The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes

All animals carry specialized microbiomes, and their gut microbiotas in particular are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and potentially alter ecosystem processes mediated by microbes. An example considered here is the hippopotamus (hippo) and the pools they inhabit. Hippo pool biogeochemistry and fecal and pool water microbial communities were examined through field sampling and an experiment. Sequencing using 16S RNA methods revealed that the active microbial communities in hippo pools that received high inputs of hippo feces are more similar to the hippo gut microbiome than other nearby aquatic environments. The overlap between the microbiomes of the hippo gut and the waters into which they excrete therefore constitutes a meta-gut system with potentially strong influence on the biogeochemistry of pools and downstream waters. We propose that the meta-gut may be present where other species congregate in high densities, particularly in aquatic environments. Significance Animals can have considerable impacts on biogeochemical cycles and ecosystem attributes through the consumption of resources and physical modifications of the environment. Likewise, microbial communities are well known to regulate biogeochemical cycles. This study links those two observations by showing that the gut microbiome in waste excreted by hippos can persist ex-situ in the environment and potentially alter biogeochemical cycles. This “ meta-gut ” system may be present in other ecosystems where animals congregate, and may have been more widespread in the past before many large animal populations were reduced in range and abundance.