This is for the midwives, the mothers, the mothers-to-be and anyone involved in the health care industry looking after mothers to be and their newborns.
Imagine if the first 1000 days of a baby’s life laid the foundation for their entire immune system, mood, allergy risk, and even metabolic health. Now imagine we could influence all of it, through the microbiomeWhen you hear the word microbiome, you probably think of the gut. Fair enough, it gets most of the attention. But what if we told you that microbes are not just hanging out 'down under'? They are everywhere. There is the oral microbiome living in your mouth, the skin microbiome covering every inch of your body, the urogenital microbiome, the lung microbiome, and, of course, the celebrity of the microbial world, the gut microbiome. These tiny organisms are not unwanted guests infact, truth be known, we are their guests. They are part of you, which helps keep you alive.. Seriously, just pause and reflect on this for a moment…
Welcome to the world of modern infant health, where Bifidobacterium breve and birth mode matter as much as sleep schedules and co-sleeping.
What are the first 1000 days?
The first 1000 days refers to the period from conception to age two. It is now considered one of the most critical developmental windows for a child’s future health, especially for establishing the gut microbiome, immune system, and even long-term risk of diseases like asthma, eczema, obesity, and type 1 diabetes.
This is not just an impressive milestone; it is microbiological, immunological, and incredibly awesome!
Microbiome 101: The gut as the training ground for immunity
The infant gut is not just a digestive tube, it is a central training ground for the immune system. In fact, 80% of the immune system is housed in the gut. Think auto-immune conditions, think obesity, think asthma, think eczema, they all have a link to the gut.
During this early window, key gut microbes educate the immune cells, influence tolerance, and help build a strong intestinal barrier.
Two key players during this time are:
- Bifidobacterium species: the ‘good guys’ that dominate the healthy baby gut
- Enterobacteriaceae family: includes E. coli, Klebsiella, Salmonella. They may sound scary but a little exposure helps immune training and yes, too much is trouble.
This early balance or imbalance sets the tone for whether a child’s immune system leans toward tolerance or inflammation.
The infant gut is not as diverse as the adult gut
In babies, we want low diversity at first because bifidobacteria should be taking up all the space. If they did not take up most of the space, then the infant’s health would be in trouble.
Meet the fantastic four of infant immunity, also known as the core four Bifidobacteria strains
When doing stool testing in infants these are your the fantastic four:
- Bifidobacterium infantis
- Bifidobacterium breve
- Bifidobacterium longum
- Bifidobacterium bifidum
These strains digest human milk oligosaccharides (HMOs) which are special prebiotics in breast milk that only these bugs can feed on.
These strains:
- Improve gut barrier function
- Produce short chain fatty acids (aka acetate and lactate)
- Compete with pathogens
- Produce B vitamins and Vitamin K
- Cross-feed other beneficial microbes like Faecalibacterium prausnitzii
- Support vaccine response
Just a note, to cross-feed means that one microbial species produces a substance as a by-product of its own metabolismMetabolism is not a calorie-burning furnace that sits somewhere near your belly button, deciding whether you can fit into last year's jeans. Metabolism is the set of chemical processes taking place inside your body every second of every day, keeping you alive., which then becomes food or fuel for another microbial species. For example,
- Acetate made by bifidobacteria can be used by Faecalibacterium prausnitzii and Roseburia to produce butyrate, a key short-chain fatty acid for gut lining health.
- Lactate can be consumed by lactate-utilising bacteria, which feeds into energy production pathways in the gut ecosystem.
Can you see, why we at the New School of Nutritional Medicine are more than partial to the microbiome?
Cross-feeding:
- builds a cooperative microbial network — one species’ activity supports the growth of others.
- helps establish a stable, balanced microbiome rather than one dominated by a single microbe (think diversity)
- amplifies the benefits of breast milk, because HMOs indirectly nourish not just bifidobacteria but a whole chain of beneficial species.
Human breast milk isn’t just food, it is a source of microbes (these microbes enter the breast milk from mom) and it is food for the microbes. There are over 200 HMOs. Breast milk composition directly reflects mom’s gut. If she’s low in bifido or high in pathogens, then the baby will inherit that through her milk.
Microbiome milestones: The timeline
Gut disruptors that ‘derail’ the 1000 Days
- C-section births
- The microbiome resembles hospital skin flora (e.g., Streptococcus, Clostridium)
- Result in lower Bifidobacterium and Lactobacillus
- Formula feeding
- creates higher early diversity (bad timing)
- results in fewer bifidobacteria
- increases the risk of eczema, asthma, obesity etc.
- Antibiotics
- Are prescribed up to 70% of infants in the U.S. and approximately 62.8% receive antibiotics in the first 2 years
- Even one course of amoxicillin can wipe out Bifidobacterium adolescentis
- Penicillin during labour (e.g., for Group B Streptococcus, GBS) reduces Lactobacillus in vaginal flora
- Linked to long-term risks: asthma, allergies, type 1 diabetes, obesity
What do we teach at the New School?
Test, don’t guess (more on functional tests HERE)
Infant gut testing (starting ~10–28 days old) which reveals:
- Levels of core bifidobacteria
- HMO-digesting capacity
- Presence of pathogens like Klebsiella, Enterobacter
- Gut maturity index (age-appropriate development)
Also test mom’s gut health, including the microbiome, during pregnancy, especially before GBS (Group B strep) testing at ~36 weeks.
Support the gut with diet and strain-specific probiotics
Probiotics are not one-size-fits-all. Strain matters. For example:
- B. infantis for restoring bifidobacteria after C-section
- S. boulardii and Bacillus clausii during antibiotics (won’t be killed)
- Don’t over-supplement, infant guts are highly malleable!
Duration of supplementation is usually:
- infants <6 months: 2–3 weeks of probiotics max
- toddlers: 4–6 weeks
- adults: 3 months
Feed the good bugs
- with breast milk (HMOs) or prebiotic-rich foods
- by introducing diverse plant fibres with solids (after 6 months)
- from giving prebiotics during antibiotics to preserve beneficials
Imagine how many future cases of asthma, eczema, and food allergies we could prevent, by simply doing gut tests on both mom and baby.
- Moms tested at their first prenatal visit
- Infants tested within 4 weeks of birth
- Retesting after any antibiotics or gut issues
- Dietary and probiotic interventions based on gut test results (to avoid over-stimulating, see later on).
Read about comprehensive stool analysis HERE.
The atopic march
The atopic march is the stepwise development of allergic and immune-related conditions, usually starting in infancy and moving through early childhood. It reflects an underlying pattern of immune dysregulation, which is often influenced by early gut dysbiosis, antibiotic exposure, birth method, and feeding practices.
Theimmune system is being trained in these early years and when the gut microbiome is disrupted (from C-sections, formula feeding, or antibiotics), this training goes ‘off course’. Instead of developing tolerance, the immune system becomes hyper-reactive. Specific microbial patterns that increase the risk of atopic march include:
Click on image for the full article
- Low Bifidobacterium (especially B. infantis, B. breve)
- Elevated Enterobacteriaceae
- Overgrowth of Clostridium species
- Low levels of HMO-digesting bacteria (due to lack of breastfeeding or maternal gut dysbiosis)
Classic sequence of the atopic march:
This results in:
- excess TH2 and TH17 responses (common in allergies and eczema)
- low levels of regulatory T cells (which normally keep inflammation in check)
- increased sIgA and IgE antibodies (seen in allergic responses)
Bifidobacterium calms the immune system as it:
- Produces short-chain fatty acids like acetate and lactate which strengthens the gut barrier
- Modulates cytokine production
- Suppresses excessive immune reactions by regulating T cells, dendritic cells, and macrophages
When Bifidobacterium is missing or too low, the immune system skews toward inflammation and allergy, resulting in the classic atopic march.
The great news is that we can intervene by testing and supporting the microbiome:
- We can prevent progression to food allergies and asthma
- We can restore immune tolerance by rebalancing the gut
- Empower mothers-to-be with knowledge about the first 1000 days as the most critical window for lifelong health.
- Equip parents and practitioners with tools like Rapid Relief Homeopathy to handle common childhood infections (earaches, chest infections, chicken pox etc) so antibiotics are only used when truly necessary.
- We can make are huge difference in the health of future generations
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A message from Chidi, Cohort 2023-2025
“When I joined the New School of Nutritional Medicine, my goal was simple: deepen my understanding of health and wellness. I expected some science, structure, and new tools. What I didn’t expect was a complete shift in how I view the body, the mind and the way we live.”
To healthy mothers and babies!
From the team at the New School Of Nutritional Medicine
Learn about the Founder & Principal of the New School of Nutritional Medicine, Dr Khush Mark PhD HERE.
