Abstract
The multi-omic integration of microbiota data with metabolomics has gained popularity. This protocol is based on a human multi-omics study, integrating cervicovaginal microbiota, HPV status and neoplasia, with urinary metabolites. Indeed, to understand the biology of the infections and to develop adequate interventions for cervical cancer prevention, studies are needed to characterize in detail the cervical microbiota and understand the systemic metabolome. This article is a detailed protocol for the multi-omic integration of cervical microbiota and urine metabolome to shed light on the systemic effects of cervical dysbioses associated with Human Papillomavirus (HPV) infections. This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches.
Highlights
A growing body of evidence, especially over the last twelve years, suggests that the composition and function of the microbiota in different human body habitats play vital roles in human development and immunity [1,2,3]
We are assisting a new stage of microbiome research, which moves beyond the typical 16S profiles listing bacteria associated to a given body site or disease, and offers the novel integration of other omics approaches, towards a better understanding of community functions in the disease, and interactions with the host
Since circulating metabolites are excreted through urine [51], recent studies suggest that exploring the association between urine metabolome and host microbiome may complement sequencing-based approaches with a functional readout of the host microbiome and its interaction with host [52,53]
Summary
A growing body of evidence, especially over the last twelve years, suggests that the composition and function of the microbiota in different human body habitats play vital roles in human development and immunity [1,2,3]. HPV infections in the vagina and cervix can produce metabolites which translocate through the host’s barriers, that could influence systemic health effects in women at risk of developing cervical cancer. Biomarkers for cervical cancer may be exfoliated as debris in urine, a kind of liquid biopsy—which could facilitate diagnostics [1] It is, important to develop protocols to help integrate information between the microbiome, viral pathogenesis, and immunity affecting cancer progression. The coupling of two omic methods is a useful approach to understand the association of the human microbiome with health status and risk of disease severity, and for the development of new point-of-care testing technologies
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