Which bugs should I have in my tummy?

Which bugs should I have in my tummy?

Margie GanderJul 23, '19

Most of my clients ask me about taking a probiotic, and I wish it was just that simple. But there is so much more to these little bugs living inside of us!

The intestinal microbiome is a large and diverse, containing about 100 trillion bacteria from 500–1000 distinct species that, collectively, provide multiple benefits to the host, being YOU! These "good bugs" contribute to nutrient absorption and maturation of the immune system, and also plays a vital role in protecting you from bacterial infection. Many "bad bugs" have developed strategies in order to be able to outcompete the friendly, intestinal bug community, leading to infection and/or chronic diseases. 

Your GUT microbiome is as ancient as the human race, and have been passed from one maternal generation to the next through birthing and breastfeeding. Your GUT flora has been living with you since your birth, and how they have survived and thrived depends mainly on your life story. Many illnesses, antibiotic treatments, stress, traveling, long nights of partying and poor diet provides a bad neighbourhood for your "good bugs" to thrive, grow, and breed. in fact, an inflamed GUT feed with sugary, processed foods results in candida and "bad bug" overgrowth!

Is there a 'GUT genotype'?

Scientists have discovered a way that bacteria in the gut can control genes in your cells. This research shows how chemicals produced by bacteria in the gut from the digestion of fruit and vegetables can affect genes in the cells of the gut lining. These molecules, called short-chain fatty acids, can move from the bacteria and into your own cells. Inside your cells, they can trigger processes that change gene activity and that ultimately affect how your cells behave. This research illustrates how important it is for us to eat our fruit and veggies! 

Although there is no one, single gene that predicts your predisposition for having GUT issues, medium to high impact genetic variations in the following genes are an indication that you may have GUT health and digestion issues:

Gene Indicates  Lab test
TNF-A Non-celiac gluten sensitivity 


HMOX-1 Leaky GUT and inflammation in the intestinal tract
BHMT Impact on the GUT-brain connection
FUT2 Prebiotic production and vitamin B12
DAO Histamine and gluten tolerance
MCM6 Lactose tolerance 
SHMT GUT inflammation
SUOX Sulfite detox


I've also found that if you have medium to high impact genetic variations in the key inflammation genes can predispose you to inflammation of the GUT lining. This results in a poor environment for healthy bacteria to thrive. 

So which bug are good guests and which are the bad ones? 

Research into the GUT microbiome has revealed that we are as dependent on our GUT flora as they are on us. Different strains of microflora have been linked to various health outcomes, and this has led researchers to conclude that the strain of probiotic that you take is very important. 

I found this table very useful in guiding my clients as to which probiotic they should be adding in:

Health Concern The probiotic strain that prevents  The probiotic strain that triggers  Product
Autoimmune disease
Saccharomyces Boulardii
An overgrowth of 
Enterococcus gallinarum
UltraFlora Spectrum 
Overweight | Obese
Bifidobacterium lactis (B420 Strain)


Changes in the ratio of Firmicutes and Bacteroidetes correlates with obesity. A high-fat diet promotes an increase of Firmicutes and relative reduction of Bacteroidete. 

UltraFlora Control


Folate levels

Hemoglobin levels

Streptococcus thermophilus
E. coli LPS 
UltraFlora Spectrum
Lactobacillus casei
People with hardened arteries have more bacteria from a group called Collinsella.
Lcasei is naturally found in the gut. Some fermentedfoods contain Lcasei, too. These include some yogurts, yogurt-like fermented milk, and certain cheeses
Recurring sinus and respiratory infections
Bifidobacterium lactis Bi-07
Dolosigranulum spp and corynebacterium spp 
UltraFlora Balance
Immune system
Lactobacillus plantarum
UltraFlora Intensive Care
rhinitis, especially lactose
Lactobacillus acidophilus 
UltraFlora Balance 
Mouth cavitites, gum disease and candida
Lactobacillus salivarius UCC118†† Culture

Salivarus can be found in living in every part of the body. Specifically, it can be found in the colon, small intestines, vagina and mouth. To keep you healthy, L. salivarus produces its own antibiotics. These antibiotics are specifically targeted against invading pathogenic bacteria.

UltraFlora Integrity
Kidney stones Lactobacillus brevis
Proteus mirabilis has been linked to causing kidney stones and difficult to tract urinary infections.
Lactobacillus brevis is a type of lactic acid bacteria found in milk products and in some plants as they decompose. Fermented products, such as pickles, use the bacteria. They are also used in making wine and beer. Lactobacillus brevis, often listed on labels as L. brevis, is in some brands of yoghurt.
Depression & post-partum depression

Lactobacillus rhamnosus HN001



Low or missing levels of 
Dialister and Coprococcus
UltraFlora Acute Care



Lactobacillus Rhamnosus gg 
Klebsiella has been linked to colic.
MetaKids Baby Probiotic
Lactobacillus helveticus 
Prevotella and klebsiella overgrowth has been linked to hypertension.
The Cultured Whey 


One of the best research pieces regarding the above is from Finnish researchers who claim that a newborn's first stool holds telltale clues about his risk of becoming an overweight 3-year-old. The clues come from the population of bacteria (microbiome) in the baby's gut. Using genetic sequencing to analyse the first stool produced by 212 newborns and another sample at age 1. The children's weight and height were checked at regular visits, and their antibiotic use recorded. Researchers found that the greater the abundance of staphylococcus bacteria in an infant's first stool, the shorter the child was at 1 and 2 years of age. Kids who were overweight by age 3 had much more (29% versus 15%) bacteroidetes in their infant microbiome than those who were not overweight.

We live in an amazing time in health and wellness where we can measure and track the types of bacteria that we have in our GUT in order to prevent disease and be optimally well! 

The role of prebiotics

Prebiotics are made up of nondigestible carbohydrates that are used by bacteria in the colon. Naturally found in food, a prebiotic is not broken down or absorbed by the gastrointestinal tract but rather used by beneficial bacteria as a food source in a process called fermentation. Prebiotics act like 'fertilizer' for good bacteria to grow in your GUT.  Examples of prebiotic foods include chicory root, dandelion greens, Jerusalem artichoke, bananas, garlic, onions, leeks, asparagus, whole grains, and already fermented foods such as kombucha, sauerkraut, and beet kvass. Your daily food choices need to include these foods so that you know that you are feeding your GUT guests!

Digestive enzymes

Enzymes are proteins that enable chemical reactions, and most of the enzymes in your body are ones that you make yourselves. Your DNA contains the instructions for building the many thousands of enzymes that your body requires to function. Most of these enzymes are involved in cellular metabolism and support. The rest helps you to digest your food by breaking down your macronutrients - proteins, fats, and carbohydrates into smaller pieces so that they can be absorbed.

Digestive enzymes are found in various places throughout your digestive tract: the saliva, stomach, and small intestine. But most of your digestive enzymes are produced by the pancreas and excreted into the small intestine, which is where most digestion and absorption of food occurs. If your pancreas is not producing enough digestive enzymes, you may not digest your food as thoroughly.

What is important to know is which digestive enzymes to take. This table will assist you in determining whether you need to add in digestive enzymes with your food. 

Symptom cause Supporting enzymes Product
Complex carbs, legumes or cruciferous veg



Colon Ecology
Gluten  Aspergillus niger SpectraZyme Gluten Digest
Dairy and lactose Lipases SpectraZyme Complete
Protein Proteases SpectraZyme Complete
Arthritis pain 
Protein-digesting enzymes bromelain, trypsin, and rutin
Acute Phase 

GUT lining

Inside your belly, you have an extensive intestinal lining covering more than 371.61216 square meters in surface area. When working properly, it forms a tight barrier that controls what gets absorbed into the bloodstream. An unhealthy gut lining may have large cracks or holes, allowing partially digested food, toxins, and bugs to penetrate the tissues beneath it. This may trigger inflammation and changes in the gut flora (normal bacteria) that could lead to problems within the digestive tract and beyond. There are many studies that show how changes in the intestinal bacteria and inflammation of your GUT lining may lead to many common chronic diseases. This becomes a really important focus area for you if you have the inflammation genotype. 

Who gets a leaky gut (and why)?

We all have some degree of leaky gut, as this barrier is not completely impenetrable (and isn’t supposed to be!). Some of us may have a genetic predisposition and may be more sensitive to changes in the digestive system, but our DNA is not the only one to blame. Your lifestyle choices may actually be the main driver of gut inflammation. There is emerging evidence that the standard American diet, which is low in fiber and high in sugar and saturated fats, may initiate this process. Too much alcohol and stress also seem to disrupt this balance.

We already know that increased intestinal permeability plays a role in certain gastrointestinal conditions such as celiac disease, Crohn’s disease, and irritable bowel syndrome. But a leaky GUT may also cause problems elsewhere in the body. Studies show that leaky gut may be associated with other autoimmune diseases (lupus, type 1 diabetes, multiple sclerosis), chronic fatigue syndrome, fibromyalgia, arthritis, allergies, asthma, acne, obesity, and even mental illness. 


Testing to determine the landscape of your microbiome is the best place to start. I love the GI MAP test, as it provides you with invaluable insight into which bacteria, parasites, pathogens are located in your GUT together with information about antibiotic-resistant strains. Instead of guessing which probiotic you should take, rather determine exactly what you need and where you need to focus your choices.




In Functional Medicine Coaching, we put all of the above into a brilliant programme called the 5R Gut Programme. If you would like assistance in getting started, you can book a session below:



Written by:
Marguerite Doig-Gander
BA (Speech, Hearing & Lang Therapy) Hons | FMCHC | ReCODE Coach | HMX Genomics & Biochemistry (Candidate) 

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