Bugs and your Gut - The Microbiota

Ever heard of the term microbiota or microbiome? Wondered what it is and what it all means? Is there such a thing as good bugs and bad bugs?

Well lets answer some of these questions.

What is the Microbiota?

When we are talking about the microbiota when are talking about the normal “flora” or commensal bacteria that lives in your body. Yes encase you didn’t know we are meant to have bug/germs/bacteria whatever you want to call it living on us and within us. If we didn’t we would be very unhealthy.

They proved this in rats where they were born and raised in “sterile” environments with no microflora. They were incredibly sick and had significant memory and functional abnormalities. In fact they documented them as having “autistic behavioural characteristics”. However when they were given faecal transplants (poo from healthy rats put inside them). Their function and behaviour dramatically improved.

Now you might not be a rat but they are doing similar studies in humans. One of which I will talk about later.

Different microbes live in different parts of the gut/body such as the mouth, skin, stomach, small intestine and large intestine. Which makes sense as they have to be adapted to that environment, survive different conditions and also play different roles. Most times though when people are referring to the microbiome they are referring to bacteria living in the lower part of the large intestine. This is because the majority of microbes live there and a lot of immune cells are also made in the large intestine. It’s quite a busy place! Also because it’s an easy place to test- just get a stool sample.

The mouth is becoming an area they are starting to research more- as we swallow a lot of the bacteria from our mouths and it can then travel down and colonise in other parts of the digestive tract.

Is it good or bad? Can you tell? Or does it seem like an illusion?

Is it good or bad? Can you tell? Or does it seem like an illusion?

But are there “GOOD” and “BAD” bacteria?

It’s not as simple to labelling bacteria as good or bad. The reality is we have a lot of bacteria that can play multiple roles. It depends on the DNA they have, the genes they contain, the environment they are living in and the fuel sources they have access to.

A good example that highlights this is the gut bug E.coli. Now you have probably heard in the news about this when there has been an outbreak. E.coli can be pathogenic (cause problems) but there are a lot of different strains of E.coli out there. Lots of E.coli strains are really healthy and good for us. They help out compete other bad bugs and prevent them growing where they shouldn’t , they help with digestion, there is probiotic that is actually based on Ecoli. But there are some E.coli strains that have acquired genes that enable them to produce toxins and these are the ones that are pathogenic. Often causing symptoms such as diarrhoea and gut pain/bloating. So when you are looking at different species, this is why its important to not only look at what type it is i.e. E.coli , but what genes it contains- to see what kind of metabolites it can produce. Like in this example produce a toxins and therefore this E.coli is playing a “bad” role.

The other thing that can make them “good” or “bad” depends on the fuel source the bacteria is feeding on. A lot of bacteria use different fuel sources such as: protein, fibre and mucus in our intestine. Fibre is not absorbed by us and travels to the large intestine to feed the bacteria in our large intestine. Most bacteria want to eat fibre preferentially and when they do they produce good metabolites that help make us healthy. If we eat excessive protein and some saturated fats that we can’t absorb it finds its way to the large intestine for our bacteria to eat and causes a downturn in bacteria.

Example of this is the bacteria Prevotella copri, it can eat fibre, protein and mucus. If it is eating fibre it will be doing us a lot of good- it will produce a lot of beneficial by-products that keep us healthy. in fact hunter gatherers have high amounts of this bacteria in their stool and they don’t have any gut problems. In western societies we have high levels of this same bug, however because we have different diets: high in protein, high in sugar and low in good carbohydrates. We are seeing this bacteria being associated with diabetes, insulin resistance and other metabolic disorders. Because when this bug is not being fed fibre and fed protein or mucus instead it is producing harmful metabolites and inflammation. It is not that this is a “good” or “bad” bacteria, it is what you are feeding it that determines what it will do.

This is why fibre is so so important in our diets, to help keep our microbiome healthy. But it’s more important to remove sugar first than simply add more fibre.

yogurt anyone?

yogurt anyone?

What about Candida I’m sure it’s a BAD bug?

Now before you start beating up Candida, even though sometimes it deserves it. Candida albicans is the most common species seen in the gut. In most cases it plays a neutral role, doesn’t do us harm or much good it just lives there and chills out. Now the time it is a problem, is when it is allowed to over grow. Typically it is unusual to happen in the gut as an overgrowth by itself (usually there are other imbalances too), more likely its a problem in other areas i.e. vaginal thrush.

When you do see an overgrowth in the gut of candida it is when antibiotics have been used -as candida is a fungi not a bacterial microbe. When the antibiotics kill off all the bacteria the candida can over grow as it was not killed by the antibiotics (as they don’t work on fungi). That in conjunction with a diet high in sugars and carbohydrates (processed) allows this to occur. Candida overgrowth can be caused also by OCP (oral contraceptive pill) use, steroid medication use and high sugar consumption. Although as already stated the most common reason is antibiotic use.

To get the gut bacteria to come back into play and decrease the candida overgrowth you need to do things such as eat fibre so the bacteria that is there can grow back and control the candida. As well as shutting off candidas food supply.

Now why the bad rap for candida? When it is allowed to overgrow it can cause intense sugar cravings and mood problems. It has been linked to anxiety, panic attacks, depression and mood swings. It also impairs fatty acid metabolism and decreases Zinc and B6. All of which are crucial for normal cognitive function and mood balance.

Tell me more about how these gut bugs make metabolites- why should I care about them? And what foods make these metabolites?

Metabolites produced by the gut bacteria are going to be more important than the species themselves. This is the way the research is heading.

Everyone has different species in their microbiome depending on where you live. People living in Asia, Europe, Australia, America etc all have different microbiota. But what these bugs are doing in our bodies is fairly consistent no matter what ones you have or where you live. They seem to be all doing the same things, breaking down protein, fibre, mucus, as well as making metabolites. It is only if you are missing certain functions that seems to be the problem rather than specific species in your gut.

When you are missing functions that is when you have gut issues or another disease process occurring. Key metabolites bacteria produce are short chain fatty acids, made from fibre as a break down product.

There are 3 primary fatty acids gut bacteria make when they break down fibre these are:

  • acetate

  • propionate

  • butyrate

The most important and most studied so far is Butyrate. Butyrate is the main energy source of our gastrointestinal cells, providing 70% of their energy needs. Butyrate also suppresses appetite by stimulating the release of hormones that have this effect. Butyrate reduces inflammation in the gut and if you aren’t eating enough fibre your gut bugs won’t be able to make this as much. This is because the bugs that feed on other food sources will outgrow the fibre loving ones and therefore they can’t make as much butyrate. Propionate seems to have a very similar role to butyrate as it decreases appetite and reduces inflammation.

When we break down protein we can also get short chain fatty acids but you also get other metabolites that may not be as beneficial for our health- which makes it more like a mixed bag. So we want to make sure we are skewing the balance in favour of the bacteria that make butyrate from fibre. For example Faecalibacterium prausnitzii is the poster child bacteria for producing butyrate in the large intestine and is a sign of good gut health.

If you are felling a lack of energy this can be from you gut bacteria not having enough energy to do what it needs to do. So feed it some fibre so it can make butyrate!

Other metabolites that can be inflammatory are made when you feed the gut bugs saturated fats. Saturated fat is the main offender as it’s metabolites can cross the intestinal barrier and enter the blood stream. One of the main metabolites that has been studied that does this is lipopolysaccharides. They are made by gram negative bacteria. When these gram negative bacteria die these metabolites get released into the gut. It then crosses the intestinal barrier into the blood (saturated fat helps these lipopolysaccharides cross into the blood). High levels of lipopolysaccharides are seen in the blood of people with metabolic diseases i.e. obesity, diabetes, cardiovascular disease etc. Now we still don’t know if it is a causative factor or not but there is definitely a strong correlation with saturated fat intake and LPS (lipopolysaccharide).

In saying this though the studies have not defined the type of saturated fat they were eating i.e. grass fed butter or a big mac and fries. So before you label all saturated fat as bad, we need the studies to be more specific on what saturated fats they are eating in these diets. As we know that a ketogenic diet is low in inflammation and this would not be possible to see these types of benefits-in numerous studies if it was destroying our microbial balance. And just so you are aware butter is also a great source of butyrate just like fibre (esp grass fed butter).

So first of all try and avoid the processed aka man made fats/oil and some vegetable ones such as:

  • Canola oil (does have some Omega 3)

  • Soybean

  • Sunflower oil

  • Corn oil

  • Safflower oil

  • Grapeseed oil

  • Margarine

  • Cottonseed oil

  • Peanut Oil

**These are high in PUFA (polyunsaturated fatty acids), high in Omega 6 & also these oils are in a large amount of processed foods.

Instead try to eat fats such as:

  • Grass fed butter

  • Tallow

  • Ghee

  • Palm oil

  • Coconut oil

  • Avocado oil

  • Olive oil

  • Fish Oil

  • Eggs

Ammonia is another metabolite that gut bacteria can produce. It is a normal by-product of natural nitrogen cycling. At normal levels it is fine, however if it is high this can cause inflammation. People with IBD tend to have a high potential to produce ammonia in their guts. IBD patients also tend to produce more hydrogensulfites- this is what give farts their “egg” smell. Ammonia at low levels suppresses inflammation but at high levels it is pro-inflammatory. It’s all about balance, you don’t want to let anything get out of control.

Branched chain amino acids- help build muscle. However when you have excessive amounts in your gut it is contributing to metabolic disorders such as insulin resistance, type 2 diabetes etc. The excess of these amino acids causes overgrowth of certain bacteria leading to an imbalance . To bring this back into alignment you need to increase fibre so that you can make short chain fatty acids over branched chain amino acids.

Trimethylamine- is another break down product that is getting a lot of attention. It has been strongly linked to cardiovascular disease. It is made in the gut and crosses the intestine, into the blood and travels to the liver where is it is oxidised to TMAO ( trimethylamine oxide). High levels of TMAO has been shown to make platelets in the blood more sticky and thus clots, atherosclerosis etc more likely to occur. It has been linked to diet but there also appears to be other factors at play for TMAO production. Especially it is formed from animal protein but we need to know more about how to affect this production. Therefore as a general rule increase fibre for now and ry not to have excessive protein.

But don’t gut bugs cause my histamine issues?

Some bugs do produce histamine, but most histamine is actually made by our human cells. So if you have histamine intolerance it might not just be the gut microbiome at play. In saying this though balancing out the gut microflora can help here, as not many species can produce histamine-it does not appear to be a common feature of the bacteria that reside in our gut. The ones that do produce it, can contribute to it being trapped in the gut and potentially causing problems. There are 4 different types of receptors in our bodies that react to histamine. Some when stimulated produce allergies, food intolerances, IBD etc. and others when stimulated that can suppress inflammation with histamine. So the importance is which receptor the histamine is linking with to produce an effect.

People with allergies tend to have more of the pro-inflammatory receptors to histamine in their gut .Which may explain why they are so sensitive to histamine. Unfortunately this is not something that can be changed with the gut microbiota as the receptors are on our human cells (we make them).

It’s interesting with Asthma patients they were found to have high levels of bacteria in the gut that can produce histamine. This is correlative, so we are not sure if the histamine is helping cause the asthma or if it is has a protective effect from these bacteria- because we are not sure which receptors they have more of in their guts i.e. the pro-inflammatory ones or the anti-inflammatory ones. Watch this space as more research is conducted.

Do the bacteria in my gut affect my mind- I keep hearing how they do?

We have a really long nerve that runs from the brain to the gut. It is a direct highway between the gut and the brain and is called the vagus nerve. We also have a whole intricate nerve network that helps our gut to move and these nerve cells are called the enteric nervous system.

Human cells produce a lot of chemicals that can either activate or suppers the nervous system. But we are also finding that there are a lot of bacteria that can produce these chemicals and then stimulate effects in our human cells.


GABA is one that is being research a lot, it is our inhibitory neurotransmitter and it is our relax chemical. People with anxiety in studies have been shown to have low levels of GABA. GABA is produced as a break down product from glutamate (a protein and neurotransmitter) . Our bodies make most of our GABA, however gut bacteria can make some (like the story with histamine). This is an emerging area of research and it was shown in a mouse study that GABA produced by bacteria is taken up by mouse cells and had a direct effect on their nervous tissue. This is exciting because we weren’t sure if bacterialy produced GABA could be used by mammalian cells. It is now looking like we can- so what does this mean for all the things being produced by the gut bacteria?? We haven’t done the studies in humans yet though. Gut bacteria not only produce GABA but also consume GABA- so with future research they will be looking at, do we have an imbalance in bacteria that is not making enough GABA, are the bacteria using our human made GABA and the gut made GABA too quickly causing overall depletion etc. This has implications for anxiety but also other conditions such as autism.


Serotonin makes us feel happy and buoyant, so it’s one we often talk about. 10% of the serotonin we produce is made in the brain and used to make us feel happy. ~90% is made in the gut and serves lots of other functions too- such as gut contraction and maintaining healthy cell barriers. Gut bacteria can make serotonin but we haven’t identified the pathways they do this by yet in the genome. Butyrate, propionate and tyramine promote the production of serotonin in our gut and help activate those serotonin pathways.

So to recap what can i do with my diet to help the microbiome?

In the research it is showing the same results over and over again. That diets high in fibre and that have a wide diversity of fibre sources such as: legumes, fruits and vegetables not just whole grains- gives us a balanced micorbiome. 

Foods that negatively affect it are mostly small studies- but we are starting to see that emulsifiers , artificial  sweetness and saturated fats have a negative impact. But most  of the larges studies we have to date are in animal models.  But just keep in your mind that a lot of processed foods have these in them i.e. emulsifiers etc.. The most important thing you can do is eat a wide variety of whole foods in your diet.

Is there anything else that upsets the microbiome apart from food?

Yes, medications can in particular and toxins, lets talk about medications first.

So we talked earlier about antibiotics as they kill off rather indiscriminately the gut microflora. And once they are wiped out they remain at very low levels and it can take up to 16months to return to normal (unless you do a faecal transplant).

Please don’t think, well i’m not going to take my antibiotics then! Because antibiotics can be life saving- if you need them you, need them, the trouble is people go the GP for a viral illness and have antibiotics uncessisarily!! This drives me bonkers- as it isn’t going to heal you or help you!!! Its only going to disturb your gut flora. We don’t need antiobics in most cases when we are sick. What we need is rest and fluids. But we don’t want to rest we want to keep “soldering on” and taking a few panadol (paracetamol) and nurofen (ibuprofen).

We are not letting out bodies do what they need to do and shift to a healing space i.e. support our immune system. If we support our body it does what it needs to do better than anything we can conjure up so far. But we push ourselves and then our body completely collapses. This then sometimes causes us to get opportunistic bacterial infections on top of a viral one.

We should NOT be letting ourselves get to this stage, we need to acknowledge we are sick, get out of our own way and let the body do what it needs to do, nourish and rest it. We need to stop rest, hydrate, increase our vitamin C and also use other supplements like elderberry, echinacea, mushrooms like reishi etc, eating garlic, onions etc. To give our body the defence support it needs to destroy the pathogens and recover.

But antibiotics are not only available from the doctor, they can be found in our tap water!!! We are drinking them without even realising and also eating them in the meat we eat. As animals are now packed into small living areas to meet human consumption demands, cramped together in dirty environments where infections can easily take hold. So they are given antibiotics “prophylactically” to prevent infections. We then eat the meat full of antibiotics which wipes out our bacteria without us even knowing.

Other medications that disrupt the microbiome include: NSAIDs (non-steroidal anti-inflammatories) such as Nurofen and the OCP (oral contraceptive pill).

Stress if it chronic opens up your tight junctions in your gastrointestinal tract making it “leaky” and also disturbs the normal bacterial balance.

Toxins can also cause havoc on our bacteria. Chlorine in water for example kills off our gut bacteria. Think about it -why is it put in tap water in the first place? Why is chlorine in swimming pools? If it is there to kill of bugs in the water, what do you think will happen when you drink it? This is why getting a good water filer is really beneficial. The company i like to use is an Australian one called the water shop they have a range of bench top, tap filter, shower filters etc.

Glyphosate aka “round up” which is used a lot on plant produce has been shown to deplete lactobacillus in our gut. It is used as a desiccant on crops 1 week before harvest and has also found its way into our water supplies. Which is why its important to have filtered water and to wash your fruits and vegetables in water with sodium bicarbonate for 15mins (if not eating organic produce). Glyphosate also reduces our ability to make amino acids, Tyrosine, Tyramine and Phenylalanine- which are important for neurotransmitter production.

Alcohol, sugar, metabolic syndrome, processed foods/carbohydrates all can upset the balance as well.

So what are somethings you can do to heal it- avoid some of these triggers/ remove the offending agents where possible. Bone broths help rebuild and repair the gut linings integrity. As discussed diet changes - very important and only then looking at supplementing secondary to that.

What about the microbiome diversity- why is it important ?

There is the correlation that with high diversity there is good gut health and low diversity is linked to having poor gut health. When we are talking about diversity its not just the number of different types of microbes but also having an even distribution. If you have 50 species but you have 1 overgrown then you are still going to have poor diversity - you want an even proportion. We do not want any species to be high or dominant in the group.

We want as many different ones to live in your gut ecosystem to have resilience. Having a wide range of bacteria with an even number allows it to deal with any stress or challenges it encounters i.e. if we get sick or have a bad day and binge on bad food- If you have diversity it can handle this. If you have something happen and one species dies off its not a big deal because you have enough diversity that another can step in and fill its role. Think of the gut microbiome like a rainforest. If you have one species of trees and a fungal infection comes in the whole forest falls over but if the forest has a wide diversity it can’t spread as quickly and all the trees won’t rot and die , so not as much damage occurs to the overall rainforest. 

Are there specific nutrients to eat that help create diversity?

It’s really just getting as many different sources of fibre into the diet as you can. This isn’t just about soluble and insoluble fibre, as there is more than just those types. Fibre is any type of carbohydrate that your body cannot digest with its own enzymes. So as it can’t be broken down in the small intestine, it passes to the large intestine where the bacteria here can eat it. As humans we are very limited in the enzymes that we produce. 

Bacteria in the gut however have a huge range of enzymes in them and they can break down way more than what we can. They can break down a lot of products including some we wuoldn’t even think of as food. People who have been exposed to hazardous chemical have up regulated bacteria in their gut that can break down polystyrene and benzene. Now we wouldn’t associate these foreign objects as food- but our bacteria can break those down and make use of them- in saying that though, those break down byproducts are probably not going to be good byproducts for us. That’s why we want to feed the bacteria preferentially fibre, so it doesn’t use other fuel sources.

So is fibre a prebiotic then?  

Prebiotics- refers to food that can’t be digested by the human body but promotes the growth of beneficial bacteria in the gut. This includes a lot of fibre, but some fibre does not promote the beneficial growth of bacteria so not all fibre is a prebiotic- but a lot is. Fibre and phytochemicals such as antioxidants are your main prebiotics. You might see prebiotics with names like fructooligosaccharide, galactooligosaccharide etc. These are just sugar molecules bound together in long chains. It is the chemical bonds that are important, some chemical bonds we can break down and then use them as fuel sources. Others like in resistant starch we can not break the bonds, so we need the gut bacteria to use their enzymes to break it down and utilise it. 

Plant polyphenols are often bound to plant polysaccharides. So we need bacteria to attack this long chain bond for us in the large intestine so we can absorb the polyphenol from the plant. If the bacteria do not breakdown the long sugar molecule we wouldn’t get the polyphenols released, so we could not absorb that component.

What happens when we don't have bacteria in there that can break down fibre etc?

It will just pass though and we wont get any benefits from these plants. Ie if you are eating a low fibre diet and suddenly start eating fibre it takes time for the bacteria to grow that can use it. Initially the fibre will just pass through and you wont get the benefit of short chain fatty acids being produced if these bacteria are absent or in low number. This can cause symptoms such as bloating, diarrhoea etc.

If absent what do we do?

We aren't sure how to treat it, probiotics don't actually re-colonise the bowels, some probiotics provide benefit but you have to keep taking them. Probiotics are beneficial strains of bacteria. The money question is how to make the bacteria we want stay and recolonise the gut. Probiotics do work but the problem is you have to keep taking them, once you stop a lot of the benefits seem to go away. There is also the question of exactly how many survive when they reach the stomach due to the acidic environment- does it actually get down to where it needs to go in the numbers we require? Is that part of the problem it can’t colonise??

 Until we figure out a way to make that happen when giving external probiotics , you can slowly but surely add fibre into your diet. Don't do it dramatically as this can be uncomfortable- you might get a “bloom” of fast growing species causing bloating or consitpation. So go slow and make incremental changes in the amount of fibre you are eating. In reality you will have bacteria there that can eat fibre- you will never be completely absent- they will just be at very low levels. So you need to encourage them to grow and become a bigger population.

Instead of buying expensive probiotics start adding fermented foods to your diet. They are more likely to survive in the acidic stomach environment, as they are the right pH to inoculate the gut and make changes. Fermented foods are pre-digested so you can easily digest and assimilate it. The fermented foods have probiotics (ancestral strains) in them but also prebiotics. They are absolutely vital in repairing and rebuilding the gut especially after having something like antibiotics wipe the slate clean in your gut. .

How long can it take for diversity to drop i.e. have a bad week of eating?

Its amazing how quickly it responds to diet changes, it is actually very fast. Animal studies with mice put on yoyo diets demonstrated this quite well. Unfortunately if you are good all week and then you binge on the weekend, you bring back the ones you were trying to reduce and you don't have the beneficial changes over all from eating healthy. You need to eat heathy all the time. Just like if you are trying to grow a lawn, you don’t trample all over it & have thing laying on it over the weekend etc. and then expect it to be green during the week. But as it responds so quickly to changes in what we eat that means there is always the possibility to make improvements, so don’t be disheartened if you have a bingey weekend, just make up for it :)

So now we know a bit about what is in the gut- how do you test what is going on in yours specifically. That will be explored in another post xo Courtney