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Pediatric GERD and proton pump inhibitor exposure are associated with reduced microbial diversityProton Pump Inhibitors Linked to Changes in Childrens Gut Health

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Key Takeaway
Note that pediatric GERD and PPI use are associated with reduced microbial diversity and altered gut composition.

This systematic review synthesizes 31 studies regarding the impact of gastroesophageal reflux disease (GERD) and proton pump inhibitor (PPI) exposure on the pediatric microbiome and associated clinical outcomes. The authors identify a consistent association between these conditions and reduced microbial diversity. Furthermore, evidence suggests changes in bacterial composition across Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria.

Specific findings include an increase in the similarity of microbiota between aerodigestive compartments, which may suggest microbial transfer via reflux or aspiration. PPI exposure was associated with increased numbers of oropharyngeal bacteria in the gut, a decrease in beneficial taxa like Bifidobacterium, and an increase in potentially pathogenic genera such as Streptococcus and Enterobacteriaceae. While an association between PPI use and small intestinal bacterial overgrowth was noted, these results were inconsistent.

The authors highlight significant limitations including heterogeneous evidence and confounding factors, which prevent the establishment of a causal relationship between GERD or PPI use and specific microbiome changes. Clinical utility is currently limited by these uncertainties; prospective longitudinal and mechanistic studies are required to clarify causality.

How this fits prior evidence

This systematic review addresses a gap in understanding how pediatric gastroesophageal reflux disease (GERD) and proton pump inhibitor (PPI) therapy affect the gut microbiome. While prior coverage established that lifestyle modification and optimized PPI therapy are first-line treatments for GERD, this review adds detail regarding the specific microbial consequences of those interventions in children, such as reduced diversity and increased risk of infections.

A systematic review of 31 studies looked at how gastroesophageal reflux disease (GERD) and the use of proton pump inhibitors (PPIs) affect the gut health of children. The researchers found that children with these conditions often had lower microbial diversity, which means fewer types of healthy bacteria in their systems.

The study also noted changes in specific bacterial groups and an increase in similarities between different areas of the digestive tract. This suggests that reflux or aspiration might cause bacteria to move between compartments. Additionally, PPI use was linked to a decrease in beneficial bacteria like Bifidobacterium and an increase in potentially harmful types like Streptococcus.

While some evidence suggested a link between PPIs and small intestinal bacterial overgrowth, these results were inconsistent across the studies. Because the data comes from many different sources, researchers cannot say for certain that these changes are directly caused by the medication. These findings highlight the need for more long-term studies to understand how these treatments affect children's health over time.

What this means for you:
PPI use in children with GERD is linked to lower gut microbial diversity and potential shifts in bacterial balance.

Common questions

How do proton pump inhibitors affect a child's gut?

The review of 31 studies found that children using these medications often show reduced microbial diversity. This means there are fewer types of bacteria in the gut. The study also noted a decrease in beneficial bacteria like Bifidobacterium and an increase in potentially harmful groups such as Streptococcus and Enterobacteriaceae.

Are there risks associated with these medications for children?

The research indicates that proton pump inhibitor use is associated with an increased risk of infections and allergic diseases. However, because the evidence is heterogeneous and influenced by many factors, a direct cause-and-effect relationship between the medication and specific microbiome changes cannot be firmly established.

Is there a link to bacterial overgrowth?

The study found some association between proton pump inhibitors and small intestinal bacterial overgrowth. However, these results were inconsistent across the different studies reviewed. Because of this inconsistency, the findings are not yet clear enough to confirm a definitive link.

Study Details

Study typeMeta analysis
EvidenceLevel 1
PublishedAug 2026
View Original Abstract ↓
IntroductionGastroesophageal reflux disease (GERD) and proton pump inhibitor (PPI) therapy have both been associated with alterations of the developing gastrointestinal microbiome and potential downstream clinical consequences in children. However, available evidence is fragmented across disease-related, treatment-related, and mechanistic studies, making the overall biological relationship difficult to interpret.MethodsPubMed, Web of Science, and Scopus databases were queried for the period January 2000 to May 2026 to synthesize evidence across the pathophysiological continuum linking pediatric GERD, microbiota alterations, inflammatory mechanisms, PPI exposure, and microbiota-associated clinical outcomes.ResultsThe review included studies evaluating children with GERD as well as mechanistic studies involving pediatric upper gastrointestinal conditions requiring PPI therapy when microbiota-related outcomes were relevant to the review objective. Study selection was performed according to PRISMA guidelines, 31 of which were included in the final analysis. The data indicate that pediatric exposure to GERD and PPI is associated with changes in the gastrointestinal microbiota at multiple levels (oral, esophageal, gastric, and intestinal). These changes include reduced microbial diversity, changes in bacterial composition (particularly Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria), and increased similarity of microbiota between aerodigestive compartments, suggesting possible microbial transfer associated with reflux or aspiration. PPI exposure has been frequently associated with increased numbers of oropharyngeal bacteria in the gut, decreased beneficial taxa (e.g., Bifidobacterium), and increased numbers of potentially pathogenic genera (e.g., Streptococcus, Enterobacteriaceae). Several studies have reported an association between PPI and small intestinal bacterial overgrowth, but the results are inconsistent. PPI use has also been reported to be associated with an increased risk of infections, allergic diseases, and other systemic effects, coupled with the recognition of limited clinical benefit of PPI therapy in GERD in infants.ConclusionPediatric GERD and PPI exposure are associated with alterations in the gastrointestinal microbiome and possible systemic clinical effects. Most evidence is heterogeneous and influenced by confounding factors, which limits the establishment of a causal relationship. Prospective longitudinal and mechanistic studies using standardized microbiome methodologies are required to clarify causality and better define the respective contributions of GERD and PPI therapy to microbiota alterations and their clinical significance.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/view/CRD420261405291, identifier CRD420261405291.
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