Gain or Loss of Specific Microbial Species May Be a Better Measure of Gut Microbiome Aging

It now costs little to determine the contents of the gut microbiome, producing a list of microbial species and their prevalence. Numerous companies offer this service. This data can be sliced in numerous ways, but as researchers note here, it is the gain and loss of specific populations with advancing age that produces contributions to aging. More general measures of diversity or change, those that give little to no weight to which specific microbial populations alter in abundance, do not produce good correlations with degenerative aging. It is important to consider the actions and mechanisms of specific microbes: are they causing chronic inflammation, are they generating beneficial or harmful metabolites, and so forth.

The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity, and infection. Aging-related health loss has been correlated with transition to different microbiome states. There is broad consensus how the microbiome changes with age, but specific intervention targets are less clear. Moreover, terms like diversity, assumed by many to be desirable, and 'uniqueness', which has been cast as a marker of healthy aging, need greater precision and should not be used agnostic of the loss or gain of specific taxa in aging. Other summary statistics include different measures of uniqueness that capture specific aspects of gut microbiome variability and are calculated using different distance measures.

This study explored whether determining the gain or loss of specific taxa represent a more precise metric of healthy/unhealthy aging than summary microbiome statistics, such as diversity and uniqueness. We analyzed microbiome diversity and four measures of microbiome uniqueness in 21,000 gut microbiomes for their relationship with aging and health. We show that diversity and uniqueness measures are not synonymous; uniqueness is not a uniformly desirable feature of the aging microbiome, nor is it an accurate biomarker of healthy aging. Different measures of uniqueness show different associations with diversity and with markers of health and disease.

The study identifies that the gut microbiome alterations associated with both aging in general and unhealthy aging are characterized by a common theme: loss of the core microbiome structure (specifically a coabundant species-level guild of the core microbiome) and concomitant increase of a specific guild of disease-associated taxa.


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