The hallmarks of dietary intervention-resilient gut microbiome

Abstract

Maintaining equilibrium of the gut microbiome is crucial for human health. Diet represents an important and generally accessible natural channel of controlling the nutrients supply to the intestinal microorganisms. Although many studies showed that dietary interventions can specifically modulate gut microbiome composition, further progress of the approach is complicated by interindividual variability of the microbial community response. The reported causes of this variability include the baseline microbiome composition features, but it is unclear whether any of them are intervention-specific. Here, we applied a unified computational framework to investigate the variability of microbiome response measured as beta diversity in eight various dietary interventions using previously published 16S rRNA sequencing datasets. We revealed a number of baseline microbiome features which determine the microbiome response in an intervention-independent manner. One of the most stable associations, reproducible for different interventions and enterotypes, was a negative dependence of the response on the average number of genes per microorganism in the community—an indicator of the community functional redundancy. Meanwhile, many revealed microbiome response determinants were enterotype-specific. In Bact1 and Rum enterotypes, the response was negatively correlated with the baseline abundance of their main drivers. Additionally, we proposed a method for preliminary assessment of the microbiome response. Our study delineats the universal features determining microbiome response to diverse interventions. The proposed approach is promising for understanding the mechanisms of gut microbiome stability and improving the efficacy of personalised microbiome-tailored interventions.

Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention

“…28 A negative correlation between the average number of genes per microbe and alpha diversity was found, suggesting that more diverse communities are formed by specialist microbes with fewer genes. 28 The microbiomes associated with industrialized countries, like the United States, often have reduced diversity and a higher abundance of Bacteroides when compared to non-industrialized countries. 29 Many Bacteroides are generalists, meaning they contain more genes and wider metabolic potentials than specialist taxa.…”

“…28 Klimenko et al found that the strongest predictor of whether an individual would respond to a dietary intervention was the average number of genes per microbe. 28 A negative correlation between the average number of genes per microbe and alpha diversity was found, suggesting that more diverse communities are formed by specialist microbes with fewer genes. 28 The microbiomes associated with industrialized countries, like the United States, often have reduced diversity and a higher abundance of Bacteroides when compared to non-industrialized countries.…”

“…Stratification of microbiomes into enterotypes has revealed enterotype-specific predictors to dietary intervention response. 28 Klimenko et al found that the strongest predictor of whether an individual would respond to a dietary intervention was the average number of genes per microbe. 28 A negative correlation between the average number of genes per microbe and alpha diversity was found, suggesting that more diverse communities are formed by specialist microbes with fewer genes.…”

“…Stratification of microbiomes into enterotypes has revealed enterotype-specific predictors to dietary intervention response. 28 Klimenko et al . found that the strongest predictor of whether an individual would respond to a dietary intervention was the average number of genes per microbe.…”

Gut physiology meets microbiome science

“…A good basic characterisation of the faecal microbiome requires repeated analysis and those could lead to a sub-clustering by what used to be called "enterotype". Although the concept of enterotypes has been questioned, a very recent study demonstrated that the outcome of any dietary manoeuvre for example depends on the starting point represented by distinct enterotypes (Klimenko et al 2022).…”