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Given the inability to consistently replicate or independently validate studies linking G. vaginalis and Lactobacillus spp. to preterm birth, differences in the ethnic or racial makeup of risk-disparate cohorts may be masking underlying true associations. As we and others have published on associations between genetic polymorphisms of the host mitochondrial genome and the microbiome, including the gut and vagina, we sought to evaluate the association of the vaginal microbiome with mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) as risk-modifiers of preterm birth (PTB).
WGS paired-end reads identified as host were aligned to the human mitochondrial reference genome (NC_012920.1) using BWA and variant calls were generated using samtools. Only SNPs were considered for subsequent analysis. Species/mtSNP associations were performed using PLINK with the variants considered a haploid genotype and taxa a quantitative trait. For associations between variants, species and PTB, we utilized the quantitative trait interaction algorithm using term and PTB as the covariate groups. Resultant p-values were corrected for False Discovery Rates (FDR).
Although a number of significant taxa-SNP associations were identified in WGS (n=1588) (Figure1A), these associations were all in relatively minor taxa and did not include the major landmark species driving the vaginal community, including L. crispatus, L. iners, L. jensenii or G. vaginalis. With respect to PTB, five SNP-species associations identified by WGS metagenomics were significantly different between term and PTB subjects (Figure1B). However, post-hoc comparisons revealed these to be minor taxa present at low abundance and frequency – Propionibacterium acnes, Haemophilus haemolytica, Veillonella atypica, Veillonella parvum, and Lactobacillus mucosa (Figure1C).
Given the significance in disparity of preterm birth between racial and ethnic groups, it is logical to consider the role of mitochondrial genetics and the microbiome. However, within this study, when we rigorously accounted for race and ethnicity using mitochondrial DNA sequencing we failed to observe an association. This was not due to underpowering, since; we identified taxa-by-mtDNA SNP associations among rare species in the vaginal microbiome. However, they were weakly predictive of PTB.