Despite the known effect of diet as a major factor that influences gut microbiome composition, the association between dietary patterns and nutrients and a certain type of gut microbiota composition in humans is not straightforward.

A new large cohort study of 3,409 healthy US individuals reveals that the correlations between gut microbiota, diet and host phenotypes depend on the individual’s underlying gut microbial communities.

Gut microbiome variation was mainly driven by the phyla Firmicutes and Bacteroidetes and the genera Bacteroides and Prevotella. However, the relationships between those abundant gut bacteria, gut microbiome composition and diversity markers were shaped by the presence of other taxa.

The findings show that the long used Firmicutes-to-Bacteroidetes ratio alone may not be a reliable indicator of gut microbiota composition and its association with overall health. In addition, in the light of the findings, it is clear that there is not a single healthy microbiome state; rather, multiple states can emerge involving different gut bacteria groups.

Many host factors were correlated with each other and were taken into account as cofounders in subsequent association analyses. Of all the lifestyle and clinical factors examined, 75 explained the highest variance in gut microbiome diversity, including blood clinical markers, anthropometrics, lifestyle/diet factors, frequency and duration of physical activity, and indicators of bowel health. Medication also affected not only the abundance of genera, but also gut microbiome functions in medication-users compared to non-users.

The findings show that the long used Firmicutes-to-Bacteroidetes ratio alone may not be a reliable indicator of gut microbiota composition and its association with overall health

More interestingly, associations between lifestyle behaviors, host factors and gut microbiome diversity differed in the context of different microbiome compositional states. While some host-gut microbiome associations were independent from the individual gut microbiota profile, multiple compositional clusters and cluster-specific associations have been found.

For instance, the authors found a correlation between higher gut microbiota diversity and higher vegetable intake, but only in participants who harbored an overrepresentation of Prevotella in their gut microbiota. Similarly, Christensenellaceae was negatively correlated with the consumption of cookies and pastries, but only in individuals with a gut microbiome enriched in Bacteroides.

Altogether, such identified associations between host diet, lifestyle factors and the gut microbiome can pave the way for designing personalized interventions that harness the gut microbiome. For example, considering specific gut microbiome clusters can help predict which individuals may respond better to particular dietary patterns.

On the whole, the findings suggest that the previously observed associations between diet and gut microbiota composition may not reproduce across the entire human population as they may depend on the underlying species diversity of each person’s gut microbiome. The current study supports the challenge of identifying causal relationships between host-associated microbiome and disease, which is largely driven by human lifestyle and physiological characteristics that should be matched in order to avoid confounding microbiota analyses.


Manor O, Dai CL, Kornilov SA, et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun. 2020;11(1):5206. doi: 10.1038/s41467-020-18871-1.