Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Abstract

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance

“…This index quantifies the availability of nearby genome representatives for each microbiome sample, and indicates the average divergence between each OTU and the reference genome in the Greengenes database (Langille et al, 2013). We obtained an average NSTI of 0.06 ± 0.01 and 0.17 ± 0.12 for wild and captive samples, respectively, which are within the previously estimated ranges for non-human mammals (Langille et al, 2013) and are coherent with scores obtained for similar studies (Mao et al, 2015; Sullam et al, 2015). These low values suggest accurate predictions for molecular functions of microbial communities in the GI tract of wild and captive Andean bears.…”

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp

“…More recently, high‐throughput sequencing of 16S rRNA gene amplicons has been used to explore the diversity and composition of gut microbiota in fish species, including three‐spined stickleback and Eurasian perch (Bolnick et al ., ), fathead minnows (Narrowe et al ., ), surgeonfishes (Miyake et al ., ), Trinidadian guppies (Sullam et al ., ), tilapia (Giatsis et al ., ), Atlantic cod (Forberg et al ., ), Atlantic salmon (Llewellyn et al ., ) and some commercially viable cyprinids (Eichmiller et al ., ; Liu et al ., ). Most of these fishes were studied in the rearing conditions fed basic diet or in wild conditions, which well demonstrated the influence of basic dietary input and environmental locations on the gut microbiota.…”

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

“…2015; Org et al. 2015; Sullam et al. 2015), widespread, evolved differences in digestive tract gene expression among populations are a potential mechanism connecting host genotype to microbial phenotype in stickleback.…”