Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

Abstract

Background Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in field conditions. To explore solutions to this limitation, we have used a noninvasive approach via fecal RNA-seq, for the quantification of gene expression markers in gastrointestinal cells of free-range primates and a forager human population. Thus, a combination of poly(A) mRNA enrichment and rRNA depletion methods was used in tandem with RNA-seq to quantify and compare gastrointestinal gene expression patterns in fecal samples of wild Gorilla gorilla gorilla ( n = 9) and BaAka hunter-gatherers ( n = 10) from The Dzanga Sangha Protected Areas, Central African Republic. Results Although only a small fraction (< 4.9%) of intestinal mRNA signals was recovered, the data was sufficient to detect significant functional differences between gorillas and humans, at the gene and pathway levels. These intestinal gene expression differences were specifically associated with metabolic and immune functions. Additionally, non-host RNA-seq reads were used to gain preliminary insights on the subjects’ dietary habits, intestinal microbiomes, and infection prevalence, via identification of fungi, nematode, arthropod and plant RNA. Conclusions Overall, the results suggest that fecal RNA-seq, targeting gastrointestinal epithelial cells can be used to evaluate primate intestinal physiology and gut gene regulation, in samples obtained in challenging conditions in situ. The approach used herein may be useful to obtain information on primate intestinal health, while revealing preliminary insights into foraging ecology, microbiome, and diet. Electronic supplementary material The online version of this article (10.1186/s12864-019-5813-z) contains supplementary material, which is available to authorized users.

Gut health, stress, and immunity in neonatal dairy calves: the host side of host-pathogen interactions

“…Isolation of mRNA from total fecal RNA may improve the sensitivity of the RT-qPCR analysis since we have previously [ 86 ] observed that total fecal RNA contains a significant amount of bacterial RNA and this has been confirmed via RNA-seq data in primates [ 89 ]. In Fig.…”

“…The intestinal epithelial cells act as a barrier against pathogens, and the daily shedding of these cells into feces has been used in rodents and humans as a source of RNA to evaluate gene expression in the gastrointestinal tract (GIT) [ 88 ]. This method has also been used to find transcriptomic similarities in the GIT between humans and wild primates [ 89 ]. Using a similar approach, RNA was isolated from fecal samples that our group refer to as “fecal RNA” from neonatal dairy calves [ 86 ].…”

“…Parallel to this increase in fecal scores, it was observed an increase in blood biomarkers associated with inflammation (i.e., IL-6, ceruloplasmin, and haptoglobin) and upregulation in pro-inflammatory genes (i.e., TLR4 , TNFA , IL8 , and IL1B ) in fecal RNA. Although this technique is promising, and it has been used by other research groups in rodents [ 90 ] and humans [ 89 , 91 ], we consider that further optimization and validation steps are required in order to improve accuracy and robustness. For instance, the migration of polymorphonuclear leukocytes (PMNL) across the intestinal epithelium is a natural pathological event of many mucosal inflammatory diseases [ 92 ].…”

“…Robust data can be generated with the application of high-throughput molecular techniques such as RNAseq to study the transcriptome in RNA isolated from fecal samples, which have been consistently reported across different species mouse [ 98 ], infants [ 91 ], wild primates [ 89 ]. However, when analyzing specific genes in fecal RNA through RT-qPCR has been proven challenging.…”

“…Thus, RT-qPCR is more suited than omics methods, to investigate specific genes in a longitudinal format, for instance, during intestinal maturation, diarrhea events, specific pathogen infections (e.g., ETEC), or heat stress. The nuance we have observed in our laboratory when optimizing an RT-qPCR protocol for fecal RNA are: Isolation of mRNA from total fecal RNA may improve the sensitivity of the RT-qPCR analysis since we have previously [ 86 ] observed that total fecal RNA contains a significant amount of bacterial RNA and this has been confirmed via RNA-seq data in primates [ 89 ]. In Fig.…”