Human gut microbiome as a composite health biomarker

Using a cohort of 893 adults who underwent medical check-ups with rich data collection across diet, lifestyle, clinical labs, cardiac stress testing, and microbiome profiling, we show that a gut microbial health index (MHI), originally defined using a large meta-analysis of various human disease cohorts, is also substantially associated with lifestyle and diet. This association persists across the overall cohort, disease-free subsets, and individuals with common medical conditions such as hypertension and dyslipidemia. The gut MHI was positively correlated with factors such as variation in cardiac stress test fitness, fiber intake, and well-being, and negatively correlated with exposure to ultra-processed foods and markers of subclinical inflammation (WBC and CRP mostly within normal limits). Lipidomics profiling of a subcohort revealed that triglycerides correlate positively with ultraprocessed foods, and negatively with unsaturated fats, olive oil, and nuts, linking diet, MHI, and lipid profile. Estimating the contribution of modifiable dietary and lifestyle factors to the MHI uncovers actionable ways to improve or worsen the personal MHI. Analyses of previously published intervention studies showed that the MHI responds quickly to dietary changes, within the predicted range. Our findings emphasize the potential of using microbiomes, and specifically the MHI, as a reporter of overall health.