How do genetics, lifestyle, diet and the environment affect the microbiome-and then affect human health and disease?

Microbiome signatures of health and disease (from Gacesa, et al., 2022)

Research has shown that the human microbiome can play a large role in a person’s health. But how do “genetics, exposome [environmental factors], lifestyle and diet” affect the microbiome?

Featured article:

*Gacesa, R., Kurilshikov, A., Vich Vila, A. et al. (2022). Environmental factors shaping the gut microbiome in a Dutch population. Nature.

“Alterations in gut microbiota composition and function are associated with a broad range of human health disorders, including gastrointestinal and metabolic diseases and mental disorders.

“The gut microbiome is associated with diverse diseases, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition.

–Linking healthy and unhealthy microbiome patterns to childhood and current exposome, diet and socioeconomics, we observed that healthier diet, childhood and current exposures to rural environment and pets, exposure to green space and higher income share signals with healthy microbiome patterns

Adult exposures also contribute to healthy or unhealthy microbiome patterns and that the environment shapes the microbiome throughout life, meaning that microbiome-targeted therapies could be effective throughout an individual’s life.

–Smoking, a high-carbohydrate diet and exposure to NO2 and small particulate matter (PM2.5) are positively correlated with disease-linked Clostridia and Ruminococcus species

–Air pollutants negatively affect the human gut microbiota and might increase the risk of gastrointestinal diseases

–Childhood exposures to smoking, pets and rural environment are associated with the adult microbiome

–Environmental exposures can have a long-lasting effect and that the microbiome reflects an individual’s history of exposures

Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.”

For more information, see:

Microbiome/microbiota: influences on disease and behavior (from Science Bibliographies Online)

Search Science Primary Literature (database)

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