Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy

Abstract

Maternal asthma status, prenatal exposures, and infant gut microbiota perturbation are associated with heightened risk of atopy and asthma risk in childhood, observations hypothetically linked by intergenerational microbial transmission. Using maternal vaginal (n = 184) and paired infant stool (n = 172) samples, we identify four compositionally and functionally distinct Lactobacillus-dominated vaginal microbiota clusters (VCs) that relate to prenatal maternal health and exposures and infant serum immunoglobulin E (IgE) status at 1 year. Variance in bacteria shared between mother and infant pairs relate to VCs, maternal allergy/asthma status, and infant IgE levels. Heritable bacterial gene pathways associated with infant IgE include fatty acid synthesis and histamine and tryptophan degradation. In vitro, vertically transmitted Lactobacillus jensenii strains induce immunosuppressive phenotypes on human antigen-presenting cells. Murine supplementation with L. jensenii reduces lung eosinophils, neutrophilic expansion, and the proportion of interleukin-4 (IL-4)⁺ CD4⁺ T cells. Thus, bacterial and atopy heritability are intimately linked, suggesting a microbial component of intergenerational disease transmission.

Keywords: Lactobacillus; asthma; atopy; immune tolerance; inherited bacteria; microbiota; prenatal; transmission; vaginal; vaginal microbiota.

Graphical abstract

Figure 1

Maternal vaginal microbiota during pregnancy stratifies into four distinct clusters (A) Schematic of the study design, harmonizing biospecimens, and metadata from the MAAP and WISC cohorts. (B) Hierarchical clustering identifies four compositionally distinct vaginal microbiota clusters (VCs I–IV; PERMANOVA R² = 0.347, p = 0.001). Shown is a principal coordinates analysis (PCoA) plot of Bray-Curtis distance using 16S rRNA gene sequence variants (SVs); each point represents a maternal vaginal profile. (C) Mean relative abundance of maternal vaginal bacteria in each VC derived from 16S rRNA amplicon sequence variant analysis. 184 biological replicates are shown. See also Figure S1 and Tables S1 and S2.

Figure 2

Shared bacterial SVs associate with VC and maternal asthma during pregnancy (A) Shared SVs, identified as those with more than 10 reads in maternal vaginal and infant stool microbiota within dyads are indicated in red; SVs not shared between mother-infant pairs are indicated in blue. Each column represents SVs shared within a mother-infant dyad. SVs are ordered by phylogeny and were included when they were shared in at least three dyads. (B) Top five shared taxa for each VC or across all clusters (right). (C) Maternal asthma status significantly relates to principal coordinate 1 (PC1; unweighted UniFrac) of shared SVs; t test for significance. 172 biological replicates are shown. See also Figure S2 and Table S3.

Figure 3

Functional capacity of shared bacteria is distinct in infants with detectable IgE at 1 year Heatmap of machine learning-selected pathways among shared metagenomic reads that discriminate infants with or without detectable IgE at 1 year of age. Shared metagenomic reads were identified by requiring identical sequence alignment between mother and infant metagenomic datasets, shown in log-transformed copies per million for each. MetaCyc annotated reactions are described by their catalyzing enzyme. 7 biological replicates are shown. See also Figures S2 and S3 and Table S4.

Figure 4

Comparative genomics of fetal L. jensenii isolates (A) Hierarchical clustering of whole-genome average nucleotide identity (ANI) of all available genomes of L. jensenii, several reference Lactobacillus genomes, and fetal meconium isolates L01 and L02 indicates greatest homology with L. jensenii. (B) Phylogenetic trees of single-copy conserved genes across select publicly available genomes within Lactobacillus and fetal meconium isolates L01 and L02 confirm greatest similarity with L. jensenii strains. (C) 16S rRNA V4 region of fetal meconium isolates L01 and L02 compared with SVs in our study indicate greatest homology with SV22 detected in maternal vaginal samples. When available strain origin is represented, hierarchical clustering was performed on ANI; an asterisk indicates a reference or a representative genome. Escherichia coli K12 and fetal M. luteus were used as outgroups in (B) and (C), respectively. See also Figure S4 and Tables S5, S6, and S7.

Figure 5

Vertically transmitted Lactobacillus isolates promote tolerance in primary human APCs (A and B) CD83 and CD86 expression is reduced (A) and CD103 expression increased (B) among live CD45⁺ HLA-DR⁺ fetal splenocytes after 4 h of treatment with fetal isolates L01 or L02 compared with the medium control and additional fetal strain Micro36 as well as non-fetal strains of L. iners and M. luteus. Representative flow cytometry plots with median ± SEM are shown on the left. Two-sided Satterthwaite’s method on the linear mixed effects (LME) model was used to test for significance, controlling for repeated measures of cell donor across treatments. Box plots indicate quartiles of the data distribution. Each dot represents a biological replicate, with at least n ≥ 3 per treatment.

Figure 6

Vertically transmitted Lactobacillus L01 and Micro36 strains ameliorate airway allergic sensitization in vivo (A) Murine HDM intra-tracheal sensitization and challenge (itHDM) scheme in animals orally gavaged with meconium-isolate L. jensenii L01 or M. luteus Micro36 or PBS. (B–D) Percentage of (B) lung eosinophils, (C) neutrophils, and (D) CD4⁺ T cells among CD3⁺ live cells in lungs of animals after HDM sensitization across treatment groups. Two-sided Satterthwaite’s method of the linear mixed effects (LME) model test for significance, with random effect attributed to experimental repeat. (E) Representative flow plots of intracellular IL-4 production in CD4 T cells within the mediastinal lymph node (medLN). (F–H) Percentage of (F) IL-4⁺ (G), IL-17A⁺, and (H) IFNγ⁺ T cells in the medLN (left) and mesenteric lymph node (MLN; right) in animals after allergic sensitization. ANOVA test for significance. .Shapes (triangles and circles) indicate mice from two independent experiments. Each treatment group had 5 mice as biological replicates, and the experiment was repeated independently twice. See also Figure S5.