Probiotics 101

What is the microbiome?

Our microbiome are the microbes that are found in the different microbial communities around our bodies, covering our skin, GI tract, and every where in between. These microbes are important for our skin barrier, nutrient absorption, gut health, immune system and neurological well-being… so basically our entire whole body health.

Ideally its foundation begins in the womb, which is then added to from the birth canal and breastfeeding. Those who have antibiotics, systemic bacterial infections during pregnancy, labour or breastfeeding, or who are surgically delivered and who have limited or no breastmilk exposure can have reduced microbial diversity, which can impact out microbiome. Current research suggests that after the first few years of life the microbiome doesn’t alter tremendously.

What are PRO-biotics?

Pro-biotics mean “for life”, this is what we call favourable bacteria. Though it is most commonly used in reference to isolated supplements; increasingly it is being used as a buzz word for microbial fortified products like foods, skin and oral health probiotics.

Traditionally foods can be rich sources of probiotic microbes, this include raw (not pasteurised) fermented foods like: sauerkraut, kimchi, kefir, milks, cheeses and kombucha. These foods can have large numbers of microbial strains and abundance in them.

Supplements called probiotics tend to focus on specific isolated strains that have been studied for therapeutic qualities. Many of these products are cultured on dairy and soya, so it can be quite expensive for low allergy risk products.

What are PRE-biotics?

Prebiotics are the food that feed our beneficial bacteria. A large part of our digestion and nutritional absorption is dependent on the microbes that work in our gut. Prebiotics feed the microbes in our gut. Fibre, resistant starches and antioxidants (like flavonoids and polyphenols) among other things in our foods feed the microbes in our gut.

Prebiotics, like FOS/GOS and inulin, are often added to probiotics supplements. These prebiotics can be problematic for some with specific sensitivities, FODMAP issues, or are sensitive to the foods they are commonly derived from (inc. chicory).

Fermenting foods that are high in FODMAPs can help those with FODMAP related reactions better tolerate them and help repopulate the gut with microbes that support their digestion.

There has also been a recent development in research, since formula companies began fortifying with GOS, that shows people can have allergic sensitisation to it, even though it is essentially a carbohydrate and the previous immunological understanding stated immune responses had to have a protein involved as a trigger.

Side note: The Nemcheck Protocol is a protocol for improving gut health which primarily focuses on the use of inulin and oil consumption. While many find it helps them, others find it can make some health issues especially Candida significantly worse, as inulin is a non-discerning food source for microbes which can be both helpful and detrimental.

What are Bio-films?

Biofilms are microbial communities in the body that have developed a protective film over themselves. These films can make some microbial infections, or dominance, particularly persistent and tricky to treat. Biofilms can act as reserves for infections that can cause the infection to become chronic or if seemingly disappeared it can cause them to flare up following periods of stress on the body.

Proteolytic enzymes like Serrapeptase, Nattokinase (soya) and sauerkraut juice can aid in the breakdown of biofilms and make anti-biotic and anti-fungal treatments significantly more effective. Though the use of these enzymes needs to be away from food so the body doesn’t use them for digestive support.

What are antibiotics and anti-microbials?

Anti-biotics, anti-virals and anti-fungals are collectively anti-microbials are anti “against” life and microorganisms. Anti-biotics indiscriminately kill-off bacteria killing off both the negative detrimental ones and the more beneficial ones that help to keep our microbes in check.

Pharmaceutical forms can be more dangerous to our good bacterial flora than natural forms. They do have their place and definitely save lives, but as is becoming increasingly understood, they have been used excessively beyond logic and are a leading cause for not only antibiotic resistant strains of bacteria. Use of daily antimicrobials in the home, such as anti-bacterial handwash, have also been shown to make some prescription antibiotics less effective. Overall, the over use of antimicrobials in our home and health care is directly linked with the tremendous decline in diversity of the microbiome of those in western societies, which has vast stretching implications for our health and environmental welfare.

Natural alternates to antibiotics can range from garlic, to oregano and colloidal silver, and so much more. Personally, I use garlic first for everything as it supports the immune system, is a naturally antiviral and immune supporting, compare to to the biocidal properties of oregano, colloidal silver and prescribed antibiotics.

Why and when do people take probiotics?

People take probiotics for various reasons. Specific strains can be taken to reduce certain health risks, like L. Rhamnosus and Bifido strains are known to stabilise mast cells and reduce allergies and L. Reuteri has been linked with reduced colic and ASD risk.

During a course of antibiotics, or natural anti-microbial, it can be important to take probiotics to reduce the impact of the treatment on your overall microbial flora diversity. To make it most effective, and not a waste of money, it is important to leave at least 2-3hrs between antibiotics and probiotics so the probiotics have enough time to get established. It can also be important to take B-vitamins (preferably optimised) and Vitamin K2 when you are on antibiotics; as these vitamins are produced by our intestinal microbes and we can become deficient in them which can slow recovery and impact overall health. Some recommend taking probiotics for up to 3 months following a course of antibiotics. Though others with more chronic issues of poor microbial diversity may need to take them therapeutic more long term.

Contraindications to taking probiotics?

There are a few reasons why despite the widely acclaimed benefits of probiotics and fermented foods, they may cause negative side effects and be contraindicated for some. Those with Small Intestine Bacteria Overgrowth (SIBO) have microbes in the body that are not where they are supposed to be, this can be linked to poor motility and hypothyroidism, probiotics can exacerbate SIBO.

Those with specific sensitivities to prebiotics added to probiotics should be diligent in avoiding known triggers, like inulin, FOS, GOS, etc. not only can these sensitivities be specific to the prebiotics, but they can also be the result of wider FODMAP issues or carbohydrate specific intolerances. These probiotics are also not “GAPS safe”. There are some low allergy probiotics out there that avoid their use such as GutPro and certain Seeking Health products.

Certain probiotics are L-Lactate or D-Lactate producing strains of probiotics. L-lactate strains are considered safer with small children. D-Lactate producing strains are known to have an inflammatory effect in some and are linked to increased neurological symptoms in some with existing conditions like Autism. Custom Probiotics, Klaire Labs and Seeking Health all have infant probiotics which do not include D-Lactate producing strains.

Those with histamine intolerance may also need to be cautious when seeking and vetting probiotics as some strains produce histamine.
Another contradiction can be the rare, but increasing in awareness neurological condition PANS/PANDAS, these are systemic infections that result in neurological symptoms.

Risks of taking probiotics?

Unfortunately there is no real long term understanding, since the research is so current, on the potential long term ramifications of probiotics usage. Specifically we do not know how much their use can potentially impact the over all development of the human microbiome and if there will be any potential negative fall out from their usage. This is one of the reasons many feel uncomfortable giving them directly to very small infants. Fortunately, those who are breastfed are able to glean the benefits of probiotic supplements transmitted through their mothers milk. Those who are formula fed do not have this intrinsic benefit of gleaning from their mothers microbiome in the same way, so are often recommended to be given probiotics along side exclusive formula feeding.

How to pick probiotics?

Make sure they are low allergy risk!

When looking for supplements the number of strains, the number of CFU (culture forming units) and additional ingredients are the primary concerns. Certain strains are known to have specific therapeutic properties. For example, there is a lot of research supporting L. Rhamnosus for improving allergies, L. Reuteri reducing colitis symptoms and the risk of ASD, Bifido Infantis for intestinal permeability and Bifido strains in general are known to support mast cell stability.

In many allergy groups people recommend probiotics with more buffer ingredients or that have been cultured on common allergens because they are only “may contain” allergens, or they have an oil in them. Seeking Health, Klaire Labs and GutPro are the most commonly recommended hypoallergenic brands in group. They each have specific products that are geared towards infant. Seeking Health also has a probiotic supplement specifically geared toward stabilising mast cells and reducing histamine issues, Probiota HistaminX.

Ferments can be a great way to get probiotics too, they can provide the beneficial microbial strains with the added benefits of nutrients, lactic acid and enzymes to aid digestion. Ferments can be an extremely cost effective way to get probiotics, they can contain 10-50+ different strains and trillions of probiotic cultures in a single jar. If they are shop bought they need to be unpasteurised to retain their microbial and enzyme properties. Fermenting foods can also improve their chances of being tolerated as the microbes breakdown many of the starches.

How do you take probiotics?

Start LOW and SLOW!!!!

Whether you start with a powder, capsule or ferment starting slowly can be essential.

When we introduce something with the potential to impact our microbial diversity – like probiotics, prebiotics, anti-microbials etc. – it can cause Herxheimer reactions; this is because when we bring in a new microbe it displaces the old causing them to “die-off” releasing toxins into the body. Typically, die-off symptoms self resolve within a few days to a week.

Generally, these symptoms can be identical to almost any (non-anaphylactic) form of reaction symptom so they can be difficult to distinguish. If you suspect die-off reducing the amount, or frequency – such as, halving the dose or alternating days – should help alleviate any symptoms. If symptoms persist or get worse then it may be a specific sensitivity to that probiotic, or it could be worth looking further into the contraindications to see if they are a factor for your little one.

Related reading:

Biofilm treatment:

Probiotics, immune function, risks and contradictions:

Free course on the Microbiome by Coursera:

GOS allergy:

Antimicrobials impairing antibiotic treatment:

5 thoughts on “Probiotics 101

  1. Hi!
    It sounds like you are super invested in you and your little ones health ๐Ÿ™‚
    Are you on Facebook? You might find out community group helpful for support.
    Unfortunately rice is a really common GI trigger, if your probiotics are hypoallergenic they may be worth keeping for a while to see how you get on? Many adapt AIP for their TEDs. Is your D3 low ingredients? Some react to bovine gelatine capsules.
    That is a big concern, fortunately the TED method is very adaptable for prioritising healing and nutrient dense foods.
    I hope you and your little one find some relief soon ๐Ÿ™‚


  2. I just joined the FB group! Not on FB, but created an account as many TED mammas recommend this group ๐Ÿ™‚
    The D3 is Pure Encapsulation brand – Other Ingredients: Hypoallergenic plant fiber (cellulose)โ€š vegetarian capsule (celluloseโ€š water). Gluten-Free / Non-GMO / Hypoallergenic.
    I’ll keep an eye out for Rice causing issues.

    I’ll try re-introducing probiotics and my multivitamin soon!

    Liked by 1 person

    1. I really hope you find the group helpful! We have so many mamas all around the world, it does make it seem so much less painful with support from people who get it. I hope that all helps ๐Ÿ™‚


  3. Do you mind deleting the comment that contains my last name? I didn’t realize that it would be published. Thank you! I prefer to be ore anonymous here.


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s