Bugs and your gut- testing

Testing your microbes in your gut is it important, should I do it? Lets explore the testing.

Why is it important to know how the gut is functioning?

The gut appears to be doing a lot of critical functions for health and overall health systems. i.e. liver function, cardiovascular, mental health, immune system etc. The body systems and the gut are in constant communication via mainly the vagus nerve. Which has more influence hasn't been determined yet, the gut telling the body or the body telling the gut. 

Who might benefit from testing?

As the gut is linked so much into our overall health, its really ideal to have it tests every 9-12mths to see how it is going. Just like you get routine blood tests to check everything is functioning as it should. But if you are experiencing a change in your health/symptoms or finished a course of antibiotics these are also ideal times to get tested and see what is going on.

Post antibiotics- what should i do?

You need to take it easy. once you have recovered from the illness it no the time to celebrate by going out partying and drinking alcohol, eating fried/fatty/processed foods or dairy. as the antibiotics have essentially wiped out your microbiota forest and you need to nature and let the healthy “seedlings” grow up rom the forest floor. If you bombard your gut with inflammatory foods at this time you can cause leaky gut and longer term problems. We need to help colonise and grow back the good bugs. People often find after hey have been sick that they are lactose intolerant as the microvilli have flattened somewhat due to the inflammation and the lactase enzymes on there are also wiped out temporarily in this process.

You should be eating easy to digest nourishing foods like bone broths, fermented foods, slow cooked foods, lots of vegetables, garlic, onion etc. Drinking lots of water and taking it easy!!! you know who you are they people that refuse to stop.

Taking probiotics post antibiotics has had mixed reports. Some showing benefits and other showing it delays the restoration of the normal microflora. They think this is because the supplemented probiotic bug take over the function of the bacteria that normally live in your gut and take up space so your natural gut bugs can’t grow back. Whether this is a good or a bad thing short term is unclear. But probiotics do not colonise your gut they only live there temporarily. Some people can take 4-6 weeks for their microbiota to come back others it can be up to 16months!

If you are taking long term antibiotics it changes the microflora permanently.

Which is what they do before you have a faecal transplant. When you have a faecal transplant they bomb your gut and sterilise it and then repopulate it with a good faecal matter in the gut.

So why test and what to test? 

We need to not only know what bugs are living in there but how many i.e. the . population density etc. and how they are functioning. 

When they test the bacteria they take the sample and strip out all the bacterial DNA present and this goes through a sequencing machine. The sequencing machine then builds together all the genome information to create a picture of what is in your gut and what it can do and in what density. 

Target PCR tests are looking for a list of organism and reporting that back of what bugs should be on the list. They don't report on any other bugs than the ones they are looking for. This testing can be great, But doesn't give the overall picture. It doesn't tell you what your balance is or how well they are functioning. We all have some unique species or pathogens in the gut, that are almost like our guts finger print. There is lots out there we don’t know what it does or its purpose yet. There is so much diversity and uniqueness in us all that we are still discovering the impacts and knowledge about the bacteria living in the gut. A single result doesn’t give all the answers you need to look at the whole picture. PCR is possibly the best way to test for acute gastroenteritis, because it’s so fast and because it tests so many organisms. And culture is likely best for things that are more chronic.

For example if you think you have a candida overgrowth that is unlikely in the large bowel. If you do have an overgrowth it usually occurs in the small bowel and is called SIBO. Faecal microba testing only looks at the bugs in the large bowel and won’t give you a clear picture if there are imbalances anywhere else. As the large bowel is the powerhouse of gut for producing metabolites, most of the bacteria live and most of the material sits there. There should be limited bacteria in the small bowel. Digestion actually starts in the mouth- how much of the digestive enzymes are in your saliva, if they aren’t there in large numbers there are knock on effect all through the gut thereafter.

Remember there is food you eat for you and your human cells i.e. sugar, protein, fats and there is food you eat for the bacteria in your gut i.e. fibre- inulin, pectin, resistant starch, cooked and cooled potatoes (to get resistant starch), rice etc.

What specific species of bacteria are found in the tests?

Within the gut there are things that are potentially good and potentially bad for you. They aren't good or evil they are just doing what they do. An example is Akkermansia muciniphila  it help the mucus in your gut grow and keeps it healthy, but if you have too much it can be a problem too. Faecalibacterium prausnitzii there are several species of this, some are good, some are neutral and some do some less than desirable things. FRPrau-B has been connected with atopic dermatitis, where as FRPrau-C produces a lot of butyrate which is great for your gut, for your energy, it feeds gut cells and also produces an anti-inflammatory compound. Both these strains look very similar on the surface, in fact they are almost identical, but a few different genes in their genomes completely change their overall behaviour and effect in the gut.

It’s what the species are doing in the gut that is important. 

As said earlier FPrau-C can produce butyrate and butyrate is a main functioning compound in the gut -many organisms in the gut can produce butyrate, it lower obesity and type 2 diabetes, it feeds your gut cells and keeps them healthy. So it is helpful to know how many bacteria in your gut can produce butyrate and to test for that. We want to be able to produce butyrate and in sufficient quantities. So if you have a good amount of bacteria (you know this from testing) that can produce it- you need to feed your gut resistant starch and because you have the right bacteria you will get a really good benefit from doing so.

If you don't have these bugs in your gut that can make butyrate. You want to change your diet so that you can encourage their growth. Then feed them the resistant starch they need to make butyrate. Trimethylamine, hydrogen sulfide, urease have impacts on health and can make things worse and these can be produced by gut bacteria, so if you test you can see if you are creating these compounds. There are neurotransmitters connected with the gut such as GABA synthesis, serotonin, vitamin synthesis- ie. certain B vitamins are produced in the gut. How well you might be making these vitamins is by looking at the genes in the bugs living there. With testing you need to look at where is the imbalance and how can I best modulate it? This makes it less like guess work and you can delve in and see what is going on and adjust it. 

It’s important if you are having testing to interpret the results with a practitioner…

If you have eaten a certain way your whole life and you know how to whip certain things up easily for yourself or your family and then all of a sudden you are told to add 6 cups of vegetables a day and eat resistant starch you might be thinking- how the hell do I cook that? It can be overwhelming, to stop or change those habits and learn new cooking strategies. To help support and drop stress levels its good to interpret your results with a practitioner, changes are not going to work if you don't have support.  

A lot of the evidence based research and practice has to do with the practitioner that you work with, the practitioner support they give, what they know and what that practitioner has learnt . Not only that but the personal situation of the person seeking treatment -what the person brings to the table -how they feel, what has happened to them with their illnesses, felling sick etc. It’s far more complex than evidence tells us we need to use “this” and then just implement “that” and “this is what will happen”. So when trying to move forward it’s our experience, our understanding, what we bring as much as what we read in the studies and what we know and how we apply it. So you need someone to help interpret some of the results you are reading and give it context. 

How do you collect the poo for testing?

New testing dosnt’t require a sample in a jar. Its not just a swob, that comes in a tube, you wipe this swob across a piece of used toilet paper. You then play the swob in the tube to preserves the sample. You place this back Into the back supplied and post it back to the lab for processing. It’s a much easier process now ( and not as gross). The amount of material is small it can give you a clue if there is parasites, but if it detects anything need to go and get a larger sample and test for that.

Is the “microba” test good compared to other tests and companies?

The tests give you a snap shot in time right now of what it is doing. And this is important to see- not what was happening 3-6 months ago or whenever you last had a test. As said it can be a good idea to have every 6-9months as routine. The microba test is very elaborate at what it looks at, due to the diversity and metabolites it shows.

Remember if you don't have bacteria to make metabolites such as tyramine you can’t make serotonin. The metabolites are important. So knowing this information about your gut you can take charge of your health. Say you aren’t making tyramine, you then know you don't need those antidepressants -if we improve your gut you can make your own serotonin. Lets fix the route cause rather than taking a pill. Instead of symptom management let’s treat the cause so we can get back to optimal health and with the doctor wean off those meds once you are feeling better/the gut is working.

Is there an age limit on testing?

2 years and above can be tested, any child below 2 years will not be tested. The reason for this is the micorbiome is still under flux. It hasn’t settled into what it will be and the immune system hasn’t decided what it likes to talk to, and the flora keeps changing. There are also no defined normal limits in these age groups for that reason.

The microbiome dose change as you get older but there is no limit to the upper age range to be tested. The are still tracking this area to see the significant of this. The production of enzymes does drop off as we age, but we aren’t sure about the impacts of the flora.

So if you are interested in testing have a look at microba website but also make sure you have a practitioner to assist you in interpreting and developing a management plan.

See also the blog on Bugs and your gut- the microbiota.

Happy testing xo