so that in general we need to eat less.

Lastly, the short-chain fatty acids in yogurt have lots of health benefits for us. They regulate the blood glucose level, insulin resistance and inhibit our appetite.

Now you have a lot of reasons to include yogurt in your daily diet plan!

What is probiotic yogurt?

Researchers found that the two starter bacteria Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus do not survive the acidity in our stomachs. Hence, they do not arrive in our guts and have no impact on our gut microbiota.

However, yogurt is a great vehicle to transport other probiotic microorganisms into our bodies. Probiotics are organisms that “when administered in adequate amounts, confer a health benefit on the host”. Also, probiotics need to be safe, well-characterized and stable while the yogurt is waiting on the shelf to be eaten.

Hence, many yogurt companies now add beneficial probiotics to yogurt. These are bacteria like Lactobacillus casei, Lactobacillus acidophilus or Bifidobacterium.

These bacteria have beneficial effects on our digestion and immune system. They help the right bacteria in our guts to grow, meaning they keep our gut microbiota healthy.

For example, in one study, researchers added a Lactobacillus casei species to yogurt and gave it to children with acute diarrhea. After a few days, these children had fewer symptoms and less abdominal pain thanks to the yogurt mix.

Is (probiotic) yogurt on your diet plan yet?

Here, we looked at two new superhero bacteria that produce the fermented creamy white dream. Even though they might not survive the passage into our bodies, they produce a lot of healthy molecules for us. Hence, they have an indirect health benefit on our bodies.

Plus, yogurt is a great vehicle to transport other probiotic bacteria into our bodies. And it seems that by eating yogurt regularly you can indeed change your gut microbiome and bring in some helpful bacteria.

So, thank bacteria for their superpowers and for providing us with this delicious food!

The post What’s in your yogurt? appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

No, but this is pretty much what happens there.

Okay, they might not sit at a table with napkins in their laps and fork and knife in hand. But bacteria do share food with each other and even feed each other with their leftovers. 

Not sure, how that might work? 

Read on to find out!

What’s in your plant food?

If you are like most people and eat a healthy balanced diet, you will probably eat a lot of plant products, including vegetables and fruits.

But think about what plants are actually made of: Their cell walls are extremely rigid and sturdy because plants need to be stable to withstand different weather conditions. So, to stabilise a vegetable or fruit, they have complex walls that we can barely digest.

And yet, they are some of the best foods you can eat…

While our own digestive system is struggling to break down plant material, we can always rely on the microbial friends in our guts. They have the necessary tools and superpowers to break up plant material, digest plant food and help us get the best from it.

But none of them can do it on their own. Also, bacteria work together and share their food to achieve that.

Let’s look at how food-sharing works between bacteria and which plant components they are digesting for us.

Arabinogalactan – a complex glycan from plants

To stabilise plant cells and make them sturdy, long and complex molecules are part of most plant cells. These are often glycans that are complex polymers with one main chain and many different side-chain branches. 

And one of these complex plant glycans is arabinogalactan – or short AG.

AG consists of very long main chains made of the same sugar molecules. And each sugar molecule consists of a ring of 5 carbon atoms. Now, these carbon atoms link to carbon atoms within the same sugar but also to carbon atoms in the next sugar.

So, within the main chain, the sugars are all linked to each other via the so-called 1,3-bond. This means, that the carbon atom at position 1 links to the next sugar molecule via the carbon atom at position 3. And between these two carbon atoms sits an oxygen atom. 

Okay, so far for the main chain.

The side chains consist of different sugar molecules. Hence, the bonds between them are different. 

Plus, the side chain is connected to the main chain via a different bond – the 1,6 bond. This means, that the carbon at position 1 from the sugar molecule of the side chain binds to the carbon at position 6 of the sugar molecule of the main chain.

Since these side chains have different lengths and lots of branches, the structure of the AG gets so complex. This is what ultimately makes it so difficult for our digestive system to break them down. We just don’t have the tools for that.

Enter our microbial friends in our guts.

Bacteria degrade complex plant polymers

Since this complex AG polymer is basically in every plant cell, we are eating a lot of it. And somehow we seem to be able to digest it. So, researchers were curious about what happens to this glycan in our guts.

And they knew already, that bacteria in our guts have really cool tools and scissors to break up complex plant sugars and glycans.

This scissor sits on the outside of a bacterium. Here, it directly chops off a piece of sugar when it comes into contact with a plant polymer.

And directly next to the scissor sits a transporter. This immediately takes the chopped off sugar molecule and imports it into the bacterium. Now, the bacterium uses this piece of sugar for energy and growth. 

One of the bacteria that break down AG in our guts is Bacteroides cellulosilyticus. Let’s call this one the Bacell-bacterium. 

These Bacell-bacteria have special scissors that cleave off the side chain of AG from the main chain. Plus, they have another set of scissors to chop off the last sugar molecule from the side chains.

However, they cannot break up the rest of the side chain. Hence, this leaves some valuable sugar chains lost in the deepest corners of our guts. 

But gladly, other bacteria pick up these yummy sugar sources and are grateful for that share of food.

Bacteria get their share of food

Researchers found that the bacterium Bifidobacterium breve uses these released sugar chains. Let’s call this bacterium the Bif-bacterium. 

Generally, the Bif-bacterium does not have these advanced scissors to break down complex glycans. But it can pick up and degrade released sugar chains from other bacteria. 

Researchers found that when they fed the Bif-bacterium with AG, it did not grow alone. However, they then added the Bacell-bacterium and fed them with AG. Now, the Bif-bacterium was growing.

This meant that the Bacell-bacteria break down certain pieces of the AG and share the leftover food with the Bif-bacteria. Since Bif-bacteria have the right scissors to break down smaller sugar molecules, they can use these now and grow.

Next, the researchers looked at what both bacteria produced from the AG.

Bacteria share food with each other and keep us healthy

They found that the Bacell-bacteria alone produce some short-chain fatty acids from the AG. These short-chain fatty acids are very helpful for our body and keep us healthy.

Yet, when the Bif and the Bacell-bacteria grew together with AG, they produced even more diverse short-chain fatty acids. This meant that the interaction between the Bif- and the Bacell-bacteria itself can be understood as a probiotic – they are healthy for us. And it also means that AGs are prebiotics – they feed healthy bacteria.

Interestingly, also other bacteria get their piece from this interaction: The probiotic bacterium Lactobacillus reuteri (Lacto-bacterium) also plays a role in sugar degradation in our guts.

The Bif-bacterium produces a molecule called 1,2-propanediol from AG. Now, the Lacto-bacterium can pick up 1,2-propanediol and make more short-chain fatty acids from it. And this also helps the Lacto-bacterium grow and keeps our gut healthy. 

So, when bacteria share food with each other, everyone wins!

Help your bacteria share food and you keep yourself healthy

From this little story, I hope it became clear again, that you are what you eat. By giving your bacteria the right food, they can feed each other so that they grow. And when the right bacteria grow in your gut, they will defend you against harmful pathogens and keep you healthy. 

So, yes, keep being nice to your bacteria! ?

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

Gladly, we learned to use some of these bacterial superpowers to improve our own lives. This means that bacteria and their superpowers are pretty much everywhere you look. You can find their impact in the food you eat, the medicine you take or the bioplastics you use.

So, yes, you probably use microbes and their superpowers daily without even realising. In this article, we listed 20 of the most fascinating bacterial superpowers and how they help not only bacteria but also us.

Bacteria know exactly where they are going

Bacteria have a so-called flagellum with which they can swim in liquids. This flagellum works together with the super responsive chemotaxis system.

This fascinating mechanism helps bacteria understand where beneficial nutrients or harmful compounds are. The bacterium then decides to swim towards or away from that compound. Chemotaxis is thus essential for the survival of bacteria.

Read Chemotaxis helps bacteria move towards goodies

Bacteria are high-speed swimmers

With the above-mentioned flagella, bacteria can move in liquids. When they rotate their flagella, they can swim in one direction which helps them find nutrients or escape harmful situations.

Interestingly, the Olympic recordist for 50 metres freestyle swims 1.17 body lengths per second. However, the bacterium Escherichia coli swims 15 body lengths per second and the tiny Bdellovibrio bacteriovorus swims even 10x faster, moving 160 body lengths in one second.

Read Bacteria wrap themselves in their swimming flagella

Floating veils for large bacteria to attach to and fetch nutrients

Bacteria produce oxygen and give superpowers to everyone

This may sound a little trivial because we take oxygen for granted. But bacteria known as cyanobacteria first produced oxygen on this planet. A large part of the atmosphere’s oxygen today is produced in oceans by these bacteria and other single-celled organisms.

You can also find more on cyanobacteria in this article.

Bacteria can produce electricity

Some bacteria can align into long filaments – so-called cable bacteria. This alignment allows bacteria to produce electrons on one side by oxidizing metals. They can then transport the electrons along the filament. Bacteria on the other side of the filament use these electrons for oxygen reduction.

Thus, bacteria produce an electric current within certain water sediments, which researchers measured. Maybe one day they can use these filaments in some kind of seawater-based batteries.

Read Cable bacteria – unusual bacteria conduct electricity

Bacteria use superpowers to align to the magnetic fields

Some bacteria, like the Magnetospirillum, that live in water, have so-called magnetosomes. These are storage units for iron crystal-like structures. The iron inside can align with a magnetic field and even along the magnetic Earth field.

These aligned magnetosomes then give magnetic momentum to the bacterium. Based on that, the bacterium aligns itself with the magnetic field and can find an optimal location in its environment.

Read How bacteria read and follow the Earth’s magnetic field

Bacteria can reduce and produce gold – highly valuable bacterial superpowers

In gold mines in Australia, researchers found bacteria that form biofilms on gold particles. For example, the bacteria Delftia acidovorans and Cupriavidus metallidurans can reduce toxic gold-ions to elementary gold.

This means that these bacteria are directly involved in the biogeochemical cycling of this precious metal.

Bacteria kill their competitors

To survive and grow, bacteria have learned to outcompete other bacteria and microbes. For this, they developed fascinating nanoweapons that kill their competitors and leave them as the sole survivor.

Interestingly, there are several different of these bacterial nanoweapons, all working slightly differently. Read more about this bacterial superpower:

Bacterial killer weapons as biocontrol to protect plants

Nanoweapons make the killer differences in bacterial siblings

Understanding the type 6 secretion system spike of a bacterial killer machine

Bacteria and contact-dependent growth inhibition: Death on a stick

Bacteria have various superpowers to protect their hosts

Microbes and bacteria live in and around bigger organisms like the human body, plants or animals. They developed fascinating mechanisms to protect their hosts and support them in different ways.

Bacteria might help them digest food, help them grow or fight off harmful intruders. For example, our bodies would not work without the microbiome – all those microbes and bacteria in and on us. Read more about the human microbiome:

How bacteria in your gut microbiome defend pathogens

Bacteria on your hands strengthen your unique skin microbiome

“Follow your gut instinct” – how your gut microbiome influences your mental health

How a healthy gut microbiome protects you and how to keep its superpower

Bacteria and their superpowers light the way

Some bacteria have the superpower to produce light in a process called bioluminescence.

Interestingly, bioluminescent bacteria often live with other organisms in symbiosis. For example, some bioluminescent bacteria occupy the lure of the female anglerfish. This fish also uses them as a fishing rod for hunting.

Bacteria withstand heat and cold

Whether too cold or too hot. Some bacteria really don’t care.

Certain bacteria can survive at temperatures as low as -20°C, which is why they are called hypothermophiles. On the contrary, other bacteria live in hot water steams up to 122°C. Similarly, these bacteria are hyperthermophiles.

These extremophiles have special repair enzymes to keep their DNA and cell envelope intact even at such extreme temperatures. Consequently, some of these enzymes are being used in research and are daily tools in each research lab. Learn more about extremophiles:

Even at the dark and cold bottom of the sea, microbes flourish

Bacteria tolerate harmful radiation

Another extreme-loving bacterium: the radiotolerant Deinococcus radiodurans. This bacterium has very efficient proteins to protect its DNA. Plus, it produces special DNA repair machines. They super quickly recognize and repair any damage in the DNA after exposure to radiation.

With these mechanisms, these extremophiles can survive exposure to ionizing radiation. Some bacteria even survive in the cooling systems of nuclear reactors.

Bacteria go to sleep by forming spores

Some bacteria can form so-called spores which are bacteria “on hold”.

Bacteria go into this state in times of greatest starvation or drought. Their aim is to keep its genetic material safe while turning down all non-essential functions. In this state, bacteria do not have an active metabolism nor do they interact with the environment. They solely wait for better times to come until nutrients become available again.

Bacteria produce some of our favourite foods

Did you know that bacteria produce many of the foods you are consuming? By fermenting sugars to alcohols or acids, lactic bacteria and some yeasts give a delicious taste to common foods like cheese, yoghurt and kefir, kombucha, kimchi and sauerkraut, beer and wine, as well as chocolate.

Reason enough to be grateful for bacterial superpowers to produce amazing foods.

Bacteria can endure high pressure in the deep sea

Researchers found bacteria that can live up to 10 km deep inside the ocean. Yes!

This means these bacteria can endure pressures of up to 100 MPa. But, researchers don’t know yet how these bacterial cells function at such high pressure. However, they think that the proteins inside these bacteria form some kind of super glue-like complexes. This would then make the bacterial content more viscous to endure the pressure.

Read Even at the dark and cold bottom of the sea, microbes flourish

Bacteria produce oil

Many microorganisms, amongst them bacteria, produce natural oils which is why they are called oleaginous microorganisms. Mainly algae, bacteria and yeasts can produce biodiesel, while fungi, and some algae can produce healthy omega-3 fatty acids.

Now, researchers focus on engineering these organisms to enhance the accumulation of produced lipids, biodiesel and omega-3 fatty acids.

Bacteria repair their DNA super efficiently

Bacteria have to endure all sorts of environmental stresses, for example, temperature changes, antibiotics or challenges by competitors. To ensure that under all circumstances, their DNA remains undamaged after an attack, bacteria developed incredibly efficient DNA repair and fixing machines. These machines recognise any small damage in the DNA.

Read

How does Salmonella deal with stress – a journey through the human body

Bacteria destroy proteins to understand the environment

Bacteria nucleate ice and let it rain

Some bacteria can trigger water to form ice crystals at temperatures close to the melting point. One of these bacteria is Pseudomonas syringae.

This bacterium has special proteins on its outer surface that interact with water and triggers ice formation. These bacteria are even used to produce artificial snow in winter sports areas around the world.

Bacteria keep our environment clean

Some bacteria surely love their heavy metals! Many bacteria have special enzymes to reduce toxic metal ions. These bacteria are even used to clean waste in industrial waters or mines and are the basis for green chemistry.

Read Microbial bioremediation: microbes cleaning-up our toxic messes

Bacteria can change our blood types for a short amount of time

Some bacteria live in our blood and when they get hungry, they start cleaving off sugar molecules from our red blood cells. While this is not harmful to us at all, in clinical tests, this may look like a different blood type than our original one.

However, as soon as the body produces new blood cells, they will have our original sugars and therefore our normal blood type.

Read Bacteria changing blood types

Some bacteria are super small

Super small but super powerful!

While bacteria have all these superpowers, I am most amazed by the fact that they are so tiny and yet SO powerful. All these superpowers in such a small box!

To actually see bacteria, we need microscopes. And to have really good photographs of them, we then need EXTREMELY good microscopes. Look at the bacterial cells in the pictures here! They are just about 2 micrometres long…

Thank bacteria and their superpowers

After having read this list of bacterial superpowers, are you even more amazed by our bacterial friends now? Which of these bacterial superpowers is your favourite? Which of them would you like to learn more about? Let us know in the comment section below or send us an email with your question. We’re looking forward to hearing from you!

The post The incredible superpowers of bacteria: unveiling nature’s tiny heroes 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