Nowak2014_Dryad

Results of individual-based simulations conducted to estimate the number of founding individuals responsible for the colonization of Mauritius by Coffea

Patterns of Gut Bacterial Colonization in Three Primate Species

<div><p>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) <i>Varecia variegata</i>, generalist <i>Lemur catta</i>, and folivorous (leaf-eating) <i>Propithecus coquereli</i>. 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.</p></div

Number of subjects and fecal samples from each lemur species.

<p>Number of subjects and fecal samples from each lemur species.</p

NowakPlastidData_4Dryad

Plastid sequence alignment used for divergence time estimation in the genus Coffea

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

<p>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.</p

Composition of Gut Microbial Communities Characterized in Different Non-human Primates.

<p>^aValues are proportions of the phylogenetic lineages reported for each next generation sequencing library.</p><p>^bLemur values are averaged over the following life stages: regular consumption of solids, weaning, weaned, and parturition.</p><p>^cXu et al. 2013[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124618#pone.0124618.ref017" target="_blank">17</a>] data reported are for metagenomic libraries sequenced from pooled samples from two wild Pygmy Lorises.</p><p>^dOchman et al. 2010[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124618#pone.0124618.ref014" target="_blank">14</a>] data are values for 16S Sanger sequencing libraries averaged within species for 2 <i>Gorilla beringei</i>, 2 <i>Gorilla gorilla</i>, 5 <i>Pan paniscus</i>, 8 <i>Pan troglodytes troglodytes</i>, 5 <i>Pan troglodytes schweinfurthii</i>, and 2 <i>Pan troglodytes ellioti</i>.</p><p>Composition of Gut Microbial Communities Characterized in Different Non-human Primates.</p

cytB and IRBP Data Set

cytB and IRBP Data Se

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.

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

Tests to detect GM differences between lemur clades.

<p>Tests to detect GM differences between lemur clades.</p

NowakSAlleles_4Dryad

Alignment of Coffea S-RNase allele sequences used for evaluating the extent of trans-specific polymorphism between Madagascan/African Coffea and Mauritian Coffea