Health disparity in early childhood caries: Unveiling the potential ethnicity-specific microbiome
Creators: name: C. Hsu, Kuei-Ling
name: Shaffer, Isaac
name: Furstenau, Tara
name: Ernst, Robert
K.
name: Y Fofanov, Viacheslav
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310204
subject: Genomics and transcriptomics
classificationCode: 310206
subject: Sequence analysis
classificationCode: 310505
subject: Gene expression (incl. microarray and other genome-wide approaches)

description: The dataset contains all of the original figures and tables for the publication. It also includes custom R scripts for performing the differential expression analysis and a Jupyter notebook for an interactive figure comparing significantly differentially expressed genes between the African American and Hispanic groups. All_Genes_AA_HIS_Summary includes raw results for all genes including those that were not significantly differentially expressed.Figures<b>Figure 1. African American and Hispanic children have both functionally and taxonomically distinct pathways for caries development.</b> In this study we compared gene expression between paired caries-active and non-caries plaque within the same children using a novel analysis tool that provides species-level gene resolution. By analyzing genes that were significantly differentially expressed in caries plaque in African American and Hispanic children, we found similar patterns of gene expression from organisms typically associated with caries formation, but we also found many differences between the two groups. We conclude that while several species act as required core species in both groups, they each follow a functionally and taxonomically unique path to caries progression.<br><b>Figure 2. Organisms traditionally associated with caries disease showed differential expression in many genes in the disease samples and this pattern was shared by both the African American and Hispanic groups.</b> Genes from other organisms showed differential expression predominantly in either the African American or Hispanic group. The figure shows the significantly differentially expressed genes for disease samples from the top organisms and functional groups. Gray lines indicate genes that were differentially expressed in both the African American and Hispanic groups. Purple and orange lines indicate genes that were only significantly differentially expressed in either the African American or the Hispanic group, respectively.<br><b>Figure 3. Genes that were significantly upregulated in both African American and Hispanic groups were predominantly associated with S. mutans and other bacterial species commonly linked with caries while the significantly down regulated genes were associated with species and functions involved in acid neutralization and inhibition of caries.</b> The figure shows the distribution of species associated with genes that were significantly upregulated (A) or downregulated (B) in caries plaque in both the African American and Hispanic groups. The values on the right side of each chart is the total number of genes in each bar. The legend on the right is proportional to the overall number of genes associated with the upregulated (N=6,967) or downregulated (N=676) genes. The functional categories shown are those that had the highest percent of shared KEGG orthologues (KOs).<br><b>Figure 4. The African American and Hispanic groups showed many functional and taxonomic differences in significantly upregulated genes.</b> The figure shows the distribution of genes that were significantly upregulated in only the African American (left, N=1,746) or Hispanic (right, N=5,683) groups. The colors represent the proportion of genes from the top 8 species in each group and the colors represent different species in each chart. Except for C. acnes, there was no overlap in the top species between the two groups. The numbers on the right of each chart are the total number of genes in each functional category. The size of the bars in the legend is proportional to the total number of upregulated genes from each species.<br><b>Figure 5. The African American and Hispanic groups showed many functional and taxonomic differences in significantly downregulated genes.</b> The figure shows the distribution of genes that were significantly downregulated in only the African American (left, N=3,224) or Hispanic (right, N=836) groups. The colors represent the proportion of genes from the top 8 species in each group and the colors represent different species in each chart. There was no overlap in the top species between the two groups. The numbers on the right of each chart are the total number of genes in each functional category. The size of the bars in the legend is proportional to the total number of downregulated genes from each species.<br><b>Figure 6. The organisms that fill certain functional roles are different between the African American and Hispanic groups.</b> The figure on the left shows KOs that are differentially expressed in both groups but by completely non-overlapping species. The colors indicate the species associated with each differentially expressed gene and the bar at the top shows the overall distribution of species shown in the table. The figure on the right shows an overview of which organisms are most commonly taking over the same functions in each group.<br>Supplementary MaterialsSupplemental Table S1: Subject metadata.Supplemental Table S2: Sequencing depth for caries and non-caries plaque samples from ECC cohort and caries-free cohort.Supplemental Table S3: Consistently dominant taxa in ECC cavity microbiome vs paired non-cavity plaque samples.Supplemental Table S4: Taxa included in the gene reference database downloaded from KEGG.Supplemental Table S5: List of genes that were significantly differentially expressed in African American and Hispanic groups.Supplemental Figure S1: Species accumulation curve from taxonomic composition analysis of ECC vs Caries-free samples.Supplemental Figure S2: Species accumulation curve from taxonomic composition analysis of Hispanic vs African American ECC samples.Supplemental Figure S3: PCA plot showing that the caries-free samples cluster similarly with the non-caries plaque from the ECC cohort.Supplemental Figure S4: The African American and Hispanic caries samples showed differences in the functional pathways that were differentially expressed.