Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model

Abstract

Red-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural lifestyle, including dietary habits such as consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure and lifestyle. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, biodiversity, and microbial function. We also identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella, which may be related to health. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

“…Our results indicate that both dietary and environmental mechanisms contribute to captivity‐induced dysbiosis. Consistent with previous research (Clayton, Al‐Ghalith, et al, ; Clayton et al, ), the captive lemurs had different proportions of Bacteroides and Prevotella , and diminished proportions of unassigned taxa, compared with their wild peers. The direction and magnitude of these wild/captive differences were host specific, however, with the specialists showing greater “effects” of captivity compared to the generalists.…”

“…Notably, the routine use of chows, domesticated produce, and carbohydrate‐based treat items generally result in fiber‐limited, but sugar‐rich (i.e., “westernized”) diets (Clayton, Al‐Ghalith, et al, ). For herbivores (animals that consume a broadly plant‐based diet) and folivores (animals that consume a specifically foliage‐based diet), increasing plant‐fiber consumption can mitigate the microbial consequences associated with captivity, as evidenced by improved GMB diversity, stability, membership, and nutrient production (Clayton, Al‐Ghalith, et al, ; Greene et al, ; Kohl et al, ). A second mechanism proposed to explain captivity‐induced dysbiosis centers around changes in environmental conditions.…”

The impact of type VI secretion system, bacteriocins and antibiotics on competition amongst Soft-RotEnterobacteriaceae: Regulation of carbapenem biosynthesis by iron and the transcriptional regulator Fur

“…For phytopathogenic bacteria, more is known about interactions within their hosts and virulence factors that these microbes recruit to successfully colonise their hosts while relatively less is known about microbe-microbe interactions and how such interactions impact on niche colonisations (1-4). Studies on the mammalian gut microbiome, the advent of new sequencing technologies, availability of many ‘omics’ data sets such as metagenomics, transcriptomics and proteomics are some of the factors that have brought microbial interactions to the fore (5-9). Thus, the past few decades have seen a rapid growth in the body of literature on microbial interactions.…”

Space, time, and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate

“…The microbiome can vary according to the host species, age, diet, health, reproductive 43 status, and external environment, but is directly linked to host health, including metabolism, 44 immunity, and development (Nishida & Ochman, 2017). The fecal microbiome is reflective of a 45 transient response to changes in the host, such as responses to dietary shifts across seasons, but 46 core groups of microorganisms are found in stable relative abundances throughout the life of the 47 host and the relative proportions of these groups can act like a signature of the host's health and 48 environment, with reductions in diversity associated closely with reductions in fitness (Amato et 49 al., 2018;Clayton et al, 2018;Donaldson et al, 2015). The stable relative abundances of the 50 core groups are directly related to the function and the demand of the core groups.…”