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Open Access Research article

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities

Jun Ma12, Cristian Coarfa2, Xiang Qin2, Penelope E Bonnen2, Aleksandar Milosavljevic2, James Versalovic23 and Kjersti Aagaard12*

Author Affiliations

1 Departments of Obstetrics & Gynecology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA

2 Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA

3 Pathology and Immunology, Baylor College of Medicine and Texas Children’s Hospital, 77030 Houston, TX, USA

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BMC Genomics 2014, 15:257  doi:10.1186/1471-2164-15-257

Published: 3 April 2014

Abstract

Background

Although our microbial community and genomes (the human microbiome) outnumber our genome by several orders of magnitude, to what extent the human host genetic complement informs the microbiota composition is not clear. The Human Microbiome Project (HMP) Consortium established a unique population-scale framework with which to characterize the relationship of microbial community structure with their human hosts. A wide variety of taxa and metabolic pathways have been shown to be differentially distributed by virtue of race/ethnicity in the HMP. Given that mtDNA haplogroups are the maternally derived ancestral genomic markers and mitochondria’s role as the generator for cellular ATP, characterizing the relationship between human mtDNA genomic variants and microbiome profiles becomes of potential marked biologic and clinical interest.

Results

We leveraged sequencing data from the HMP to investigate the association between microbiome community structures with its own host mtDNA variants. 15 haplogroups and 631 mtDNA nucleotide polymorphisms (mean sequencing depth of 280X on the mitochondria genome) from 89 individuals participating in the HMP were accurately identified. 16S rRNA (V3-V5 region) sequencing generated microbiome taxonomy profiles and whole genome shotgun sequencing generated metabolic profiles from various body sites were treated as traits to conduct association analysis between haplogroups and host clinical metadata through linear regression. The mtSNPs of individuals with European haplogroups were associated with microbiome profiles using PLINK quantitative trait associations with permutation and adjusted for multiple comparisons. We observe that among 139 stool and 59 vaginal posterior fornix samples, several haplogroups show significant association with specific microbiota (q-value < 0.05) as well as their aggregate community structure (Chi-square with Monte Carlo, p < 0.005), which confirmed and expanded previous research on the association of race and ethnicity with microbiome profile. Our results further indicate that mtDNA variations may render different microbiome profiles, possibly through an inflammatory response to different levels of reactive oxygen species activity.

Conclusions

These data provide initial evidence for the association between host ancestral genome with the structure of its microbiome.

Keywords:
HMP; Mitochondrial DNA haplogroup; Association; Microbiome; mtDNA SNP