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Borrego-Ruiz et al. Microbiome Res Rep. 2025;4:20 https://dx.doi.org/10.20517/mrr.2024.78 Page 5 of 22

Avershina L. rhamnosus strain GG Infants in the probiotic group exhibited a higher relative abundance of L. rhamnosus at ten days
[41]
et al. and three months of age compared to the control group. However, this difference was not
sustained at twelve months or two years. No significant differences were observed between the
probiotic and placebo groups in terms of α- or β-diversity of the total microbiota in infant stool
samples at three months or two years of age
Korpela Probiotics: B. breve, P. The probiotic supplementation had a significant overall impact on microbiota composition, but
et al. [42] freundenreichii subsp. shermanii the effect was influenced by the diet of the infant. In breastfed infants, those receiving
strain JS, and L. rhamnosus probiotics showed a higher relative abundance of lactobacilli and bifidobacteria compared to
strain GG controls. However, other taxa (clostridia and Gammaproteobacteria) were less abundant in the
Prebiotic: GOS probiotic group. In formula-fed infants, there was a slight but significant decrease in total
bifidobacteria in those supplemented with probiotics. In addition, the genera Anaerostipes,
Klebsiella, and Veillonella were more abundant in the formula-fed probiotic group compared to
the formula-fed control group
Pärnänen Combination 1: L. rhamnosus No significant differences were observed in the abundance of antibiotic resistance genes
et al. [43] strain LPR and B. longum between the probiotic and placebo groups in the infants
Combination 2: L. paracasei and
B. longum

Plummer B. longum subsp. infantis strain Infants who received probiotics had a higher abundance of Bifidobacterium and a reduced
[44]
et al. BB-02, Streptococcus presence of Enterococcus compared to the placebo group during the supplementation period
thermophilus strain TH-4 and B.
animalis subsp. lactis strain BB-
12
Castanet Probiotic: B. animalis subsp. A significant correlation between changes in microbiota composition and the gut maturation
[45]
et al. lactis marker calprotectin was found. While B. animalis subsp. lactis increased in the probiotic-
Prebiotic: BMOS supplemented groups, it remained a minor part of the overall fecal Bifidobacterium composition.
The authors concluded that the prebiotic component of the synbiotic mixture had a more
substantial impact on the observed shift in gut microbiota than the probiotic component
[46]
Martí et al. L. reuteri strain DSM 17938 Probiotic supplementation led to greater bacterial diversity and an increased abundance of L.
reuteri during the first month. At one week, supplementation also resulted in a reduced
abundance of Enterobacteriaceae and Staphylococcaceae. No significant effects were observed at
two years
Bargheet B. longum subsp. infantis strain Both microbiota-altering treatments (antibiotics and probiotics) were associated with an
et al. [47] ATCC 15697 and Lactobacillus increased presence of mobile genetic elements in preterm infants compared to term controls.
acidophilus strain ATCC 4356 Thus, antibiotics and probiotics contribute to dynamic changes in the resistome, mobilome, and
gut microbiota, which are relevant to infection risk
GM: Gut microbiome; GOS: galactooligosaccharide; BMOS: bovine milk-derived oligosaccharides.

shifts in other bacterial groups . Ismail et al. found no significant impact of prenatal L. rhamnosus strain
[35]
GG supplementation on infant microbial diversity . Probiotic treatment had varying effects on the GM
[36]
composition of Finnish and German infants, attributable to discrepancies in feeding modes and early
commensal microbiota. The authors also reported that maternal administration of L. rhamnosus strain GG
during the late stages of pregnancy did not modulate diversity in the early infant gut microbiota, despite
promoting a beneficial bifidobacteria profile. Pärtty et al. reported that 94 preterm infants receiving
L. rhamnosus strain GG, prebiotics, or placebo did not show significant effects on overall microbial
diversity, but the probiotic group had lower Clostridium histolyticum levels . Furthermore, the provision of
[37]
early prebiotic and probiotic supplementation was shown to mitigate symptoms related to crying and
fussing in preterm infants, suggesting a novel preventive approach for this prevalent disturbance in early
life. Enomoto et al. showed that probiotic supplementation with Bifidobacterium longum (B. longum) and
B. breve resulted in higher Bacteroidota abundance in infants at 4 months, although no differences were
observed at 10 months . These findings indicate that the administration of bifidobacteria during the
[38]
prenatal and postnatal periods is effective in preventing allergic diseases. Bisanz et al. noted that
L. rhamnosus supplementation to mothers led to higher Bifidobacterium relative abundance in infants at 10-
[39]
25 days . The consumption of Moringa-supplemented probiotic yogurt was shown to enhance
Bifidobacterium relative abundance and to reduce the presence of Enterobacteriaceae in the feces of
newborns. However, these effects were not observed in the maternal microbiota across all body sites. The
oral and gut microbiota remained stable throughout pregnancy, while the vaginal microbiota exhibited a
substantial increase in diversity around birth and in the postpartum period. Rutten et al. pointed out that a