Baby Gut Microbiome Development: What To Expect


  • Ideally, baby gut maturation is low in the early days and steadily increases until it reaches adult-like maturity.
  • Breastfeeding sets the pace of baby gut development.
  • Formula-feeding and early introduction of solids accelerate baby gut maturation.
  • Too fast microbiome maturation may be linked with increased BMI, eczema, and asthma.

In the same way that your baby hits motor milestones with turning over, sitting, and walking - the baby gut microbiome goes through its own stages of development. While there’s a rough trajectory that we like to see with gut microbiome development, what takes shape is something that’s unique to each baby.

Factors like breastmilk, formula, how your baby is born, and medication can have a big impact.

What is seeding?

Starting from birth, your baby’s gut picks up, selects for, and feeds a collection of microbes. This is known as seeding and selection.

The microbes your baby picks up change over time [1]. During the first years of life, these changes follow a defined pattern known as gut microbiome maturation [2]. Typically, the gut microbiome reaches full, adult-like maturity by the time your child is 3-5 years old [2], [3].

But first, what is seeding? And how does selection take place?

We can define seeding as the event when microbes colonize the baby’s entire body, from their skin and mouth to their digestive tract. A wide variety of microbes have the ability to seed your baby’s gut [4].

These microbes mostly come from you - during birth and breastfeeding - and the environment [5], [6].

Selection happens when factors like the temperature, oxygen availability, and pH of the gut allow some microbes to thrive while others pass through or die off. Certain types of bacteria will take up residence in the gut when conditions are right. After conditions change, they will fade out while other types of bacteria grow. 

Tip: Make sure your baby’s gut doesn’t mature too quickly

As you might imagine, the gut microbiome plays a big role in gut development.

The first year or so of life is when your baby’s gut develops into a digestive and immune system organ [7], [8]. It’s when the gut learns to deal with whatever enters it: helpful nutrients, particles from the environment, friendly and unfriendly microbes.

Ideally, the timing between gut development and microbiome maturity lines up. But without a well-composed cast of microbes in place at the right times, baby gut development could go off course [9].

With overly-rapid or out-of-sync maturation, you’re more likely to see:

  • Increased body mass index (BMI) or obesity [9]–[11]
  • Infections [12]
  • Type 1 diabetes [13], [14]
  • Asthma [15]
  • Atopic dermatitis, or eczema [16]

The key to protecting and nurturing your baby’s microbiome is to keep it from maturing too quickly [3].

How breastfeeding sets the pace of baby gut development

After birth, breastmilk can be the next source of protective microbes seeding your baby’s gut [17], [18]. With many compounds that nourish friendly bacteria, it’s also a means of selection.

Certain friendly bacteria called bifidobacteria are key players in your baby’s gut development. This is because they:

  • Fend off unfriendly bacteria [12], [19], [20]
  • Help your baby’s immune and metabolic systems develop [19], [21]–[23]
  • Provide nutrients that your baby needs [24]

An important source of bifidobacteria is a baby’s birthing mother [25], [26]. If the mom’s gut has bifidobacteria, they can transfer to her baby during delivery [27].

If breastfeeding, then breastmilk becomes the major source of bifidobacteria.

Once bifidobacteria are established, an ongoing supply of breastmilk sustains them. They thrive on human milk oligosaccharides (HMOs), which are the sugars found in breastmilk.

Feeding on HMOs gives beneficial bifidobacteria a competitive edge over other microbes. When these bifidobacteria flourish, they produce enough acid to make your baby’s gut inhospitable to unfriendly bacteria [12], [20]. 

In breastfed babies, bifidobacteria outcompete other microbes and assume a dominant role [2], [13], [28]. Because of this, the overall diversity - or variety of bacteria in the gut - is low, which is ideal for young babies.

As long as your baby is breastfed, there’s a good chance that bifidobacteria will remain high during their first 6 months [13]. This is important because low levels of bifidobacteria in babies are linked to chronic diseases, including autoimmunity, asthma, and obesity [29]–[31].

It’s important to note that not all mothers have bifidobacteria. Microbiome testing before birth helps to make sure that a mother has bifidobacteria to pass along to her baby. If no bifidobacteria are found, this would be a good time to supplement with probiotics.

How formula feeding sets the pace of baby gut development

The gut microbiome of formula-fed babies is different from that of breastfed babies [32]. This can include:

  • Different types of bacteria [13]
  • Lower levels of bifidobacteria [13]
  • Greater diversity [2], [13], [32]
  • A more mature microbiome [32]

In short, formula feeding speeds up baby gut microbiome maturation [32].

The unique combination of the probiotic and prebiotic components of human breastmilk provides breastfed babies with a stable and relatively uniform gut microbiome compared with formula-fed babies. Some formulas contain prebiotics like HMOs that help to feed beneficial bacteria.

Breastmilk remains the ideal source of nutrition for babies.

If it’s available to you, continue to breastfeed even if feeding your baby formula. This is because it’s been found that breastmilk seems to suppress baby gut microbiome maturation in formula-fed babies [13].

There are only a few studies on the effects of mixed formula and breastfeeding on the baby gut microbiome. That means we don’t know what the threshold is. We don’t know how much breastmilk it takes to hold off the maturing influence of formula.

If you choose to supplement breastmilk with formula, we suggest:

  • Tip the breastmilk/formula balance as far in favor of breastmilk as you can
  • Wait as long as you can to introduce formula; holding off until a baby is 4-6 months old may reduce the risk of obesity later in childhood

Microbiome maturation speeds up when a baby stops breastfeeding

Complete weaning - or no longer giving your baby breastmilk - drives the maturation of a baby’s gut microbiome [2]. While breastfeeding, bifidobacteria tend to dominate the baby’s gut, even with the introduction of solid food [17].

Like breastmilk, solid food helps to shape which microbes flourish and which do not. If you continue breastfeeding, then introducing solids will only bring on a slight increase in maturation [13].

But when a baby or toddler weans and stops breastfeeding, their gut microbiome matures rapidly, moving towards a diverse, adult-like composition [32]. These bacteria act together to break down all the different foods your child eats [13].

After weaning, your baby’s gut microbiome will continue to change through early childhood before stabilizing at around 3-5 years [3], [28], [33].

It’s worth keeping in mind that food isn’t the only factor shaping your baby’s gut microbiome. Between weaning and full maturity, other environmental factors come into play. This includes:

  • Close contact with caretakers [6]
  • Geographical location [32]
  • Air quality [32]
  • Pet and animal exposure [34], [35]
  • Daycare [32], [36]
  • Playing in soil, grass, and leaves [36]


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