Milk Consumption and Blood Microbiome in Healthy Volunteers

eDNA (ecological DNA) is a concept that is gaining popularity for making comprehensive descriptions of all organisms present in an ecosystem. Gut microbiomes can be considered a specific variant of eDNA. In theory, a description of the gut microbiome should contain all different kinds of microorganisms in our gastrointestinal tract, including bacteria, viruses, archaea, fungi and other organisms (e.g. worms and phages). In practice, making such descriptions is challenging because of spurious temporal changes and technical challenges (e.g. the commonly used 16S rRNA approach ignores many organisms). Nevertheless, making accurate descriptions is essential as it is generally accepted that the gut microbiome plays critical roles in maintaining host homeostasis and health.

To overcome the challenges in sampling the intestinal microbiome, most investigators currently rely on probing faeces. We have pioneered the field in developing improved technical approaches; for example, we previously performed a double-balloon endoscopic study in healthy volunteers to characterize this microbiome in its entirety. Problems with the faecal microbiome include its poor capture of the adherent flora (which seems the most relevant concerning human physiology), it is highly heterogeneous and can cause results to differ depending on which part of faecal samples was taken, and technological challenges, as many eukaryotes are quite resistant to DNA isolation protocols. Additionally, the faecal microbiome is dominated by diet, which can vary substantially from day to day in humans. For example, faecal material deriving from breakfast can have a significantly different microbiological composition compared to that derived from dinner. Hence, there is a call for alternatives.

The blood microbiome is a newly discovered way of probing the microbiome, integrating the colonization of all kinds of body sites, particularly the intestinal tract. It is speculated that the DNA fragments of various microorganisms enter the circulation through mechanisms that are yet fully understood. The gastrointestinal microbiome is considered a major source of blood microbiome, especially in the case of an impaired gut barrier, which can occur in various chronic diseases.

The description of the entire body of cell-free DNA fragments that derive from non-human origin is called the blood microbiome, even though it does not constitute living organisms, but rather their remnants. The blood microbiome signature has been reported as a predictable biomarker in differentiating patients with cancer from healthy individuals and even for distinguishing between different cancer types. However, the approach remains very controversial due to bioinformatical pitfalls. While we have invested substantial energy in resolving the issues involved, the field requires a formal proof-of-concept to progress. The current study is meant to provide this.

• Changes in other microbial DNA counts [Time frame: 10 days before milk consmuption, 0, 1, 2 and 7 days during milk consumption]