The Baby Biome – And Why You Should Support It

adorable baby beautiful child
What a cutie!

For years, I have encouraged Mums-To-Be (and Dads pre-conception) to look after their gut bacteria because that can have such an effect on baby’s health in the womb and out of it. To go with my microbiome (gut bacteria balance) series of blog posts this week (see oral and vaginal), I thought this piece from Biocare about the Baby microbiome was a useful one because people rarely think about their new baby’s microbiome.

My main aim has been to make sure baby has a good, strong immune system and to prevent allergies, which I note they mention here. They have a Baby Bioflora product here (not dairy free) or Baby Infantis, the dairy free one I have recommended myself for years. Either will help make sure your new bundle of joy is healthy and strong in early and later life.

For more info, check the Pregnancy factsheet out and the Probiotics one here.



Are you expecting a new arrival in the family? Or have you recently given birth and want to give your baby the best start in life? One of the best things you can do is to look after the 4.4 trillion of bacteria that live in their gut! Let’s find out how probiotics can support your baby’s immune system, digestion and development from birth and through childhood.

But first, what is the microbiome?

There are approximately 39 trillion microbial organisms living in an adult human bodyand they are collectively referred to as our microbiome. Having such a large community of other organisms living inside us might sound somewhat scary, but we have evolved together and depend on each other2. These bacteria, also called probiotics, live, eat and reproduce in our gut and their activity supports our own health in multiple ways.

How does our microbiome develop?

Up until recently, it was believed that a baby’s first exposure to bacteria occurred during birth. But a recent study has identified a unique placental microbiome to which the baby is already in contact with in the uterus.3 However, the impact of this microbiome is still unclear, and the most significant exposure is still believed to be to the mother’s vaginal microbiome during natural birth or to the hospital environment in the case of a C-section delivery. This initial exposure will determine the composition of the baby’s gut and is crucial to enable beneficial bacterial to colonise it and help build the newborn’s immunity.

The baby’s diet and exposure to the environment in the first months and years continue to shape the microbiome until around 3 years of age, after which it settles into an adult-like microbiome.4 Once fully established, the composition of this microbiome is relatively stable but can be affected by the use of antibiotics, infections, and a whole host of dietary and lifestyle factors.

What can affect the baby’s microbiome?

As already touched upon, the first factor affecting the infant’s microbiome is the method of birth. Compared to babies born vaginally, babies born by C-section have reduced populations of Bifidobacterium5, a type of bacteria associated with health benefits and a stronger immune system6.

How a newborn is fed can also majorly impact the development of the gut microbiome during the first few months of life.7 Breast milk informs the baby’s immune system about the environment8 and provides beneficial bacteria9,10 which are transferred from the mother’s gut to the mammary glands.11 Breast milk also contains large amounts of oligosaccharides, a type of carbohydrate that functions as a fertiliser for beneficial bacteria in the gut and helps to promote their activity12.

Early use of antibiotics can also reduce the number and diversity of beneficial bacteria in the gut.

How gut health affects our immunity and overall health?

A balanced and diverse microbiome is essential to help program the immune system of new born babies, so it is able to respond to pathogens, but at the same time, does not overreact to environmental allergens and to foods introduced during weaning.

The beneficial bacteria form a physical barrier in the gut and prevent pathogens from entering the body. They also keep the immune system in alert so it can respond quickly and effectively to invaders. Numerous studies have shown that when children are supplemented with probiotics, they get fewer colds 13 and respiratory tract infections,14 and recover more quickly when they get ill.15

An imbalanced microbiome following birth by C-section can double the risk of developing egg and milk intolerances,16 a factor involved in the development of both eczema and asthma. Antibiotic use during infancy can also increase the risk of developing allergic diseases,17 asthma18 and Inflammatory Bowel Disease (IBD) later in life.19

How to improve your baby’s microbiome…

…Before Birth

The first thing to do if you are expecting a baby is to look after your own microbiome by supplementing with probiotics that are suitable during pregnancy, and by increasing your intake of fibre-rich foods. This will help to ensure your baby benefits from your beneficial bacteria during birth and breastfeeding. If a C-section is planned or performed in an emergency, you can give your baby a probiotic supplement straight from birth to support their gut microbiome.

…At Birth

You can supplement your baby with probiotics that are well researched and safe for their immature gut. One landmark study found that babies supplemented with a blend of 4 strains of bacteria (including Lactobacillus paracasei and salivarius), at 10 billion per day for 6 months were 57% less likely to develop allergic eczema than those receiving placebo and 44% less likely to develop allergic reaction to pollen, cow’s milk, egg, and house dust mite.20

In premature babies, supplementation with probiotics has also been shown to halve the risk of a severe and fatal condition called necrotizing enterocolitis, which is common in preterm infants.21

…In the first few months

Once your baby starts weaning, slowly introduce a variety of fruits and vegetables rich in prebioticfibres, such asavocado, banana, onions and leeks.

You can also introduce fermented foods in small amounts which naturally contain beneficial bacteria, such as organic yoghurt or kefir.

Lastly, if your baby needs to take antibiotics, giving them a probiotic supplement both during and after treatment can help to reduce disruption to their gut bacteria and the risk of side effects. Just make sure that they take the probiotic supplement at least 2 hours away from the antibiotics to protect the beneficial bacteria.

Biocare have also added some other really useful info here on when you might consider giving probiotics:


Have you been reading about probiotic supplementation and feeling confused over whether they are suitable, why, or how is best to best give them to your child?

Our gut microbiome plays a central role in supporting our health in a variety of ways. You may have recently read numerous blogs or research papers focusing on the positive impact of live bacteria on our immunity, digestive function and even the ability to alter our attention, behaviour and mood.1,2 Perhaps you would like to support your child’s health by optimising their gut flora, yet have a few questions we aim to answer.

The number of bacteria in the body, including our gut microbiome lining the gastrointestinal tract outnumbers even the body’s own cells. It has been known for a long time that the bacteria play a role in digestion yet a new field of study is finding that these bacteria can influence many organ systems in the body, including diseases of the digestive tract, immune system and even the brain.

Over the past decade or so, we’ve seen a huge growth in childhood allergies, behavioural problems and chronic disease. Many experts now consider disrupted microbiome as a major contributory factor, and one that is possible to do something about using simple appropriate dietary changes and supplements.

Baby’s initial exposure to bacteria via their mother’s placenta, birth canal or hospital environment in the case of Caesarean section births is essential for training the immune system to respond appropriately to recognise potential pathogens, such as viruses or bacteria.3 Once fully established, the composition and diversity of the microbiome is relatively stable, yet can be affected by dietary and lifestyle factors, such as the use of antibiotic medication.4

Why and when to consider probiotics for your child:

  • My baby was born via C-section

Significant differences in infant microbiome have been noted depending on methods of birth. Babies born by C-section have lower bacterial counts and reduced populations of Bifidobacteria at 1 month compared to those born vaginally.5 However, the simple solution to this is to populate your babies’ microflora as soon as is possible after birth, by giving a daily probiotic bacteria supplement for a minimum of 6 months.6

Certain probiotics have been designed to include the prebiotic GOS (galactooligosaccharides) in order to most closely emulate breastmilk.

  • Following Antibiotic Medication

Whilst it is sometimes important to give prescribed antibiotics to your baby, it is also vital to consider the longer term effects of this. Antibiotic medication not only destroys harmful bacteria, it does not discriminate therefore also affects beneficial microflora. This can leave us susceptible to recurrent infections, therefore following antibiotics it is vital to replenish healthy gut flora to enhance immune resistance.

  • Lactose Intolerance – breast or bottle-fed?

Whether you are breast or bottlefeeding your baby, milk contains the sugar, lactose, which can be difficult for some babies to digest efficiently. If your baby has been checked over by their GP and is still experiencing stomach pain, diarrhea, bloating or excessive wind (usually within 1-3 hours after a feed), it can be helpful to try lactase enzyme to predigest lactose, added into formula or expressed milk.Probiotic supplementation has been shown to support lactose digestion.7

In rarer cases; 4-7% of bottle fed babies and 0.5% of breastfed babies,8 can experience more severe reactions, for example, swelling of the lips or wheezing, as an immune response allergic reaction to the proteins in milk such as casein. This would need further GP investigation and possibly prescription of suitable hypoallergenic milk formula.

For breastfeeding mums, it may be beneficial to take a daily probiotic supplement and eliminate your intake of cow’s milk protein. Although breastmilk does by nature contain some lactose, this would limit exposure and improve microbial diversity of breastmilk.9

  • Baby Thrush & Feedback to Mum

Baby thrush (e.g. white tongue coating) can be stubborn to alleviate and incredibly painful for mum on feeding. Low amounts of healthy gut bacteria (e.g. following antibiotic medication) can leave individuals susceptible to recurrent infections or thrush, due to overgrowth of yeast.

It may also be helpful for feeding mums to temporarily avoid all sources of refined sugar, yeast, alcohol and fizzy drinks, until significant improvement is seen.

  • Colic / Reflux

Colic symptoms such as intense prolonged periods of crying (over 3 hours) and arching their back be disturbing and difficult to manage for parents desperately trying to relieve their discomfort, often feeling helpless.

Growing evidence suggests the infant’s immature digestive system may be responsible for this, the proteins present in milk in particular being particularly difficult to digest.10 Probiotics may be helpful in supporting efficient digestion and movement of food through the gastrointestinal tract. Whilst your child is under GP investigation, it may be helpful to choose a simple probiotic product to start with.

As they grow older, review your baby’s progress and adapt their supplement programme as necessary for their specific age and needs. You could also consider visiting a local registered cranial osteopath, many of which specialise in infant colic.

  • Recurrent Infections

A healthy gut wall is vital as our structural first line of immune defense, acting as a barrier with the environment. Lactobacillus species have been found to stimulate our immune system’s natural function. The “PROCHILD” study in 2015 involved giving children aged 3-6 years, a combination of probiotics containing Lactobacillus acidophilus, Bifidobacterium lactic and Bifidobacterium bifidum, alongside a small amount of vitamin C daily, for 6 months. The results showed a 50% reduction in coughs and colds, antibiotic use and reduced absence from school.11

  • Allergies/Skin conditions

Common skin conditions such as eczema, psoriasis or milia (“milk spots”) can be incredibly sore and also distressing for parents trying to alleviate discomfort and determine possible underlying factors such as food allergy/intolerance or stress. Food allergies are an increasing concern in young children, where the incidence of food allergy is estimated to be greater in toddlers (5-8%) than in adults (1-2%).12

Extensive research has shown live bacteria strains LAB4B, given during infancy can reduce incidence of allergy in children and improve symptoms of atopic eczema.

Would you like to try a probiotic for your child but you’re not sure how to administer it?

It’s quite easy once you find what suit you and your child. Most high strength live bacteria products for children come in a powder. For infants, they can be mixed with a little milk and ingested directly from mum’s nipple, or sucked from her finger/a dummy. The powder can also be given directly into their mouth before a feed. Practically, try whichever method best suits you and your baby.

For toddlers, the powder can be dissolved into milk/juice, onto a spoon to ensure they ingest it all, or into their porridge, yoghurt or mashed banana. The prebiotic often used, FOS, tastes sweet, therefore taste isn’t a concern and they often like it!

We all want the best for our children’s health. Digestion plays a crucial role in regulating immune function, in addition to supplying the body with the nutrients it requires during this critical period of growth and development. Adequate intake of vegetables, fruits, fibre and fluid encourages regular bowel movements, essential for effectively eliminating toxins. Taking a daily probiotic supplement provides a safe and effective way to support their immunity, digestion and even improve their mood, behaviour, learning and concentration.

For toddlers and older children, you might look at Biocare’s Biomelts for children over 3.  MindLinx would be good for over 2s who are showing signs of allergy (colic, eczema, food regurgitation) as it contains leaky gut-healing glutamine as well as the probiotics. Banana or Strawberry Acidophilus is a good all-rounder probiotic for children 6m and up.

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