MICROBIOME, GUT
FUNCTION AND IMMUNITY
Ella Allred Dip CNM Nutritional Therapist mBANT CNHC

WHAT IS THE MICROBIOME?
• The microbiome can be put simply as the balance of bacteria, yeasts, virus’s, protozoa
and parasites that live in your body.
• There are over 40,000 species identified to date.
• The average human microbiome weights 2.2kg.
• The amount of DNA owned by our microbiome is 200 times our own DNA.
• We need a balance of at least 80% beneficial microbiome in order to maintain good
health.
• Therefore, we should not be referring to ourselves as ‘me’, rather ‘us’ would be a better
description!
• When you have a bowel movement, most of the weight of the faecal matter is
microbiome, rather than anything else

WE ARE MOSTLY
MICROBIOME

WHERE DOES IT ALL START?
• Previously, we thought that babies were sterile in their mother’s womb, and they
were first exposed to microbiome in the birth canal.
• However, we now know that the placenta has its own microbiome, and that our life
long microbiome balance is started at the moment of conception.
• The placenta microbiome is based on our mothers. This is why it is really important
to plan pregnancy, and to ensure that the mother is in a good state of health.

WHERE DOES IT ALL START?
• The next stage of microbiome conditioning is birth.
• As the baby passes down the birth canal, its face, eyes, ears and mouth are covered
in secretions from the birth canal, which give the baby a heavy dose of his life long
microbiome.
• 3 weeks before the birth, (if the birth is at the expected time) the mothers body will
populate the birth canal with billions of beneficial bacteria and yeasts, in
preparation for the baby to swallow and set the standard for health.

WHERE DOES IT ALL START?
• Problems occur when:
• The baby is premature and the appropriate microbiome has not been place in the birth
canal
• The mother is on antibiotic before or during the birth
• The mother as an infection in the birth canal during the birth
• The baby is born by caesarean

WHERE DOES IT ALL START?
• Studies show that babies who are born via caesarean, have a microbiome that is
similar to that of the surgeons hands. Even as adults, people born via caesarean
show distantly different gut microbiome to those who were born via vaginal birth.
• C section babies are colonised by staphlococcus and other hospital bacteria and
have much higher rates of eczema, asthma and other immune conditions.
James J. Goedert et al. Diversity and composition of the adult microbiome associated with a history
of caesarean birth or appendectomy: analysis of the American gut project. EBioMedicine 2014

WHERE DOES IT ALL START?
• The third stage of microbiome transmission is skin to skin contact.
• Skin to skin transfers the microbiome of the skin from the mother to the babies skin.
• This is why imitate skin to skin contact is so important.
• If we miss out this vital stage, then the baby will pick up the microbiome from the
environment around him. This can be a problem if it is a hospital birth or if the
mother is too unwell to care for her child.

WHERE DOES IT ALL START?
• The forth stage of microbiome transmission is through breastmilk.
• Breastmilk is a power house of bacteria! The bacteria line the digestive tract of the
baby and prepare the baby’s gut for foods later on.

BREAST MILK IS AMAZING!
• Breast milk changes in composition according to the babies needs. The babies saliva
enters the mother nipples through a vacuum that is produced by the sucking action
of the baby.
• If the baby has an infection, the mothers body will respond to this by creating
antibodies for that infection, and within half an hour, these antibodies are showing
up in breast milk.
• Breastmilk also contains sugars that the baby cannot break down, and therefore
their only purpose is to provide a food source for the microbiome.
• Amazing!

HOW DOES MICROBIOME IMPACT HEALTH?
-Immune system
-Digestive system
- Skeletal system
-Cardiovascular
system
-Endocrine system
-Nervous system
-Respiratory system
-Urinary system
-Reproductive system
-Detoxification
-Energy and
methylation
-Nutrition status

EPIGENETICS
• Microbiome has more of an impact on the expressions of genetic related conditions,
than genes do.
Examples
• BRCA1 / BRCA2 genes (breast cancer)
• HLA genes (autoimmune genes)
• FTO (fat gene)
• Ageing

NUTRITION
• They produce short chain fatty acids (butyric acid) which are needed as fuel for the
gut cells.
• They excrete vitamins k2 (more than we get from diet)
• B12 is also produced, however not enough in isolation
• B1, B2
• Vitamin C
• Over 200 digestive enzymes

GUT HEALTH
• 70% of your immune system comes from you gut microbiome.
• They have a huge impact on the Gut Associated Lymphoid Tissue and the regulation of
immune cells.
• They alter the PH of the gut. Beneficial bacteria produce lactic acid, which is helpful for
protection against pathogens and needed for good digestion.
• The gut is where you digest and absorb foods and provide your whole body with
nutrition. Humans naturally produce 22 digestive enzymes to break down foods,
however, your microbiome excrete over 200 digestive enzymes! They are as important for
digestion as your bodies natural function!
• The majority of digestion is done by microbes.

GUT
• Sibo – excessive bacteria in the small intestine.
• Excess bacteria metabolise fermentable fibres in the small intestine causing gas and
bloating.
• FODMAP – Fermentable oligosaccharides, disaccharides, monosaccharides and
polyols.
• Lactose - troublesome sugar.

IBS
• There is a lack of beneficial bacteria in the colon, and therefore, not enough short chain
fatty acids are produced i.e butyric acid. Short chain fatty acids fuel the gut cells and
allow for effective peristalsis = constipation.
• Or, too many pathogenic organisms in the colon causing irritation = diarrhoea.
- What are the typical symptoms of IBS?
- How do we treat IBS naturally?
- What other symptoms in IBS could signal SIBO?
- Anxiety?
- Irritability?
- Food intolerances?

IBD
• GALT (gust associated lymphoid tissue)
• The gut microbiome shapes the intestinal immune response, and is directly indicated in
Irritable bowel diseases such Crohn’s, Colitis and ulcerative Colitis, as well as all other
auto immune conditions.
• The use of microbiome therapy for IBD remission has so far been impressive. Therapies
such as the use of probiotics – particularly E.coli Nissel, and faecal rectal infusion are
showing great results.
• What does this mean for the current use of immunosuppressant's and steroids for IBD’s?
• How does faecal rectal infusion work and are there any risks?
• What other diseases benefit from faecal rectal infusion?
June L Round , et al. The gut microbiotica shapes intestinal immune response during health
and disease. Nature Reviews Immunology 2009

DEPRESSION AND ANXIETY
• Pathogens have the ability to affect the behaviour of the host. Studies show that
patients with IBS and altered microbial diversity have demonstrated poorer
emotional functions such as anxiety and depression. Pathogenic bacteria release a
substance called lipopolysaccharides. These are able to pass the blood brain barrier
where they can effect emotions. Consider the microbiome affect on:
• Suicide rates – (Toxaoplasma gondii - protozoa)
• Anti depressant use
• Other mental illnesses
Blanchard EB, et al. The role of anxiety and depression in irritable bowel syndrome. Behav
Res Ther 1990.

LIVER DETOXIFICATION
• Beneficial bacteria stimulate the enzyme production of the liver needed for certain
detox pathways.
• Consider the implications of microbiome and liver detox pathways:
• Drug metabolism
• Nutrient metabolism
• Skin health
• Immune health
• Moods and mental health
Claus SP, et al. Colonization-induced host-gut microbial metabolic interaction. Mbio 2011

CHOLESTEROL
• Some bacteria are efficient at reducing cholesterol levels. There are certain microbes
called bile salt hydrolase active (BSH active) bacteria.
• They metabolise and break down some of your bile. Bile is made from cholesterol, so
your body has to call on its reserves to make more, decreasing blood cholesterol
levels.
• Consider the implication for reduced cholesterol on rates of:
• Atherosclerosis and heart blockages / ischemic stroke
• Coronary artery disease and poor blood flow
Mitchell L Jones et al. cholesterol lowering with bile salt hydrolase active probiotic
bacteria, mechanism of action, clinical evidence, and future direction for heart
health applications. Expert opinion on biological Therapy 2013

WHAT CAUSES A BAD MICROBIOME?
• Our mothers health at the time of conception and birth
• The way in which we were born, and weather or not we undergo vaginal seeding
• Weather we were breast fed or formula fed
• Antibiotic use – it is estimated that over 50% of antibiotics are inappropriately
prescribed
• The use of Non Steroidal Anti Inflammatory (NSAID’s). They case irritation in the
gut which stops the adherence of the microbiome to the gut wall.
• Stress can have a profound detrimental affect on microbiome.
• Poor diet.
Baily MT et al. Exposure to social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain behave
immune 2011

WHAT CAN WE DO?
• Your microbiome changes within just one day of you changing your diet. This means
that we have a very powerful tool at our finger tips.
• Exclude sugar and refined carbohydrates, which reduces inflammation in the gut
and has a negative affect on the gut microbiome.
• In the words of Michael pollan “Eat food. Not too much. Mostly plants”

WHAT CAN WE DO?
• The diet impacts microbiome, and microbiome impacts your diet. Your microbiome
released chemicals into your brain, giving you cravings for food that supports their
growth. Since we know that sugar is detrimental to the microbiome and sugar
cravings come from negative microbiome such as candida species.
• What we need for a good gut garden is the same as how we would grow a real
garden:
• less chemicals
• more nutrition
• And a bit of dirt

WHAT CAN WE DO?
• Eat fermented foods daily. Fermented foods contain billions of organisms and a huge
variety of species and strains.
• Sauerkraut contains Bacillus clausii, also found in healthy soil and plants. Bacillus
Clausii is particularly beneficial for the upper respiratory tract. It is also antibiotic
resistant!
• Nato contains Bacillus Subtillus which break down hydrocarbons in the gut. They
colonise mostly in the small intestine.
• Saccharomyces boulardii is a beneficial yeast and is related to bakers yeast. It
produces lactic acid and supports GALT, modulates immunoglobulins. Good to take
with antibiotics to help decrease the risk of a candida overgrowth.

KEFIR DRINK CONTAINS…
• Lactobacillus acidophilus
• Lactobacillus brevis
• Lactobacillus casei
• Lactobacillus delbrueckii- bulgaricus
• Lactobacillus delbrueckii- delbrueckii
• Lactobacillus delbruckii- lactis
• Lactobacillus helveticus
• Lactobacillus kefiranofaciens- kefiranofaciens
• Lactobacillus kefiri
• Lactobacillus paracassi- paracasi
• Lactobacillus plantarum
• Lactobacillus rhamnosus
• Lactobacillus sake
• Lactococcus lactis- cremoris
• Lactococcus lactis- lactis
• Lactococcus lactis
• Leuconostoc mesenteroides- cremoris
• Leuconostoc mesenteroides- dextranicum
• Leuconostoc mesenteroides- mesenteroides
• Pseudomonas fluorescens
• Pseudomonas putida
• Streptococcus thermophiles
• Candida humilis
• Kazachstania unispora
• Kazachstania exigua
• Kluyveromyces siamensis
• Kluyveromyces lactis
• Kluyveromyces marxianus
• Saccharomyces cerevisiae
• Saccharomyces martiniae
• Saccharomyce unisporus

WHAT CAN WE DO?
• Consume fibre to provide a food source for the beneficial microbiome.
• Ensure that HCL levels are normal.
• Avoid constipation.
• De-stress.
• Get back to nature.
• Take a probiotic supplement.
• Remove sugar from the diet.
• Ensure you are consuming enough omega 3.
• Eliminate and food intolerance.
• Consume a diet that consists of at least 80% beneficial and nutritious foods.
• Avoid antibiotics, antibacterial products and chlorine in drinking water.
• Go oraanic.

THANKYOU FOR LISTENING
I hope you enjoyed ‘our’ talk!