Multiomics characterization of the zoo-housed gorilla gut microbiome reveals loss of bacterial diversity besides abundant fungal cellulose-degrading and archaeal methanogenic activity

Abstract

AbstractWe carried out a comparative analysis between the microbiota composition of zoo-housed western lowland gorillas (Gorilla gorilla gorilla) and their counterparts living in the wild through 16s rRNA gene amplicon sequencing. In addition, we characterized the carbohydrate active potential and activity of the zoo-housed gorilla microbiome through shotgun metagenomics and RNA-seq. Alpha and beta-diversity indices significantly decreased in the zoo-housed gorilla microbiota compared to those of their wild fellow species. Abundant fiber-degrading native bacterial taxa of the wild gorilla gut, Chloroflexi andOlsenella, vanished, whereas oligosaccharide-consumingLactobacillusspecies blossomed in presumably, the upper gastro-intestinal-tract of the zoo-housed gorilla. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA-sequencing revealed diverse cellulase and hemi-cellulase activities in the zoo-housed gorilla gut, contributing to a total of 268 identified carbohydrate active enzymes. We demonstrated for the first-time major activity of the cellulose-degrading fungi Neocallimastigomycetes and methanogenic archaea in the gorilla gut, the latter known to feed on hydrogen produced by the anaerobic fungi. We propose that the zoo-housed gorilla microbiome is adapted in composition and reduced in bacterial diversity due to lifestyle effects, while a previously unacknowledged fiber-degrading capacity is sustained by anaerobic gut fungi. Our study shows the added value of RNA-seq in a multiomics approach and highlights the contribution of eukaryotic and archaeal activity to the gorilla gut microbiome.