Patterns of gut bacterial colonization in three primate species

Abstract

Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

Fig 1. GIT diagrams [49] and feeding strategies for (A) Varecia variegata, (B) Lemur catta, and (C) Propithecus sifaka, projected onto a phylogenetic tree [28].

H: If the succession process in lemurs is similar to that described in humans, then microbial diversity should be lowest in samples from birth and increase with age until weaning, with decreasing intraspecific variability as individuals approach adulthood and their GMs approach the climax community. We refer to this as the “life stage” hypothesis.

Fig 2. Composition of 16S libraries sequenced in duplicate from 58 fecal samples, collected from 15 lemurs belonging to Varecia variegata, Lemur catta, and Propithecus coquereli.

Samples were collected from infants at (i) birth, (ii) nursing, (iii) introduction of solid foods, (iv) regular consumption of solid foods, (v) weaning, (vi) weaned, and from dams at parturition (p). Infants’ ages are listed below each life stage. The samples collected from each species during the introduction of solid foods are also bracketed and indicated with asterisks. Technical duplicates sequenced from each sample are paired and arranged so that infants’ results are repeated in the same order within each life stage and so that dams’ order corresponds to their infants’. Results are shown at the (A) phylum level and (B) genus level.

Fig 3. Weighted PCoA of OTU beta diversity between libraries.

The distance in PCoA vector space represents community membership (i.e. taxa in Fig 2). Each data point in represents a library (i.e. bar in Fig 2). The distance between points represents unique branches on a phylogenetic tree (i.e. evolutionary history not shared between libraries in Fig 2). Closer points share more branch length, while points more distant from one another have more unique or disparate GMs. Dashed lines connect samples from a representative individual from each species, and represent species-specific trajectories. Representative individuals were chosen based on the completion of longitudinal sampling and quality of sample sequencing. Dashed circles indicate samples collected from animals after they begin consuming solid foods regularly.

Fig 4. Inter-individual GM variation within species.

Weighted UniFrac distances were averaged to plot GM variation at each life stage. The distances between replicate libraries (sequenced from the same fecal sample) were omitted from average calculations. Distance could not be calculated for Propithecus coquereli at birth or for Varecia variegata at parturition because only one sample was collected at these time points.

Fig 5. Shannon-Weaver biodiversity values, averaged at each life stage within species.

Fig 6. Bacterial lineages that distinguish 16S libraries sequenced from fecal samples collected from lemurs at (A) introduction of solid foods and (B) regular consumption of solid foods.

Differentially distributed lineages are ranked based on their linear discriminant analysis effect size. The average percent contribution of each lineage is listed in parentheses.