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Page 8 of 20 Linehan et al. Microbiome Res Rep. 2025;4:24 https://dx.doi.org/10.20517/mrr.2024.92

mother’s vaginal microbiome; (E) Number of ASVs shared between mother oral and infant meconium dyad samples; (F) Relative
abundance of infant meconium microbiome shared with their mother’s oral microbiome; (G) Number of ASVs shared between mother
vaginal and infant meconium dyad samples; (H) Relative abundance of infant meconium microbiome shared with their mother’s vaginal
microbiome. ASVs: Amplicon sequence variants.

Impact of perinatal factors on the meconium microbiome
Maternal antibiotic usage modestly impacted meconium beta diversity (R = 0.0764, P = 0.069). In the “no”
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antibiotic group, 16 ASVs were differentially abundant at the genus level, including Eubacterium hallii
group and Dialister, with 8 significant ASVs at the species level, such as Blautia obeum and Bacteroides
fragilis [Figure 3A]. In the “yes” group, 15 ASVs, including Pantoea and Enterobacter, were significant at the
genus level, with 8 species-level differences, including Ruminococcus bromii and Gemella sanguinis
[Figure 3A]. The “yes” group was also associated with the enrichment of heme biosynthesis pathways
[Supplementary Figure 7A]. C-section delivery increased species richness (Chao1, P = 0.07). NB infants had

10 differentially abundant ASVs at the genus level, such as Cloacibacterium and Bifidobacterium, and 8 at
the species level, including Bifidobacterium longum [Figure 3B]. CS-born infants showed 21 significant
ASVs at the genus level, including Fusicatenibacter and Eubacterium eligens, with 7 species-level differences
like Veillonella tobetsuensis [Figure 3B]. NB infants were associated with heterolactic fermentation
[Supplementary Figure 7B]. Breastfeeding was associated with 21 differentially abundant ASVs at the genus
level, including Delftia, and 11 at the species level, such as Bacteroides vulgatus [Figure 3C]. Formula-fed
infants showed 14 genus-level differences, including Eubacterium eligens group, and 7 species-level
differences, such as Blautia obeum [Figure 3C]. Breastfeeding was associated with fatty acid oxidation
pathways [Supplementary Figure 7C]. Gender differences revealed 10 significant ASVs in males, including
Gemella, and 11 at the species level, such as Anaerostipes hadrus [Figure 3D]. Females showed 15 genus-
level differences, including Massilia, with 7 species-level differences like Rothia dentocariosa [Figure 3D].
For PROM births, 29 ASVs were more abundant in the “no” group at the genus level, including
Eubacterium eligens group, with 12 species-level differences, such as Blautia obeum [Figure 3E]. The “yes”
group showed 8 genus-level differences, including Delftia, and 8 species-level differences, such as
Ruminococcus bromii [Figure 3E].

Impact of perinatal factors on the infant oral microbiome
In this study, maternal antibiotic usage, PROM, and gender had no significant effects on the infant oral
microbiome. Regarding delivery mode, six ASVs were differentially abundant in NB infants at the genus
level, most significantly Parvimonas, Anaeroglobus, and Oribacterium. At the species level, 12 ASVs were
differentially abundant in NB infants, most significantly Bifidobacterium longum, Veillonella atypica, and
Veillonella parvula [Figure 4A]. In CS-born infants, 18 ASVs were differentially abundant at the genus level,
most significantly Lautropia, Enhydrobacter, and Kocuria, with 16 ASVs differentially abundant at the
species level, including Lautropia mirabilis (L. mirabilis), Corynebacterium durum, and Veillonella rogosae
[Figure 4A]. NB infants were associated with peptidoglycan biosynthesis, while CS-born infants were
enriched in L-tryptophan biosynthesis and fatty acid salvage pathways [Figure 4B and C]. Feed type had a
significant effect on beta diversity (R = 0.1148, P = 0.049). In breastfed infants, 27 ASVs were differentially
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abundant at the genus level, most significantly the Eubacterium brachy group, Parvimonas, and
Anaeroglobus, with 27 species-level ASVs, including Prevotella saccharolytica, Treponema maltophilum, and
Johnsonella ignava [Figure 4B]. Formula-fed infants had 14 genus-level differences, most significantly
Lautropia, Acinetobacter, and Escherichia-Shigella, with 15 species-level differences, including Streptococcus
oralis, Gemella morbillorum, and Veillonella atypica [Figure 4C]. Breastfeeding was associated with hexitol
degradation, while formula feeding was linked to fatty acid salvage [Figure 4D].