Page 143 - Read Online

Linehan et al. Microbiome Res Rep. 2025;4:24 https://dx.doi.org/10.20517/mrr.2024.92 Page 9 of 20

Figure 3. Bar plots of differentially abundant ASVs within meconium samples at the species level. Perinatal factors are shown as green
(representing one condition) and red (representing another condition). (A) Mother antibiotic usage; (B) Delivery mode; (C) Feed type;
(D) Gender; (E) PROM. Differentially abundant ASVs were identified using the ANCOM method. Only statistically significant ASVs that
fall within a distribution based on W values, are shown. ASVs: Amplicon sequence variants; PROM: premature rupture of membranes;
ANCOM: analysis of composition of microbiomes.

Impact of perinatal factors on the maternal oral microbiome
Maternal antibiotic usage significantly affected the beta diversity of the maternal oral microbiome (R =
2
0.0877, P = 0.013). In the “no” antibiotic group, seven ASVs were differentially abundant at the genus level,
most significantly Mycoplasma, Filifactor, and Anaeroglobus. At the species level, 20 ASVs were
differentially abundant, including Streptococcus mutans, Leptotrichia hongkongensis, and Granulicatella
elegans [Figure 5A]. In the “yes” group, four ASVs were differentially abundant at the genus level, most
significantly Oribacterium and Mogibacterium. At the species level, 16 ASVs were significant, including
Oribacterium sinus and Prevotella_7 denticola [Figure 5A]. Mixed acid fermentation was associated with
antibiotic exposure [Figure 5B]. Regarding delivery mode, four ASVs were differentially abundant in the NB
group at the genus level, such as Anaerococcus and Candidatus Saccharimonas, while seven ASVs were
significantly different at the species level, including Haemophilus haemolyticus and Veillonella massiliensis
[Figure 5C]. CS-born mothers exhibited nine genus-level differences, including Filifactor and Mycoplasma,
and 18 species-level differences, such as Prevotella oris and Veillonella parvula [Figure 5C]. CS delivery was
associated with cell wall recycling pathways [Figure 5D]. PROM significantly affected the beta diversity (R
2
= 0.0874, P = 0.022). In the “no” PROM group, 15 ASVs were significant at the genus level, predominantly
Staphylococcus and Filifactor, with 36 ASVs at the species level, such as L. hongkongensis and V. parvula
[Figure 5E]. In the “yes” group, six genus-level ASVs, including Scardovia and Anaerococcus, were
significantly different, with 10 species-level differences, such as O. sinus and Capnocytophaga leadbetteri
[Figure 5E]. Thiazole biosynthesis was associated with the “no” PROM group, while nitrate reduction was
linked to the “yes” group [Figure 5F].

Impact of perinatal factors on the maternal vaginal microbiome
Maternal antibiotic usage significantly influenced the vaginal microbiome. In the “no” group, two ASVs
were differentially abundant at the genus level, most notably Clostridium sensu stricto 1 and Staphylococcus.
At the species level, Bifidobacterium longum and Lactobacillus iners were differentially abundant
[Figure 6A]. In the “yes” group, nine ASVs were differentially abundant at the genus level, with Fenollaria,