The resident microorganisms in the human body, termed the microbiota, represent diverse communities of microbial species comprising a complex ecology of tens of trillions of mainly bacterial cells.

Our gut microbiota, the largest and most diverse of these communities, is in constant interaction with our body’s cells and systems (such as the immune system), and it both shapes, and is being shaped by, our health status. The particular composition and diversity of the gut microbiota are associated with many health conditions.

However, it is usually not known whether such associations are just correlative or a consequence of the health condition, or whether they might cause, or contribute to, the illness. Addressing this problem is highly challenging because of the many physiological and lifestyle differences that can exist between individuals who are healthy and those who have the illness of interest.

Such confounders — the variables that correlate with both microbiota and health status — might underlie the many discrepancies observed between the outcomes of different studies linking the composition of the gut microbiota and human health.

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