Background The gut microbiome is crucial for maintaining overall host homeostasis and metabolism, but it can be significantly affected by dietary changes, leading to substantial temporal variations in microbial composition both within and between individuals. Despite these variations, fecal sampling remains the standard for microbiome assessment. Recently, the blood microbiome, which reflects the microbial DNA circulating in the bloodstream, has emerged as a potentially more stable and integrated alternative. Preliminary data suggest that analyzing blood microbiomes may provide more consistent insights than fecal samples.

Method/Design This study will test the validity of the blood microbiome as a representative of the gut microbiome. Using a prospective, single-arm crossover trial, the researchers will evaluate the effect of milk consumption on the composition of milk-associated intestinal bacteria (MAB) in the blood of healthy volunteers aged 18-65. Participants will first abstain from dairy products, which is expected to reduce MAB cell-free DNA in the bloodstream. They will then reintroduce milk, during which MAB DNA is anticipated to reappear in the blood. Changes in blood MAB levels will be tracked using shotgun sequencing. Longitudinal sampling of this process will provide critical evidence for the existence of a common blood microbiome and refine the bioinformatic pipeline for its analysis.

Conclusion This pilot trial will determine whether blood MAB is a valid surrogate marker for gut MAB, potentially offering a more consistent alternative to traditional microbiome assessments.

Clinical Trial Registration NCT06944002

The authors have declared no competing interest.

NCT06944002

This project is funded in part through a grant (KICH2.V4P.22.015) of the Dutch Organization for Scientific Research and the Dutch Cancer Foundation.

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Ethics committee of Erasmus Medical University Center Rotterdam gave ethical approval for this work

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