ProbiotikaguidenGut Flora & Recipes
Watercolour drawing of a small, newly sprouted garden in a soft nest of leaves, held safely by two large hands. Small, round bacteria are gently moving in between the first shoots.

Colic and probiotics: What do we know about baby gut flora?

By Published 6 min read

A newborn baby has almost no gut bacteria. Over the first days, months and years, billions move in, and how that happens depends on things such as the birth and whether the baby is breastfed.

Many parents are therefore told that a caesarean section "ruins" the gut flora, or that probiotics can help with colic. Here is what the research actually shows.

Birth leaves a clear mark

A large English study followed 596 children and analysed 1,679 stool samples from early in their lives. In children born by caesarean section, the mother's Bacteroides bacteria were passed on less often, and more of the children picked up bacteria that belong to the hospital environment, such as Enterococcus and Klebsiella [1].

The same pattern was seen to a lesser degree in children born vaginally whose mother was given antibiotics during labour, and in children who were not breastfed. The difference after caesarean section could be seen throughout the first month and into infancy [1].

A Swedish study similarly found that the gut flora of children born by caesarean section resembled their mother's less than that of children born vaginally [2].

Breastfeeding matters most

The large American-European TEDDY study followed 903 children from 3 months to just under 4 years of age. Breast milk, whether exclusive or partial, was the factor most strongly linked to the gut flora. Breastfed children had more bifidobacteria, and when breastfeeding stopped, the gut flora matured faster [3].

The Swedish study pointed the same way: it was stopping breastfeeding, not the first baby porridge, that made the gut flora resemble an adult's [2].

Siblings and furry pets were also linked to the child's gut flora [3].

The differences even out with age

The TEDDY study described three phases: a developmental phase from 3 to 14 months, a transitional phase up to 30 months and then a stable phase. The mode of delivery mattered mainly in the first phase [3].

In adults, the mode of delivery cannot be seen at all. A Belgian study of over 1,100 adults, repeated in a Dutch one, found that the mode of delivery was not reflected in the gut flora [4]. Read more about what shapes the gut flora in adults in the article What shapes your gut flora?.

And later illness?

Here a Danish study is worth knowing about. Researchers from COPSAC followed 690 children and found that children with an immature gut flora at age 1 had a higher risk of asthma at age 5. But only in children of mothers with asthma [5].

This is an association. It does not show that the gut flora causes asthma, and it does not mean that children born by caesarean section will get asthma. Caesarean sections save lives, and nothing in the research here is a reason to turn one down when it is needed.

Colic: One strain, in breastfed babies

Colic means that an otherwise healthy baby cries intensely for at least three hours a day, at least three days a week, for at least three weeks [6]. It is hard on the whole family.

One particular bacterial strain, Lactobacillus reuteri DSM 17938, has been studied as a treatment. A pooled analysis of four double-blind trials with 345 babies with colic found [7]:

  • The babies cried and fussed on average 25 minutes less a day after three weeks than with placebo.
  • In breastfed babies the effect was clear: for every 2 to 3 babies given the strain, one baby got noticeably better.
  • In bottle-fed babies there was no significant effect. The researchers write that there are not enough data to conclude anything for them.

So this is one strain, few trials and an effect that has only been shown in breastfed babies. It does not apply to probiotics for babies in general.

Prevention is less well documented. A Cochrane review of six trials with 1,886 newborns found no clear evidence that probiotics given from birth prevent colic. The babies cried a little less, but the evidence was of low quality [6].

Stomach infection: Probably no difference

It has long been common to give probiotics to young children with acute diarrhoea and vomiting. Two large trials from 2018 called this into question:

  • An American trial with 971 children aged 3 months to 4 years at ten emergency departments found no difference with L. rhamnosus GG. The diarrhoea lasted just as long in both groups, about two days [8].
  • A Canadian trial with 886 children and a combination of two other strains also found no difference [9].

A 2020 Cochrane review of 82 trials therefore concluded that probiotics probably make little or no difference to whether the diarrhoea lasts more than two days. Many of the trials had a high or unclear risk of bias, and there were signs that negative results were not published [10].

The European society for paediatric gastroenterology (ESPGHAN) still gives weak recommendations for a few strains, but writes that it could not find two high-quality trials showing an effect of any strain [11]. The most important thing with a stomach infection in young children is still that the child gets enough fluids.

Premature babies: A decision for the doctors

In premature babies, a serious bowel disease called necrotising enterocolitis (NEC) can develop. A Cochrane review of 60 trials and over 11,000 babies found that probiotics probably reduce the risk of NEC in babies born before week 32 or with a birth weight under 1,500 grams. But in the smallest babies, under 1,000 grams, there was no clear effect [12].

The American Academy of Pediatrics advises against routinely giving probiotics to all premature babies, especially the smallest, partly because in the USA the products are sold as dietary supplements and not as approved medicines [13]. In premature babies, probiotic bacteria have also, in rare cases, been found in the blood. Read more in the article on who should not take probiotics.

Whether a premature baby should be given probiotics is decided by the neonatal unit. It is not something parents should buy themselves.

What you can do

  • Breastfeed if you can and want to. Breast milk is what is most strongly linked to the baby's gut flora. But if you cannot, it is not a reason to worry. The differences even out with age.
  • If your baby has colic, talk to your health visitor or doctor. Crying can have other causes that need to be ruled out. If you are considering probiotics, ask about the strain that has been studied, and be aware that the effect has only been shown in breastfed babies.
  • With diarrhoea and vomiting, fluids are the most important thing. Contact your doctor if the child becomes lethargic, passes very little urine, cannot keep fluids down or has blood in their stool.
  • If your baby was born prematurely, let the neonatal unit make the decision about probiotics.

The bottom line

  • Caesarean section and breastfeeding clearly affect a baby's gut flora in the first months. Breastfeeding matters most.
  • The differences even out with age, and in adults the mode of delivery cannot be seen in the gut flora.
  • One strain, L. reuteri DSM 17938, has reduced crying in breastfed babies with colic in a few trials. In bottle-fed babies the effect has not been shown.
  • For acute stomach infections in young children, probiotics probably make no difference.
  • Probiotics for premature babies are a decision for the doctors.

Sources

  1. Shao Y et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature. 2019. PMID 31534227
  2. Bäckhed F et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015. PMID 25974306
  3. Stewart CJ et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018. PMID 30356187
  4. Falony G et al. Population-level analysis of gut microbiome variation. Science. 2016. PMID 27126039
  5. Stokholm J et al. Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun. 2018. PMID 29321519
  6. Ong TG et al. Probiotics to prevent infantile colic. Cochrane Database Syst Rev. 2019. PMID 30865287
  7. Sung V et al. Lactobacillus reuteri to Treat Infant Colic: A Meta-analysis. Pediatrics. 2018. PMID 29279326
  8. Schnadower D et al. Lactobacillus rhamnosus GG versus Placebo for Acute Gastroenteritis in Children. N Engl J Med. 2018. PMID 30462938
  9. Freedman SB et al. Multicenter Trial of a Combination Probiotic for Children with Gastroenteritis. N Engl J Med. 2018. PMID 30462939
  10. Collinson S et al. Probiotics for treating acute infectious diarrhoea. Cochrane Database Syst Rev. 2020. PMID 33295643
  11. Szajewska H et al. Use of Probiotics for the Management of Acute Gastroenteritis in Children: An Update. J Pediatr Gastroenterol Nutr. 2020. PMID 32349041
  12. Sharif S et al. Probiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants. Cochrane Database Syst Rev. 2023. PMID 37493095
  13. Poindexter B et al. Use of Probiotics in Preterm Infants. Pediatrics. 2021. PMID 34031231

This article is general information and not medical advice.