Probiotics for Infants: Evidence-Based Strains for Colic, Gas, and Constipation
What the clinical research says about infant gut health—and how your baby's microbiome starts with you
Few experiences unsettle new parents quite like a baby who won't stop crying, won't pass gas comfortably, or strains with constipation. These common infant digestive issues—colic, gas, and constipation—affect an estimated 5% to 40% of infants in their first months of life, depending on how they're defined.[1] And while they're usually benign, the impact on family wellbeing can be profound.
Over the past two decades, research into the infant gut microbiome has reshaped our understanding of why these issues arise—and how specific probiotic strains may help resolve them. The evidence is increasingly clear: the microbial communities that colonize a baby's intestines in the earliest weeks and months play an outsized role in digestive comfort, immune development, and long-term health.
What makes this research particularly compelling for parents is that it's not generic. Specific strains—not just broad categories like "probiotics"—have demonstrated measurable benefits in randomized, placebo-controlled clinical trials. And critically, the foundation for an infant's microbiome begins before birth, shaped by the mother's own gut health during pregnancy and the mode of delivery.
This guide examines the peer-reviewed evidence behind the probiotic strains most studied for infant digestive health, explains how the maternal microbiome influences early colonization, and outlines what parents should look for when evaluating probiotic options for their family.
Key Takeaways
- Lactobacillus reuteri DSM 17938 is the most extensively studied probiotic for infantile colic, with multiple meta-analyses confirming significant reductions in daily crying time in breastfed infants.[1][2]
- Bifidobacterium infantis is uniquely adapted to metabolize human milk oligosaccharides and is considered the keystone species of the healthy breastfed infant gut.[3]
- Bifidobacterium breve has demonstrated potential in promoting early bifidobacterial colonization and may reduce the risk of necrotizing enterocolitis (NEC) in premature infants.[4]
- Maternal probiotic supplementation during pregnancy can modulate the mother's gut and breast milk microbiota, with evidence of vertical microbial transmission influencing neonatal colonization.[5][6]
- Multi-strain formulations that combine Bifidobacterium and Lactobacillus species may address the complexity of infant gut development more comprehensively than single-strain products.
- Infants with colic consistently show lower proportions of Bifidobacterium and Lactobacillus with higher Escherichia coli populations—a microbial imbalance that targeted probiotics can help correct.[7]
Your Infant's Developing Gut Microbiome
At birth, a baby's gastrointestinal tract transitions rapidly from a relatively sterile environment to one of the most densely populated microbial ecosystems in the human body. This colonization process isn't random—it follows a predictable developmental arc shaped by genetics, mode of delivery, feeding method, and environmental exposures.
In healthy breastfed infants, Bifidobacterium species historically dominated the gut microbiome, sometimes comprising up to 80% of the total bacterial population.[3] This dominance was driven by human milk oligosaccharides (HMOs)—the third most abundant component of breast milk—which selectively nourish beneficial bifidobacteria while creating an inhospitable environment for pathogens.
The Modern Infant Microbiome Crisis
Research has revealed a troubling trend: a generational loss of Bifidobacterium in breastfed infants from industrialized nations over the past century, accompanied by higher levels of potential pathogens and elevated fecal pH.[8] This shift is attributed to the cumulative effects of widespread antibiotic use, cesarean deliveries, and formula feeding—all of which disrupt the natural mother-to-infant microbial transfer that once occurred seamlessly.
When beneficial microbes fail to colonize the infant gut during this critical developmental window, the consequences extend beyond temporary digestive discomfort. Early-life gut dysbiosis has been associated with increased risk for allergic diseases, immune dysfunction, and metabolic conditions later in childhood.[3] This growing body of evidence underscores why restoring and supporting the infant microbiome has become a major focus of pediatric research.
What Happens When Beneficial Bacteria Are Missing
Infants with colic consistently demonstrate a distinct microbial signature: lower populations of Lactobacillus and Bifidobacterium, combined with higher levels of gas-producing Escherichia coli and other proteobacteria.[7] This microbial imbalance creates a cycle of excessive intestinal gas production, inflammation, and altered gut motility that manifests as the persistent crying, fussiness, and apparent abdominal discomfort that defines infantile colic.
The Maternal Microbiome Connection: It Starts Before Birth
One of the most impactful revelations in infant microbiome research is that a baby's gut colonization doesn't begin at birth—it's shaped by the maternal microbiome throughout pregnancy. The mother's gut bacteria influence the infant through multiple pathways: amniotic fluid exposure, vaginal delivery, skin-to-skin contact, and most significantly, breast milk.
Vertical Microbial Transmission
Studies have confirmed that maternal gut microbes—not vaginal bacteria, as previously assumed—are the primary contributors to early infant gut colonization.[5] This means the diversity and health of a mother's own microbiome directly shapes her baby's initial microbial landscape. Mothers who harbor robust populations of beneficial Lactobacillus and Bifidobacterium species are more likely to pass these protective organisms to their newborns.
A 2022 systematic review examining the effects of maternal nutritional supplementation found that probiotic consumption during pregnancy and lactation resulted in colonization of the breast milk microbiota, with pooled data showing significantly increased odds of probiotic presence in breast milk among supplemented mothers.[6] Furthermore, a large Norwegian randomized controlled trial demonstrated that maternal supplementation with Lactobacillus rhamnosus, Lactobacillus acidophilus, and Bifidobacterium lactis from 36 weeks of gestation through 3 months postpartum resulted in detectable L. rhamnosus colonization in infant stool at 10 days and 3 months of age.[6]
The Breast Milk Microbiome
Breast milk is far more than nutrition. It contains its own microbiome—a community of living bacteria that directly seed the infant gut with each feeding. It also delivers HMOs specifically designed to nourish beneficial bifidobacteria, along with immunoglobulins and antimicrobial compounds that shape which bacteria thrive and which are suppressed.
Maternal probiotic supplementation during pregnancy has been shown to modulate key microbial taxa in both the maternal gut and breast milk, potentially influencing microbial recognition and immune signaling between mother and infant.[9] This understanding has led researchers to advocate for supporting maternal gut health as a primary strategy for optimizing infant microbiome development.
Supporting the Maternal-Infant Microbiome Pathway
For mothers looking to support their own gut health during pregnancy and postpartum, a comprehensive probiotic that includes clinically relevant Bifidobacterium and Lactobacillus strains may be worth considering. MicroBiome Restore contains 26 probiotic strains—including Bifidobacterium infantis, Bifidobacterium breve, Lactobacillus reuteri, and Lactobacillus rhamnosus—along with Jerusalem artichoke and acacia prebiotic fiber to nourish those strains. Always consult your healthcare provider before beginning any supplement during pregnancy or breastfeeding.
Lactobacillus reuteri: The Colic Specialist
No probiotic strain has accumulated more clinical evidence for infant colic management than Lactobacillus reuteri DSM 17938. This strain—which produces a broad-spectrum antimicrobial substance called reuterin—has been the subject of multiple randomized controlled trials and meta-analyses, making it the most thoroughly evaluated probiotic intervention for excessive infant crying.
The Meta-Analysis Evidence
A landmark individual participant data meta-analysis published in Pediatrics (the journal of the American Academy of Pediatrics) pooled raw data from four double-blind RCTs involving 345 infants with colic. The probiotic group averaged significantly less crying and fussing time than placebo at all measured time points, and was nearly twice as likely to experience treatment success by day 21.[2]
An earlier meta-analysis of six RCTs encompassing 423 infants confirmed these findings, demonstrating that L. reuteri significantly increased colic treatment success rates at two and three weeks of supplementation.[1] A network meta-analysis comparing L. reuteri against all other colic interventions—including dietary modifications, herbal remedies, and pharmacological treatments—concluded that L. reuteri and dietary approaches were superior to all other evaluated treatments.[10]
Lactobacillus reuteri — At a Glance
Primary evidence: Infantile colic (breastfed infants), functional constipation, prevention of functional GI disorders
Key findings: Significantly reduces daily crying time; nearly 2x treatment success rate vs. placebo at day 21; positive effects on bowel movement frequency in constipated infants
Clinical dosage studied: 108 CFU per day (100 million CFU)
Safety profile: Well-tolerated with no adverse events reported across all included trials; FDA GRAS status in the United States[11]
Beyond Colic: Constipation Benefits
L. reuteri's benefits extend beyond colic relief. A double-blind RCT published in The Journal of Pediatrics evaluated the strain in 44 infants aged 6 months and older with functional chronic constipation. Infants receiving L. reuteri had significantly increased bowel movement frequency at weeks 2, 4, and 8 compared with placebo, with no adverse effects reported.[12]
A subsequent multicenter RCT in France confirmed these findings, demonstrating improvements in spontaneous bowel movements and quality of life in constipated children aged 6 months to 4 years after 8 weeks of supplementation.[13] Additionally, a 2014 multicenter trial showed that prophylactic L. reuteri supplementation beginning in the first week of life reduced the overall incidence of colic, gastroesophageal reflux, and constipation in both breastfed and formula-fed newborns.[11]
An Important Note About Feeding Method
While the evidence for L. reuteri in breastfed infants with colic is robust, results in formula-fed infants have been less consistent. The AAP's individual participant data meta-analysis concluded that L. reuteri can be recommended for breastfed infants with colic, but noted that its role in formula-fed infants requires further research.[2] If your infant is formula-fed, discuss probiotic options with your pediatrician.
Bifidobacterium infantis: The Breast Milk Expert
If L. reuteri is the colic specialist, Bifidobacterium longum subsp. infantis (B. infantis) is the foundational architect of the healthy infant gut. This subspecies is evolutionarily unique in its comprehensive ability to metabolize HMOs—the complex sugars in breast milk that no human enzyme can digest. B. infantis essentially converts breast milk's prebiotic components into short-chain fatty acids (primarily lactate and acetate) that nourish the intestinal lining, lower gut pH, and suppress pathogenic bacteria.[3]
Persistent Colonization
A follow-up study to a randomized controlled trial published in Pediatric Research demonstrated that B. infantis supplementation beginning at 7 days of age produced persistent colonization detectable through at least 12 months—far outlasting the 21-day supplementation window. Fecal B. infantis levels were 2.5 to 3.5 log units higher in supplemented infants compared with unsupplemented controls at 6 through 12 months.[8]
More recently, a 2025 randomized placebo-controlled trial confirmed that B. infantis supplementation in exclusively breastfed infants aged 2 to 4 months produced rapid and abundant colonization persisting at least one month after cessation, and this effect was observed at all tested doses.[14] This is notable because it demonstrates that effective colonization is achievable even beyond the immediate neonatal period.
Why B. infantis Matters for Infant Digestion
The mechanisms by which B. infantis supports infant digestive health are multifaceted. Published reviews identify five key pathways: metabolizing HMOs for competitive advantage over pathogens, producing substances that promote innate immune maturation, reducing intestinal inflammation, decreasing intestinal permeability (addressing "leaky gut"), and producing beneficial short-chain fatty acids.[3]
For infants experiencing gas and digestive discomfort, these mechanisms are directly relevant. When B. infantis dominates the gut, the acidic environment it creates through SCFA production makes it harder for gas-producing pathogenic bacteria to thrive. The result is less intestinal gas, reduced inflammation, and improved digestive comfort.
The Disappearing Microbe
A cross-sectional study of breastfed infants across eight countries found three distinct patterns of Bifidobacterium colonization—and alarmingly, infants from countries with historically lower breastfeeding rates frequently lacked any detectable Bifidobacterium at all.[15] This finding has led some researchers to warn that B. infantis may be at risk of functional extinction in industrialized populations, making probiotic supplementation increasingly relevant for supporting healthy infant development.
Bifidobacterium breve: The Early Colonizer
Bifidobacterium breve occupies a unique ecological niche in the infant gut. While B. infantis specializes in HMO metabolism, B. breve is among the earliest and most prominent Bifidobacterium species to colonize the newborn gut, playing a critical role in establishing a healthy microbial foundation during the first weeks of life.
Clinical Evidence in Vulnerable Populations
Much of the clinical evidence for B. breve comes from studies in premature infants—a population especially vulnerable to gut dysbiosis and its consequences. A comprehensive review published in Nutrients synthesized the evidence for B. breve M-16V, finding that this strain promotes early bifidobacterial colonization, may help regulate immune balance and inflammatory responses, and shows potential for reducing the risk of necrotizing enterocolitis in preterm neonates.[4]
In a randomized double-blind placebo-controlled trial involving 159 preterm neonates, B. breve supplementation significantly increased fecal Bifidobacterium counts compared to placebo, with no adverse events reported.[4] A retrospective cohort study of over 1,700 preterm neonates further supported these findings, suggesting reduced incidence of serious gut complications in the supplemented group.
Allergy Prevention
Beyond digestive health, B. breve has demonstrated promise in modulating immune responses relevant to allergic disease. Clinical studies have shown that B. breve supplementation in infants with atopic dermatitis can improve allergic symptoms while favorably shifting gut microbiota composition—increasing Bifidobacterium populations and decreasing potentially problematic aerobes.[4]
A pilot trial evaluating B. breve in infant formula showed that supplemented infants had significantly lower rates of gastrointestinal and respiratory tract infections and reduced antibiotic use compared with controls, alongside increased fecal bifidobacteria and short-chain fatty acid concentrations.[16]
Supporting Strains for Infant Gut Health
While L. reuteri, B. infantis, and B. breve carry the strongest individual evidence bases for infant applications, several additional strains contribute meaningfully to the broader microbial ecosystem that supports infant digestive health.
Lactobacillus rhamnosus
Lactobacillus rhamnosus GG is one of the most extensively studied probiotic strains worldwide, with specific pediatric evidence. Among newborns and infants, LGG colonizes the GI tract readily and has been detected in stool up to two weeks after supplementation.[17] A 2024 systematic review and meta-analysis concluded that LGG is effective in treating infantile colic, with reductions in both crying time and fecal calprotectin (a marker of intestinal inflammation).[7] LGG also demonstrates strong evidence for preventing antibiotic-associated diarrhea in children, with a meta-analysis showing it reduced the risk from 22.4% to 12.3%.[18]
Bifidobacterium lactis
Bifidobacterium lactis has been studied in pediatric contexts particularly in combination formulations. In a large RCT involving nearly 1,100 preterm infants, a probiotic combination that included B. lactis alongside B. infantis and Streptococcus thermophilus significantly reduced the incidence of NEC, with associated increases in fecal Bifidobacterium counts.[3]
Bifidobacterium bifidum and Bifidobacterium longum
Bifidobacterium bifidum and Bifidobacterium longum are among the natural residents of the healthy infant gut and contribute to the overall bifidobacterial ecosystem. Their presence supports microbial diversity and helps maintain the competitive exclusion of pathogenic organisms. Cross-sectional analyses of breastfed infants globally confirm that multiple Bifidobacterium species work together to establish gut health, with B. bifidum showing particular prevalence in populations with historically high breastfeeding rates.[15]
Streptococcus thermophilus
Streptococcus thermophilus is a well-characterized lactic acid bacterium naturally found in breast milk and commonly used in probiotic combinations for infants. Studies in premature infant populations have included S. thermophilus as part of multi-strain formulations showing reduced NEC incidence.[3] Its presence in breast milk also connects maternal yogurt consumption (which contains S. thermophilus and Lactobacillus bulgaricus) to favorable shifts in infant gut composition.[19]
Multi-Strain vs. Single-Strain Probiotics for Infants
One of the central debates in pediatric probiotic research is whether single-strain or multi-strain formulations better serve infant gut health. The answer isn't entirely straightforward and depends on the specific clinical scenario.
The Case for Targeted Single Strains
For specific, well-defined conditions like infantile colic, the evidence is clearest for single-strain interventions—particularly L. reuteri DSM 17938 in breastfed infants. Clinical guidelines from ESPGHAN (the European Society for Paediatric Gastroenterology, Hepatology and Nutrition) provide strain-specific recommendations precisely because efficacy varies dramatically between strains, even within the same species.
The Case for Multi-Strain Formulations
However, the infant gut is not dealing with just one challenge. Colic, gas, constipation, immune development, and pathogen resistance are all occurring simultaneously during a period of rapid change. A multi-strain approach may better address this complexity by providing complementary strains that occupy different ecological niches, metabolize different substrates, and produce different beneficial metabolites.
The clinical literature supports this reasoning. When B. infantis is combined with other probiotic strains, colonization and overall gut health improvements are enhanced.[3] Multi-strain probiotic combinations including Bifidobacterium and Lactobacillus species have shown benefits in reducing NEC in preterm infants and supporting broader microbiome diversity.
What matters most is that the strains included have individual evidence of benefit, are present at clinically meaningful doses, and are formulated without additives that could compromise their effectiveness. A well-formulated multi-strain probiotic provides the breadth of microbial support that matches the complexity of infant gut development.
Comprehensive Probiotic Support for the Whole Family
MicroBiome Restore contains 26 clinically relevant strains at 15 billion CFU—including Lactobacillus reuteri, Bifidobacterium infantis, Bifidobacterium breve, Lactobacillus rhamnosus, and 22 additional strains—alongside 9 organic prebiotics including acacia fiber and Jerusalem artichoke inulin. Delivered in gut-friendly pullulan capsules with zero synthetic fillers or flow agents.
What Parents Should Look For in an Infant Probiotic
Navigating the infant probiotic market can be overwhelming. Products range from single-strain drops to multi-strain powders, with wildly varying quality standards. Here's what the evidence suggests matters most.
Strain Specificity
Not all probiotics are interchangeable. The AAP has noted that benefits are strain-specific, meaning that evidence for L. reuteri DSM 17938 cannot be assumed to apply to other L. reuteri strains or to Lactobacillus species broadly. Look for products that identify specific strains, not just species names.
Clinically Studied Dosages
The effective dosage for infant colic studies with L. reuteri has typically been 108 CFU (100 million) per day. For B. infantis, successful colonization studies have used doses ranging from 109 to 1010 CFU per day. Any product making health claims should provide colony counts that align with the doses studied in clinical research.
Clean Formulation
Infants are especially vulnerable to unnecessary additives. Many probiotic products contain fillers like microcrystalline cellulose, titanium dioxide, and synthetic flow agents that serve no health purpose and may negatively impact the developing gut. When evaluating products, reading the full ingredient label—including the "other ingredients" section—is essential.
Prebiotic Support
Prebiotics feed and sustain probiotic organisms. For infants, breast milk naturally provides HMOs as prebiotics. For mothers seeking to support their own gut flora, look for prebiotics from whole-food sources like inulin from Jerusalem artichoke, acacia fiber, and maitake mushroom rather than synthetic alternatives.
Strain Evidence Summary
| Strain | Primary Infant Evidence | Strength of Evidence |
|---|---|---|
| L. reuteri DSM 17938 | Colic, constipation, GI disorder prevention | Strong (multiple meta-analyses) |
| B. infantis | Gut colonization, HMO metabolism, immune development | Strong (RCTs, mechanistic studies) |
| B. breve | NEC risk reduction, early colonization, allergy prevention | Moderate-Strong (multiple RCTs) |
| L. rhamnosus GG | Colic, antibiotic-associated diarrhea prevention | Moderate (emerging meta-analyses) |
| B. lactis | NEC prevention (in combination), GI health | Moderate (combination studies) |
| S. thermophilus | NEC prevention (in combination), natural breast milk organism | Moderate (combination studies) |
Always Consult Your Pediatrician
While the probiotic strains discussed in this article have strong safety profiles in healthy term infants, probiotic use in premature infants or immunocompromised infants should only occur under direct medical supervision. The FDA has issued specific guidance about probiotic products in hospitalized preterm infants, and clinical decisions for these vulnerable populations should always be made in consultation with neonatal specialists.
Frequently Asked Questions
What is the best probiotic strain for infant colic?
Based on the strongest available evidence, Lactobacillus reuteri DSM 17938 has the most clinical support for reducing colic symptoms in breastfed infants. Multiple meta-analyses of randomized controlled trials show it significantly reduces daily crying time and approximately doubles the likelihood of treatment success compared with placebo. Lactobacillus rhamnosus GG has also shown emerging evidence of efficacy for colic management.
Are probiotics safe for newborns?
The probiotic strains discussed in this article—particularly L. reuteri DSM 17938, B. infantis, and B. breve—have strong safety records in healthy term infants, with no adverse events reported across numerous clinical trials. L. reuteri has FDA GRAS (Generally Recognized As Safe) status, and B. breve M-16V holds GRAS status for use in infant formula. However, you should always discuss probiotic supplementation with your baby's pediatrician before starting.
Can maternal probiotics during pregnancy help my baby's gut?
Research suggests yes. Maternal probiotic supplementation during pregnancy and lactation has been shown to result in probiotic colonization of breast milk and, in some studies, detectable colonization of the infant gut. Strains like Lactobacillus rhamnosus supplemented maternally have been found in infant stool samples at 10 days and 3 months of age. Supporting your own gut health with a comprehensive probiotic formulation during pregnancy may contribute to your baby's microbial foundation.
Will probiotics help my gassy baby?
Excessive gas in infants is closely linked to gut microbiome composition. Infants with higher populations of gas-producing bacteria (particularly E. coli) and lower levels of Bifidobacterium and Lactobacillus tend to experience more gas discomfort. Probiotic strains like B. infantis, which lower gut pH through SCFA production and competitively exclude gas-producing organisms, and L. reuteri, which has anti-inflammatory effects in the intestine, may help reduce gas-related discomfort by rebalancing the gut microbial environment.
Can probiotics help with infant constipation?
Clinical evidence for L. reuteri DSM 17938 specifically shows improved bowel movement frequency in constipated infants, with significant improvements observed as early as two weeks into supplementation. While the evidence is preliminary, the safety profile is strong and the mechanism—supporting healthy gut motility through microbial balance—is well-established.
Should I choose a single-strain or multi-strain probiotic for my infant?
For a specific condition like colic in a breastfed infant, single-strain L. reuteri drops have the strongest direct evidence. However, for broader gut health support during the critical developmental window, a multi-strain approach that includes multiple evidence-based Bifidobacterium and Lactobacillus species may better address the complexity of infant microbiome development. Discuss your specific situation with your pediatrician.
Is Bifidobacterium infantis safe for babies?
B. infantis is not just safe—it's the bacterial species most closely adapted to the healthy breastfed infant gut. It has evolved specifically to thrive on human milk components and has been used safely in clinical trials involving newborns, including preterm infants. Multiple studies confirm persistent, beneficial colonization with no adverse events.
Conclusion: Building Your Baby's Microbial Foundation
The science of infant gut health has advanced remarkably in the past decade. We now understand that the microbes colonizing a baby's intestines in the first months of life aren't passive bystanders—they're active participants in digestion, immune training, and protection against pathogens. When this microbial ecosystem is disrupted, the clinical consequences—colic, gas, constipation, and potentially longer-term health issues—are increasingly well-documented.
The encouraging news is that specific, well-studied probiotic strains can help. Lactobacillus reuteri for colic, Bifidobacterium infantis for foundational gut colonization, Bifidobacterium breve for early microbial establishment, and Lactobacillus rhamnosus for immune and digestive support each bring evidence-based benefits to the developing infant microbiome.
Equally important is the understanding that gut health starts with the mother. Maternal microbiome quality during pregnancy, delivery mode, breastfeeding, and skin-to-skin contact all contribute to the microbial legacy passed to each new generation. Supporting maternal gut health with evidence-based probiotic and prebiotic supplementation represents a promising—and increasingly validated—strategy for giving infants the best microbial start.
Whatever path you choose, make decisions guided by clinical evidence, not marketing claims. Look for strain-specific research, clinically relevant dosages, clean formulations free of unnecessary fillers, and the guidance of your child's healthcare provider.
Discover Filler-Free Probiotic Support
MicroBiome Restore brings together 26 evidence-based probiotic strains—including every infant-relevant strain discussed in this article—with 9 organic prebiotics and 80+ trace minerals. No microcrystalline cellulose. No magnesium stearate. No titanium dioxide. Just research-backed ingredients in pullulan capsules designed to support your microbiome.
References
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