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Page 10 of 20 Linehan et al. Microbiome Res Rep. 2025;4:24 https://dx.doi.org/10.20517/mrr.2024.92

“yes” group was enriched in pathways including the reductive TCA cycle and L-methionine biosynthesis

Figure 4. Bar plots of differentially abundant ASVs within infant oral samples at the species level and the impact of perinatal factors on
oral microbiome functionality. (A) Delivery mode. (B) Feed type. Differentially abundant ASVs were identified using the ANCOM
method, with only statistically significant ASVs based on W values shown (see Supplementary Table 1 for W values); (C) Delivery mode:
Functional pathways associated with NB and CS groups; (D) Feed: Functional pathways associated with the “Breast Feeding” and
“Formula” groups. (C and D) Extended error bar plots represent the mean proportion of PICRUSt2-predicted KEGG functions, with error
bars showing the difference between groups. Bar color indicates the group with the higher proportion for the respective function.
Welch’s t-test for unequal variances was applied. Statistical significance was set at P < 0.05 (two-sided) following adjusted measures.
ASVs: Amplicon sequence variants; ANCOM: analysis of composition of microbiomes; NB: natural birth; CS: cesarean-section.

Fastidiosipila, and Alloscardovia being the most significant. Five ASVs were differentially abundant at the
species level, including Alloscardovia omnicolens (A. omnicolens), Corynebacterium coyleae, and
F. nucleatum [Figure 6A]. Hexitol fermentation was associated with the “no” antibiotic group, while the

[Figure 6B]. Regarding delivery mode, CS delivery significantly increased species richness in vaginal
samples (Chao1, P = 0.091). Following NB, five ASVs were differentially abundant, including
C. pyruviciproducens, L. iners, and B. longum [Figure 6C]. NB was associated with pathways such as
menaquinol biosynthesis, while CS delivery was linked to the Calvin-Benson-Bassham cycle and pentose
phosphate pathway [Figure 6D]. PROM significantly increased alpha diversity (Chao1, P = 0.085; Shannon,
P = 0.015). At the species level, A. omnicolens, F. nucleatum, P. lymphophilum, and B. longum were
differentially abundant in the “yes” group [Figure 6E]. In PROM comparisons, the “no” group was
associated with adenosine biosynthesis and pyruvate fermentation, while the “yes” group was enriched in
TCA cycle and glucose degradation pathways [Figure 6F].