Abstract
Simple SummarySince the advent of microbiome research, this field has seen an explosion of both techniques and subfields. Researchers have aimed not only to classify microbiome membership and diversity among varying hosts, but to also identify and understand new and novel microbial lineages. This wealth of knowledge continues to grow, and with it the potential to use microbiome databases as diagnostic tools. This diagnostic application is of great importance and interest in zoological settings, as it may provide a non-invasive assessment of animal health. However, before this tool can be utilized in zoos, more data are needed to assess the extent of microbial variation characteristics to each host species to know what may be problematic versus normal. The aim of this research was to characterize variation of the microbiome at the individual level within managed populations of western lowland gorillas in three zoological institutions.The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the “normal” state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish “typical” patterns of GI microbial richness and diversity, as well as inter-individual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three zoological institutions in North America. Fecal samples were collected from 19 western lowland gorillas every two weeks for seven months (n = 248). Host identity and host institution significantly affected GI microbiome community composition (p < 0.05), although host identity had the most consistent and significant effect on richness (p = 0.03) and Shannon diversity (p = 0.004) across institutions. Significant changes in microbial abundance over time were observed only at Denver Zoo (p < 0.05). Our results suggest that individuality contributes to most of the observed GI microbiome variation in the study populations. Our results also showed no significant changes in any individual’s microbial richness or Shannon diversity during the 7-month study period. While some microbial taxa (Prevotella, Prevotellaceae and Ruminococcaceae) were detected in all gorillas at varying levels, determining individual baselines for microbial composition comparisons may be the most useful diagnostic tool for optimizing non-human primate health under human care.
Highlights
The richness and Shannon diversity of a host’s microbiome are affected by a multitude of factors including the host’s age, diet, health, phylogeny, season, and sex [1,2,3,4,5,6,7,8,9,10]
After rarefaction a total of 196 samples remained for downstream analysis
We identified 10,446 distinct operational taxonomic unit (OTU) across all samples, with 9722 of these OTUs classified beyond the domain level (Figures 1 and 2)
Summary
The richness (the number of distinct microbial taxa in a biological sample) and Shannon diversity (which incorporates richness as well as the relative evenness of representation of taxa) of a host’s microbiome are affected by a multitude of factors including the host’s age, diet, health, phylogeny, season, and sex [1,2,3,4,5,6,7,8,9,10]. Other studies have assessed disease or life stage effects, such as development of the microbiome within human infants and non-human primates [7,9,14,15,16,17,18]. These studies, were frequently restricted by which host species were included, a low number of individuals sampled over time, and/or short sampling periods. Few other host species have large enough datasets that include longitudinal sampling from sufficient individuals to determine whether their microbiomes display the same plasticity across individuals as the human microbiome [1]. While the gut microbiome may provide useful indicators of several life stages and health conditions, its current utility is currently limited
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