Estimating the causal effect of body mass index on gut microbiota variation

The gut microbiome is a complex ecosystem which has population-level variation in composition and abundance known to be associated with body mass index (BMI). The nature of these relationships is largely unknown and potentially confounded by environment, diet and other behavioral traits. We used fecal 16S rRNA data from 2,225 individuals from the Flemish Gut Flora project to derive 368 microbiota traits (MTs) including diversity, abundance, presence, or absence, enterotype class and abundance ratio. We assessed the relationship between BMI and those traits in observational and Mendelian randomization (MR) frameworks, the latter being used to estimate a causal effect of BMI on MT variation. We found that 141 (38%) of MTs associated with BMI in observational analyses. These estimates showed concordance with those from MR, suggesting that BMI has a broad influence on gut MTs. Evidence here was strong enough to suggest causal BMI effects for 41 MTs (11% of all those tested). This included a reduction in overall diversity, a decrease in the abundance of genera Barnesiella of phylum Bacteroidetes (B) and a decrease in the abundance of genera Sporobacter of phylum Firmicutes (F) with higher BMI. There was also an increase in the ratio of genera Roseburia to genera Sporobacter (F/F), genera Oscillibacter to Sporobacter (F/F), genera Bacteroides to Sporobacter (B/F), and Bacteroides to Barnesiella (B/B) with increases in BMI. The log-odds of assignment to enterotype Bacteroides2 increased and – in females – the presence of genera Adlercreutzia decreased with higher BMI. Previous studies have implied that variation in the gut microbiome influences BMI, but the present results support the conclusion that relationships between BMI and microbiome variation are, at the very least, bi-directional.