Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions

Abstract

Complex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.

Opportunistic pathogens are abundant in the gut of cultured giant spiny frog (Paa spinosa )

“…However, only 12 phyla dominated each of the P. spinosa gut microbial communities and freshwater microbial communities (their relative abundances were more than 1% in at least one sample; Figure a). Similar to previous reports in other amphibians (Bletz et al., ; Colombo et al., ; Kohl et al., ), Firmicutes and Bacteroidetes were the predominant organisms detected in the P. spinosa gut microbial communities. However, Bacteroidetes and Proteobacteria were the predominant organisms in freshwater microbial communities (Figure a).…”

“…Despite the importance of gut microbiota in host health, the gut microbiota are not constant. Their structures are changed by host development, diet and habitat (Bletz et al., ; Salmerón, ; Schwartz et al., ; Wang et al., ). Analysing the effects of changes in the host habitat on gut microbiota is still a main research focus (Falony et al., ; Stappenbeck & Virgin, ).…”

Manipulation of gut microbiota during critical developmental windows affects host physiological performance and disease susceptibility across ontogeny

“…However, as these larvae neared metamorphosis (stage 35), relative community composition of the gut microbiomes converged among the three treatments. This convergence may be a result of colonization by microbes from dietary and ecological sources, whereby as amphibian gut physiology and morphology change across ontogeny, environmental microbes may displace early colonizers (Bletz et al., ; Knutie et al., ). While the above speculation is tentative at the moment, because of our small sample size for microbial sequencing, these findings are supported by our earlier study.…”

The influence of diet and environment on the gut microbial community of field crickets

“…Although Ruminococcaceae has been shown to play a key role in polysaccharide degradation (Flint, Scott, Duncan, Louis, & Forano, ), there was no significant difference in the carbohydrate metabolism between wild and CD crickets, despite huge differences in abundance. However, this could be compensated by the sheer abundance of Porphyromonadaceae in crickets on a CD diet, as there is evidence that Porphyromonadaceae also possesses genes involved in the degradation of complex carbohydrates (Hahnke et al., ), resulting in convergence of functions even though there was a difference in gut microbial composition (Bletz et al., ; Muegge et al., ). Based on the decrease of Firmicutes to Bacteroidetes ratio observed from wild crickets to those fed on CC and CD diets, we predict a shift in diet from one that is high in plant material in field populations to a laboratory diet higher in protein (David et al., ).…”