Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging

elderly subjects have a statistically significantly higher GM biodiversity than young controls, elderly subjects classified as unhealthy have a statistically significantly lower GM biodiversity than both healthy elderly and young controls. The analysis of the ELDERMET T0 data set also allowed us to confirm the results about the consistence and statistical power of the estimate of biodiversity obtained from the 2NB model. When performing the hypothesis tests based on classical biodiversity indices, in fact, we obtain results that are in agreement with those revealed by θrare and θabundant (S9 Fig), even if not all classical indices are able to detect all the differences between the three groups (S9 Fig). More- over, when ranking biodiversity indices according to the p-values, it turns out that the most significant results are obtained with θrare or θabundant for all comparisons, except that of healthy versus unhealthy elderly subjects, in which Simpson obtaines the smallest p-value (0.0028), fol- lowed by θrare (p-value = 0.0165), while none of the other indices detects a stastically significant difference (Fig 5 and S9 Fig). This supports the hypothesis that estimating biodiversity through the 2NB model provides more statistical power. GM biodiversity predicts health status in old age We assessed the ability of the GM biodiversity estimated by the 2NB model to predict the health status in the elderly considering the ELDERMET T0 data set. To this aim, we fitted a lin- ear regression model between health status and GM biodiversity adjusted for sex and total

number of reads, and we evaluated the results obtained with GM biodiversity estimated by Fig 3. Spline model for θabundant. The splines model corresponding to each individual data set is shown. In each plot, dots correspond to subjects, the x-axis is given by the subject age and the y-axis is the standardized value of θabundant. Black lines and gray shadows represent the data set specific regression lines and confidence intervals. https://doi.org/10.1371/journal.pone.0237207.g003 PLOS ONE Gut microbiota biodiversity and healthy aging PLOS ONE | https://doi.org/10.1371/journal.pone.0237207 October 30, 2020 9 / 23