Faecal proteomics as a novel method to study mammalian behaviour and physiology

Abstract

Mammalian faeces can be collected noninvasively during field research and provide valuable information on the ecology and evolution of the source individuals. Undigested food remains, genome/metagenome, steroid hormones, and stable isotopes obtained from faecal samples provide evidence on diet, host/symbiont genetics, and physiological status of the individuals. However, proteins in mammalian faeces have hardly been studied, which hinders the molecular investigations into the behaviour and physiology of the source individuals. Here, we apply mass spectrometry-based proteomics to faecal samples (n = 10), collected from infant, juvenile, and adult captive Japanese macaques (Macaca fuscata), to describe the proteomes of the source individual, of the food it consumed, and its intestinal microbes. The results show that faecal proteomics is a useful method to: (i) investigate dietary changes along with breastfeeding and weaning, (ii) reveal the taxonomic and histological origin of the food items consumed, and (iii) estimate physiological status inside intestinal tracts. These types of insights are difficult or impossible to obtain through other molecular approaches. Most mammalian species are facing extinction risk and there is an urgent need to obtain knowledge on their ecology and evolution for better conservation strategy. The faecal proteomics framework we present here is easily applicable to wild settings and other mammalian species, and provides direct evidence of their behaviour and physiology.

Keywords: Japanese macaque; breastfeeding and weaning; diet; intestinal condition; proteomics.

FIGURE 1

Schematic illustration of known breastfeeding and weaning patterns in Japanese macaques (see Supporting Information for more details) and the details of the analysed faecal samples (see Table S1 for more details)

FIGURE 2

Number of protein groups detected from Faecal samples by the age of the individuals at the time of sample collection. Schematic illustrations of the amount of consumed breast milk and solid foods during infancy are also shown. (a) Number of macaque, food, and bacterial protein groups. (b) Number of milk‐specific and antimicrobial protein groups. (c) Number of food protein groups. (d) Number of Bifidobacterium and Lactobacillus protein groups

FIGURE 3

Venn diagrams of the macaque protein groups detected from breast milk (Beck et al., 2015), faeces of breastfed individuals (MF06, MF07, MF10, and MF11), and faeces from nonbreastfed individuals (MF05, MF12, MF03, MF02, MF00, and MF01). See Table 1 for the detailed information of the milk proteins shown