Microbiome sampling time series and developmental milestones for the Amboseli baboons.

Plot (A) shows microbiome samples from female baboons, and plot (B) shows samples from male baboons. Each point represents a microbiome sample from an individual subject (y-axis) collected at a given host age in years (x-axis; n=8,245 samples from 234 females shown in yellow; n=5,231 samples from 197 males shown in blue). Light and dark point colors indicate whether the baboon was sexually mature at the time of sampling, with lighter colors reflecting samples collected prior to menarche for females (n=2,016 samples) and prior to testicular enlargement for males (n=2399 samples). Due to natal dispersal in males, we have fewer samples after the median age of first dispersal in males (n=1,705 samples, 12.6% of dataset) than from females after the same age (n=4408 samples, 32.6% of dataset). The timelines below the plots indicate the median age in years at which (C) female baboons attain the developmental milestones analyzed in this paper—adult rank, menarche and first live birth—and (D) males attain adult rank, testicular enlargement, and disperse from their natal groups (55, 56). The age at which 75% of animals in the population have died is shown to indicate different life expectancies for females versus males (63). Baboon illustrations courtesy of Emily (Lee) Nonnamaker.

Microbiome features change with age.

(A) and (B) show the percent mean relative abundance of microbial phyla across life for females and males respectively. Panel (C) shows the estimates of the linear associations between mean-centered age for metrics of microbiome alpha diversity and principal components of microbiome compositional variation that exhibited significant associations with age (FDR < 0.05). Positive values are more abundant in older hosts. Panel (D) shows the estimate of the linear association between mean-centered age and the top 50 microbiome features that exhibited significant associations with age. Positive values are more abundant in older hosts. Panel (E) shows the average value of the microbiome features from (C) as a function of age, across all subjects. Note that sample sizes for patterns beyond age 20 years rely on 256 samples from just 18 females; hence, we interpret the pattern in these oldest animals with caution. Panel (F) shows the average prevalence of the higher taxonomic designations from (D) as a function of age, across all subjects. In (C-F) points are colored by the category of the feature (see legend). UC is an abbreviation for uncharacterized. Features that had a significant quadratic age term are indicated by * (see also Figure S2; Table S1).

Microbiome clock age predictions in wild baboons.

Panels (A) and (B) show predicted microbiome age in years (agem) from a Gaussian process regression model, relative to each baboon’s true chronological age in years (agec) at the time of sample collection. Each point represents a microbiome sample. Panel (A) shows linear fit for all subjects in the model; (B) shows separate linear fits for each sex (Table S4). Dashed lines show the 1-to-1 relationship between agec and agem. Panel (A) also shows the measurement of sample-specific microbiome Δage compared to chronological age. Whether an estimate is old- or young-for-chronological age is calculated for each microbiome sample as the difference between agem and agec. Because of model compression relative to the 1-to-1 line, we correct for host chronological age by including chronological age in any model. An example of an old-for-age sample is shown as a red point, with dashed lines showing the value of agec for a given sample with its corresponding agem.

Comparison of Gaussian process regression model performance between sexes. Model accuracy was determined based on the correlation between known chronological age (agec) and predicted age (agem), the variance explained in agec by agem (R2), and the median absolute difference between agec and agem

(40).

Social and environmental factors predicting variation in microbiome Δage in female and male baboons. Models below only show variables that minimize the Akaike information criterion (AIC) for each model; see Table S6 for full models. Coefficients for social dominance rank are transformed so higher values reflect higher rank/social status (see footnotes).

Social dominance rank predicts gut microbiome Δage in male and female baboons (corrected for confounders).

Panels (A) and (B) show the relationship between host proportional dominance rank and corrected gut microbiome Δage in (A) males (blue points) and (B) females (yellow points). Each point represents an individual gut microbiome sample. Corrected microbiome Δage is calculated as the residuals of agem correcting for host chronological age, season, monthly temperature, monthly rainfall, and social group and hydrological year at the time of collection.