Data from: The meta-gut: community coalescence of animal gut and environmental microbiomes
This is the data and R code necessary to reproduce the findings in the manuscript, "The meta-gut: community coalescence of animal gut and environmental microbiomes." 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, and share gut microbiota between individuals.
Steps to reproduce
Microbial sequences were obtained from an Illumina Miseq then processed using Dada2 on an Amazon Machine Image (AMI) of RStudio. A Phyloseq object was then created. These analyses begin with the phyloseq object. There are two folders in this dataset, 2017 and 2018. Sampling took place in two separate years. Only samples sequenced together were analyzed together. Raw sequences will be deposited in Genbank. The dada2.R file was used to process the sequences on a server. There are .RMD files in each folder. These are the R Markdown files that were used to run a full set of analyses from the phyloseq objects (ps2017.rds and ps2018.rds). The HTML file with the same name as the .RMD file is the compiled output from the .RMD file.