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BMC Genomics. 2019 Jun 14;20(1):493. doi: 10.1186/s12864-019-5813-z.

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

Author information

1
Department of Animal Science, University of Minnesota, Twin Cities, USA.
2
The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.
3
Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic.
4
Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Praha, Czech Republic.
5
Vanderbilt University medical center Technologies for Advanced Genomics, Vanderbilt University medical center, Nashville, TN, USA.
6
WWF Central African Republic, Bangui, Central African Republic.
7
Department of Anthropology, University of Colorado, Boulder, CO, USA.
8
Loyola University Chicago, Quinlan Life Sciences Building, Chicago, IL, USA.
9
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.
10
Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, MN, USA.
11
The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic. petrzelkova@ivb.cz.
12
The Czech Academy of Sciences, Biology Centre, Institute of Parasitology, Branišovská 31, 370 05, České Budějovice, Czech Republic. petrzelkova@ivb.cz.
13
Liberec Zoo, Lidové sady 425/1, 460 01, Liberec, Czech Republic. petrzelkova@ivb.cz.
14
Department of Animal Science, University of Minnesota, Twin Cities, USA. gomeza@umn.edu.

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.

KEYWORDS:

Gene expression; Nonhuman primate; Noninvasive method; RNA-seq

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