Table 2.

Descriptive summary of item selection.

Authors (Year)	Study Design	Number of Patients	Materials and Methods	Outcomes
K. Korpela et al., 2018 [83]	Randomized clinical trial	428 infants	The study conducted an analysis of the GM composition in 428 infants at 3 months of age using fecal samples and 16S rRNA gene amplicon sequencing. Mothers were randomized into control and treatment groups during pregnancy, with the treatment group receiving a mixture of specific bacterial strains. Infants continued to receive these capsules after birth, and fecal samples were collected for analysis. Information on birth mode, breastfeeding, formula feeding, and antibiotic use was obtained through questionnaires.	Newborns’ microbiota composition was significantly influenced by probiotic supplementation; breastfed newborns had higher levels of bifidobacteria and lower levels of proteobacteria and clostridia. Probiotics reversed or lessened the effects of antibiotic usage and birth mode, which were linked to altered microbiota in the placebo group.
B. C. Wilson et al., 2021 [84]	Randomized clinical trial	47 babies	Healthy babies born through cesarean delivery were randomly assigned to receive either sterile water (CS-placebo, n = 13) or a 3 mL solution of maternal vaginal microorganisms (CSseeded, n = 12). Neonatal infants born vaginally (VB, n = 22) served as the reference control. Clinical evaluations were performed within the first two hours after birth as well as at one and three months of age. Shotgun metagenomic sequencing was performed on maternal vaginal extracts and infant stool samples from CS women. The composition of the GM at one month of age was the main result. The functional potential of the gut microbiome, maternal strain engraftment, anthropometry, body composition, and adverse events were all secondary outcomes.	The results showed that vaginal seeding had no discernible effect on the microbiome development of CS-born infants, particularly with regard to Bacteroide colonization, regardless of the dosing technique. Therefore, for infants born through CS, maternal fecal microbiota transplantation (FMT) might be a more successful strategy. Additionally, it was discovered that intrapartum antibiotic prophylaxis (IAP), which is frequently used during CS, decreased the exposure of newborns to maternal microbes and might have a deleterious impact on the survivability of transplanted microbes. In summary, this pilot study suggests that the oral administration of maternal vaginal microbiota did not significantly affect the early gut microbiome of CS-born infants, questioning the utility of this procedure in reducing disease risk.
K. M. Tonon et al., 2021 [85]	Cross-sectional study	48 infants	This study involved a subset of mother–infant pairs participating in a cross-sectional observational study aimed at identifying factors associated with human milk oligosaccharide (HMO) concentrations. The participants included healthy full-term singleton infants who were exclusively breastfed and had not received antibiotics, probiotics, water, or any other food besides human milk. Human milk and infant fecal samples were collected at one month postpartum and processed for analysis. Human milk samples were stored at −20 °C for HMOs analysis. Infant feces were collected from disposable diapers, preserved in an ASL buffer, and stored at −20 °C for DNA extraction. The study involved analyzing the fecal microbiota composition through 16S rRNA gene sequencing, and the main bacterial genera and species were quantified using a qPCR with specific primers. Standard curves for quantification were created using reference gene fragments, and results were expressed as bacterial units per gram of feces (U/g of feces). The detection limit for all organisms was 1 cell/g.	The researchers found that infants born through cesarean had lower levels of Bacteroides, less B. longum, and higher levels of Akkermansia as well as Kluyvera in their GM. Despite these differences, the overall composition of the microbiota did not differ significantly between infants born through cesarean and those born vaginally, provided they were breastfed by secretory mothers. In addition, the study noted an increased presence of Verrucomicrobia and Akkermansia, mainly in CSe+ infants. Akkermansia is a bacterium involved in immune regulation and promotion of the intestinal barrier function, which also is associated with lower risks of obesity and allergies in infants. Another distinctive observation was the higher prevalence of proteobacteria, particularly Serratia and Kluyvera, in this group. This differed from previous studies, probably because of socioeconomic differences between the populations.
C. Mei Chien et al., 2017 [86]	Randomized Clinical Trial	152 babies	Infants were given either a non-hydrolyzed cow’s milk-based formula (control formula), a prebiotic formula supplemented with 0.8 g/100 mL of scGOS/lCFOS, or a synbiotic formula supplemented with B. breve M-16V (Morinaga Milk Industry Co. Ltd.) at a dose of 7.5 108 cfu/100 mL. As a reference group, vaginally delivered infants were included. From birth (1–3 days at the latest) until 16 weeks of age (the intervention phase), and study formulae were given. At day 3, day day 5, week 2, week 4, week 8, week 12, and week 22, stool samples were taken.	This study showed that supplementation with scGOS/lcFOS and B. breve M-16V contributes to the early colonization of bifidobacteria in infants born through CS, reproducing the physiological conditions of the intestinal microbiota observed in vaginally born infants. Positive effects have also been observed in terms of the reduction in adverse events such as skin disorders, particularly eczema/atopic dermatitis.
Ilias Lagkouvardos, 2022 [87]	Randomized Clinical Trial	540 infants	-Synbiotic intervention formula (IF) containing Limosilactobacillus fermentum CECT5716 and galacto-oligosaccharides. -Measurement of metabolites (e.g., short-chain fatty acids) and milieu parameters (e.g., pH, humidity, and IgA) in stool samples.	-Fecal microbiota analysis through 16S rRNA amplicon sequencing at 4, 12, and 24 months of age. -Significant changes in microbiota profiles with age. -Closer overall phylogenetic profiles of infants receiving IF to those fed with human milk at month 4. -Association of these microbiota states with higher prevalence of infants born through CS.
Wenqing Yang et al., 2021 [88]	Observational Cohort Study	26 neonates	-Neonates divided into four groups as follows: VD (natural delivery neonates, n = 3), CD (cesarean-born neonates, n = 9), CDL (cesarean-born neonates supplemented with a probiotic at a lower dosage, n = 7), CDH (cesarean-born neonates supplemented with a probiotic at a higher dosage, n = 7) -Sequencing of the V3–V4 region of the 16S ribosomal ribonucleic acid gene through next-generation sequencing technology	-α-diversity of intestinal microbiota significantly lower in cesarean-born neonates on the 28th day compared with naturally delivered neonates (p = 0.005). -Abundances of Lactobacillus and Bifidobacterium significantly increased from the 3rd day of probiotic supplementation. -Impact of probiotic supplementation on the diversity and function of GM.
Christophe Lay et al., 2021 [89]	Double-blind randomized controlled study	153 infants	Newborns’ microbiota compositions were significantly influenced by probiotic supplementation; breastfed newborns had higher levels of bifidobacteria and lower levels of proteobacteria and clostridia. Probiotics reversed or lessened the effects of antibiotic usage and birth mode, which were linked to altered microbiota in the placebo group.	Babies delivered vaginally had an environment in their guts that was hypoxic and acidic, with a higher concentration of stringent anaerobes (Bifidobacteriaceae). Enterobacteriaceae enrichment is a sign of a damaged microbiome in infants born after cesarean delivery.
Joanne E Sordillo et al., 2017 [69]	Clinical trial	333 infants	Microbial diversity was calculated using the Shannon index, and 16S rRNA gene sequencing was employed for infants’ stool samples.	White race/ethnicity was associated with lower diversity but higher Bacteroidetes coabundance scores. CS birth was associated with higher diversity but decreased Bacteroidetes coabundance scores. Infants born through CS had higher firmicutes scores. Infants that were breastfed showed reduced levels of Clostridiales. Vitamin D in cord blood is associated with a rise in Lactococcus but a decrease in lactobacteria.
Pin Li et al., 2023 [90]	Randomized, placebo-controlled trial	109 infants	Saliva and stool samples collected at weeks 0, 4, 8, and 12 from infants aged 6–24 months born through CS.	-Fecal pH increase in the control group (p = 0.003). -No change in fecal pH in the experimental group. -Salivary cortisol decrease in the experimental group (p = 0.023). -Little change in cortisol in the control group. -No obvious effect on fecal calprotectin and saliva sIgA. -Enhancement of Lactobacillus content.
Thomas Dierikx et al., 2022 [91]	Randomized controlled trial	CS group (n = 40); vaginal group (n = 23)	Microbiota analyzed through 16S rRNA gene sequencing and whole-metagenome shotgun sequencing. Data collected at 1, 7, and 28 days after birth and at 3 years.	-Microbial diversity and composition compared between CS and vaginal groups in the first month of life. -Abundance changes in specific bacterial genera noted. -Comparison of microbiome at 3 years of age. -Confirmation of CS delivery’s impact on microbiome colonization.
Yang Liu MD et al., 2023 [10]	Randomized clinical trial	A total of 120 pregnant women were divided into two groups as follows: a “vaginal seeding” group (n = 60) and a control group (n = 60).	This randomized controlled trial was conducted at the Liuyang Maternal and Child Health Care Hospital in China to investigate differences in GM between infants born through cesarean delivery and those born through natural childbirth. In the “vaginal seeding” group, sterile gauze soaked in sterile saline solution was inserted into the maternal vagina one hour before delivery and then used to gently swab the infant’s body after birth. In contrast, the control group received standard care.	The results of the study revealed that there were no significant differences in the GM between the two groups of infants. The analyses found that changes in gut bacterial composition were similar in both the “vaginal seeding” group and the control group. In addition, no significant differences in BMI (body mass index) or allergy risks were found between the two groups during the infants’ first 2 years of life.
Joanna Hurkala et al., 2020 [72]	Randomized clinical trial	The recruited infants (148) were divided into two groups as follows: the intervention group (71) and the control group (77).	Newborns were divided into two groups as follows: one group received a probiotic product with specific strains of Bifidobacterium and Lactobacillus shortly after birth, while the other group served as the control. The study aimed to investigate the impact of probiotic supplementation on the early GM of newborns born through CS. Stool samples were collected on days 5 or 6 after birth and again after one month. These samples were analyzed to assess the presence and quantity of bacterial genera and species, including beneficial ones like Lactobacillus and Bifidobacterium as well as potentially harmful bacteria.	The intervention group showed a significant increase in Lactobacillus and bifidobacteria levels in their fecal samples compared with the control group. Lactobacillus levels were high, while bifidobacteria levels were higher, indicating the effectiveness of probiotic supplementation in infants.