Why Is My Baby Crying? Gut Health Tips That Help

It’s 6pm, your baby has been crying for what feels like forever, and nothing you try makes any difference to help them settle and sleep.

I remember those long evenings so well with my firstborn, who screamed from teatime until late most nights, which nearly broke me. Over my 30 years in clinic, I have sat with hundreds of shattered parents feeling the same way. Thankfully, there are gentle, natural and well-researched ways to soothe your baby that you can try straight away.

Baby crying is just so tough on exhausted parents, and luckily there has now been quite a bit of research into why some babies cry more than others. Much of this points to a link between crying and the bacterial balance in a baby’s little belly, called the gut microbiome. At NatureDoc, we find that making small adjustments to your baby’s gut ecosystem, through what you feed them and live bacteria supplements, can bring them real comfort, so this can mean you all get more downtime and more sleep.

Why explore the gut? When a baby’s crying feels excessive, this can often boil down to difficulty digesting milk proteins, whether breast or formula, or to excess gas or wind from fermentation in the gut. Both of these can be made worse by an underdeveloped gut microbiome, where not enough of the friendly bacteria have populated yet. An unsettled tummy and the balance of bacteria in your baby’s gut are very often part of the story.

How much crying is normal?

If you are reading this in the middle of the night and you are worried something is wrong, be reassured that most baby crying is completely normal. It tends to be at its most heightened in the first six weeks before it eases up, as their tummy gets bigger and their gut microbiome starts to mature.

Do use your parental instinct though and seek medical advice if you feel your baby is in great discomfort or has other symptoms that do not seem quite right. If reflux or spitting up is heavy, frequent, or coming with real distress and poor feeding, it deserves a proper look, because it may be more significant reflux. It can occasionally be a condition called pyloric stenosis, where the vomiting is forceful and projectile and a small operation might be needed to put it right.

All babies cry, and it is how they tell you that they are hungry, need winding, over tired, too hot, too cold, in need of a nappy change, or simply wanting a cuddle. When researchers pooled crying diaries from thousands of babies, they found that newborns cry for around two hours a day on average, and that crying stays high for the first six weeks or so before dropping quite a bit after eight to nine weeks.

And if you suspect it is colic, this is the word medical professionals use when a baby cries for more than three hours a day, on three or more days a week, with no obvious cause. Colic is common, it is exhausting, and luckily it usually settles on its own with time.

British babies, by the way, are among the most tearful in the world, so if your evenings feel full of crying all round, there are plenty of other parents around the country living the same experience.

How can you spot if their crying is gut-related?

A baby with an uncomfortable tummy will be fussy when they feed, pull their knees up, arch their back, strain, or pass a lot of wind. Many babies wake and cry around 15 to 45 minutes after being put down, which frequently points to gut discomfort. Some want to feed almost constantly in the evening, because sucking helps to soothe their sore belly. Trapped wind, bringing up milk, and a slow bowel (constipation or straining) are all very common in the early months, and any one of them can be behind a whole lot of crying.

Soothing your baby straight away

While you work on the gut side of things (read more below), there is a lot you can do to soothe them, and this is the part you can start on right now if they are crying whilst you are reading this blog.

Newborns spent months in the snug, noisy, constantly moving world of the womb, and calm often comes from giving them a little of that feeling back. Many babies have what is best described as a calming reflex in the first three or four months, and holding, movement and sound together are what switch it on. The lovely thing is that none of this involves any shopping, and you can begin straight away.

A soothing sequence to try, in order

Rather than trying everything at once, work through these one at a time and give each a minute or two to take effect. Layer the next one on top if you need it, and follow your baby’s lead.

Hold your baby along your forearm, on their side or tummy, with your hand supporting their chin and cheek and their head higher than their bottom. This position alone settles a lot of babies, and it eases a windy tummy. It is simply a holding position in your arms, and never a sleeping position.
Add slow, steady movement. A gentle sway from side to side, a soft bounce, a walk around the room, a sling, or a push in the pram all work well. The rhythm matters more than the speed, and it is the same reason a car journey so often does the trick.
Add a shushing sound, close to their ear and roughly as loud as their crying to begin with, softening as they settle. A low, droning white noise from your dishwasher or washing machine, a running tap, or a shush from you all mimic the constant whoosh they heard before birth. Silence can feel strange to a newborn, so sound is a real comfort.
Offer something to suck. A clean finger, a dummy, or the breast can bring a fractious baby into deep calm, because sucking lowers their heart rate and settles them. If you are breastfeeding, it helps to wait until feeding is well established before introducing a dummy.
Try a warm bath and plenty of skin to skin. Bare cuddles against your chest calm both of you, and they are one of the nicest ways to ride out a difficult evening together.

Winding and a gentle tummy massage

Trapped wind is behind a great deal of evening crying, so it is worth winding your baby partway through a feed and again at the end. Hold them upright against your shoulder, or sit them on your lap supporting their chin, and rub or gently pat their back until the wind comes up. Take your time, because a good burp is often what a grizzly baby is waiting for.
Between feeds, a gentle tummy massage can help things move along. Lay your baby on their back, and with warm hands stroke softly around their tummy in a clockwise direction, which is the way the bowel naturally runs. You can follow this by bicycling their legs and bringing their knees up towards their tummy to release trapped wind.

Massage has a mixed picture in the research, with some studies showing less crying and others showing little difference beyond the natural settling of colic, so think of it as a low-risk way to soothe and connect rather than a guaranteed fix. Most babies enjoy the warmth and closeness of it, and that alone is worth a great deal at the end of a long day.

The vital gut connection

Here is what I have learned about the gut-crying connection from decades of working with little ones. A baby’s belly is home to trillions of microbes, and the balance of these bugs shapes their digestion, wind, mood and immunity. Several things influence the development of a healthy balance, including birth by caesarean section, early antibiotic use for mum or baby, and the way a baby is fed, as all of these can shape how the microbiome develops.

One family of friendly bacteria that every expectant or new parent needs to know about is Bifidobacterium. It is the first bacterium to populate a baby’s gut when they are first born, and we should all have plenty of Bifidobacterium populating our guts. This is because they help with digestion, the break down starches and fibres from the food we eat, they produce short-chain fatty acids that reduce inflammation, and crowd out harmful bacteria such as E. coli. They also make folate, which is a vital B vitamin for baby development.

Having enough Bifido in a baby’s belly really counts when it comes to preventing colic. When researchers compared the gut microbiomes of colicky babies with those of settled babies, the crying babies tended to have more inflammation, a lower diversity of beneficial bacteria overall, and fewer of this calming Bifidobacterium.

Good sources of this mighty bacterial strain include probiotic yoghurts and kefir, and it flourishes when you eat prebiotic-rich foods like bananas, oats, onions, garlic, and chicory root. Ideally, your baby would be breast fed, and you would be eating plenty of these foods, but I totally understand that this is not everyone’s reality nowadays and even if you do prioritise these measures, your baby could still have a shortfall. Let me explain.

Breast milk is usually a wonderful source of beneficial bacteria and very much reflects the mother or donor’s gut microbiome. The bacteria from the woman’s intestines cross her gut wall, are captured by their immune cells, and then travel via the internal circulation system to the mammary glands, which is called the entero-mammary pathway. The key bacteria in breast milk is Bifidobacterium infantis, along with sugars known as human milk oligosaccharides (HMOs), which help to feed this vital Bifido, and together these help to set up the gut immune system in the first months of life and help the baby to settle.

Sadly, breast milk is often not quite as protective as it once used to be. A century ago, breastfed babies were found to have Bifidobacterium infantis as the dominant bacteria in their gut, while bottle-fed babies had far less. Fast forward a hundred years and this vital strain has become much harder to find in the guts of most Western babies, even in breastfed babies who have never had antibiotics. This generational decline is thought to be linked to a century of antibiotic use, more caesarean births and our modern reliance on disinfectants and hand sanitisers. So, it is more likely than not that your baby could do with more of this bifido strain, which not only helps to reduce crying but is also linked to protection from serious infections, allergies and eczema.

The gut and the brain are in constant conversation too, and friendly bacteria like Bifidobacterium also help to make some of the calming chemicals a baby’s brain relies on, including GABA, which supports settling and good sleep. Emerging studies even link higher levels of Bifidobacterium and its cousin Lactobacillus with how settled and soothable a baby is during their first year. So, supporting your baby’s gut microbiome may help both their tummy comfort and their contentment.

The good news is that if you breastfeed and you have a healthy gut microbiome yourself, you are likely to be passing some Bifidobacterium on to your baby. It is harder for a formula-fed baby to build up this Bifidobacterium, even though some formulas now add prebiotics to try and encourage it and this is where I woud encourage live bacteria supplementation. And it is also worth adding a live bacteria supplement containing Bifidobacterium and Lactobacillus strains if your baby is crying more than they should, or if you suspect the crying is down to digestive issues.

It’s not just Bifidobacterium

Bifidobacterium is not the whole microbiome story when it comes to crying babies. The most studied live bacteria supplement for helping to reduce baby crying is a specific strain called Lactobacillus reuteri. In a trial of breastfed babies, those given this strain cried and fussed far less than those given a placebo. A large analysis that pooled the raw data from several trials found that it reduced crying and made babies roughly twice as likely to settle well, with the clearest benefit in breastfed babies. Across the reviews, crying often falls by around 25 to 50 minutes a day when supplemented with this live bacteria strain.

Other strains show promise too. A 2023 review of 15 different bacteria, including Bifidobacterium animalis lactis, found an average reduction of about 51 minutes of crying a day, with the biggest difference in exclusively breastfed babies. A blend of Lactobacillus rhamnosus and Lactobacillus reuteri given alongside vitamin D also lowered crying time.

Starting these probiotic drops early may even head off problems before they take hold, and one large trial found less colic, less reflux and less constipation in babies given daily drops from birth. If you would like to try a live bacteria supplement for your baby, always choose a product specifically made for infants.

Could it be dairy?

For breastfeeding mums, a small number of babies react to milk proteins that pass into your breast milk, most commonly from cow’s milk dairy. If you suspect a food reaction in your baby, it is worth reducing your own dairy intake for two to three weeks and see if they are more settled and comfortable. Cow’s milk protein allergy can show up in breastfed babies as crying, reflux, mucousy or bloody stools, and eczema.

For babies who are formula fed, cow’s milk protein allergy can cause similar upset. If you suspect this, some babies do better on goat’s milk formula or specialist hydrolysed formulas where the cow’s milk proteins have been softened and are easier to digest. However, a high proportion of babies who react to cow’s milk protein often react to goat’s milk formula too, and the usual next step is a properly hypoallergenic formula prescribed and reviewed by your doctor.

Interestingly, Lactobacillus strains help with dairy digestion, so sometimes it is not the cow’s milk proteins which are upsetting them; it is purely that they are not digesting the proteins that well due to an immature and underpopulated gut microbiome. And I find that often after a few weeks or months of taking a Lactobacillus supplement, there is increased tolerance to these proteins and they can begin to start climbing the milk ladder (under guidance).

The role of vitamin D

Vitamin D deserves a special mention when it comes to crying babies, because it is anti-inflammatory and can help the gut microbiome to populate with beneficial bacteria, which is why it is often combined with live bacteria in supplements for babies.

We get little sun overall in the UK, and studies have found that many newborns are low in vitamin D, more so in winter. The NHS recommends that breastfed babies have a daily vitamin D supplement of around 10 micrograms, which is 400 IU, from birth. Babies having more than 500ml of formula a day already get enough, because it is added in, so it is worth keeping that in mind. Breast milk contains only a small amount of vitamin D, so you will need to top your baby up with a supplement if they are exclusively breastfed or mixed fed.

Since every single cell in the body has a vitamin D receptor, even a shortfall is thought to affect a baby’s immunity, bone health and gut. Newer research is exploring vitamin D’s role in gut comfort, with some studies pairing it with live bacteria for a dual effect on crying and on a baby’s ability to self-soothe.

Round Up

Long evenings of crying are one of the hardest parts of early parenthood, and you are doing a wonderful job. Remember that most crying is normal and fades with time, that an unsettled gut is often part of the story, and that friendly bacteria and vitamin D can make a real difference. Whilst this is taking effect, reduce likely trigger foods such as dairy thoughtfully, soothe your baby gently, and always get medical advice if you are worried about them.

If your little one is really struggling, we are there to help and get in touch with our NatureDoc Baby Gut Health team for individual support. Please also share this blog with any friend or WhatsApp group where a new parent is pacing the floor tonight, because a little knowledge passed on can bring a lot of comfort to them.

Ask me what supplements can help… or anything else!

Why is my baby crying so much, and how can you help them?