Gut microbiome and epigenetics analysis of common long-tailed macaque macaca fascicularis fascicularis and burmese long-tailed macaque m. fascicularis aurea in different habitat types

Abstract

Macaca fascicularis (long-tailed macaques) occupy a wide habitat range in Southeast Asia and are divided into 10 subspecies. Among the 10 subspecies, M. f. fascicularis (Mff) encompassed the largest distribution, and M. f. aurea (Mfa) was the only Old-World monkey reported using stone as tools to forage encased food. Previous studies indicated the distinctive genetic characteristics between the two subspecies, and Mfa primarily inhabited coastal and estuary habitats to a greater extent than the overall Mff populations. Thus, the ecological conditions appeared to be conducive to natural selection of stone-tool use behavior. Based on the current interest in an association between gut microbiota and brain development, namely the gut-brain axis, this study aimed to investigate the effect of host genetics (Mff and Mfa), habitat types (mangrove and island) and diets (human-fed foods or natural foods) on gut microbiota composition. Two populations, each of Mff and Mfa, residing on the island and in mangrove forests were recruited. In addition to their natural foods, only Mff could access to human-fed foods during the field survey. Fecal specimens (n = 30 for each population) were collected for gut microbiota analysis using 16S rRNA gene sequencing on Oxford Nanopore Technologies. Mff populations exhibited higher bacterial species richness (alpha diversity) in their gut microbiota compared to respective Mfa populations living in the same habitat types. The dominant bacterial phyla in the gut microbiota of both subspecies were Firmicutes and Bacteroidetes; however, Mfa exhibited a significantly higher relative abundance of these phyla compared to the Mff. This denoted that the composition of gut microbiota primarily differed based on variations in diet, although the influence of host genetics and habitat type should not be disregarded. Since the fecal specimen collections were performed during the COVID-19 lockdown (12 July – 6 August 2022) when the human-fed foods were diminished, an island-living, namely Koh Ped, Mff faced food scarcity. They developed stone-tool use “pound-hammering-like” behavior to forage for natural foods, i.e., oysters, which was less proficient than the pound-hammering behaviors previously reported in the Mfa and Mfa x Mff hybrids, suggesting a potential genetic contribution of Mfa to the skill of stone-tool manipulation in M. fascicularis. Koh Ped-Mff stone tool users were mostly adults and subadults, and 88% were males which might be because of the higher weight of stones used. To understand the association between gut-brain axis and stone-tool use behavior, plasma tryptophan (Trp) and serotonin (5-HT) levels were subsequently determined using the HPLC technique and compared between the Mff non-stone-tool users and the Mfa stone-tool users living in mangrove forests. Because of the very low levels of 5-HT in plasma, the current HPLC method was unable to detect it, and only Trp levels were compared in this study. Categorizing animals into three age-classes (adult, subadult and juvenile), plasma Trp levels were not significantly different within and between populations, except that the Mfa adults had higher plasma Trp levels than the Mff adults which were associated with the higher prevalence of stone-tool use. Thus, this study revealed an association of gut microbiota, dietary adaptations, and cultural behaviors, particularly stone-tool use, in these macaques, contributing to the knowledge of complex interactions between host genetics, diet, and gut microbiota.