Browsing by Author "Clayton, Jonathan B"

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Open Access
Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model.
(Scientific reports, 2018-07-24) Clayton, Jonathan B; Al-Ghalith, Gabriel A; Long, Ha Thang; Tuan, Bui Van; Cabana, Francis; Huang, Hu; Vangay, Pajau; Ward, Tonya; Minh, Vo Van; Tam, Nguyen Ai; Dat, Nguyen Tat; Travis, Dominic A; Murtaugh, Michael P; Covert, Herbert; Glander, Kenneth E; Nadler, Tilo; Toddes, Barbara; Sha, John CM; Singer, Randy; Knights, Dan; Johnson, Timothy J
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.
Open Access
Captivity humanizes the primate microbiome.
(Proc Natl Acad Sci U S A, 2018-03-01) Clayton, Jonathan B; Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M; Al-Ghalith, Gabriel A; Travis, Dominic A; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E; Johnson, Timothy J; Knights, Dan
The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.
Open Access
Dietary choices by four captive slender lorises (Loris tardigradus) when presented with various insect life stages.
(Zoo Biol, 2011-03) Clayton, Jonathan B; Glander, Kenneth E
The slender loris (Loris tardigradus) is a rare, nocturnal prosimian found only in the tropical rainforest of southern India and Sri Lanka. Little is known about their diet, though it is assumed that insects comprise a majority of their wild diet. Based on this assumption, captive lorises are offered a variety of insects or insect life stages; the species of insect or the life stage is often determined by what is easiest to buy or rear. Captive lorises at the Duke Lemur Center (DLC) were offered the opportunity to choose which life stage of mealworms (Tenebrio molito), superworms (Zophobus morio), or waxworms (Galleria mellonella) they preferred. The DLC captive lorises did not select the largest life stages of any insect offered. They preferred the larvae stage to the adult stage in all three insect species, and males and females had different insect species and life stage preferences.
Open Access
Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.
(Microbial ecology, 2023-05) Greene, Lydia K; McKenney, Erin A; Gasper, William; Wrampelmeier, Claudia; Hayer, Shivdeep; Ehmke, Erin E; Clayton, Jonathan B
Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.
Open Access
The gut microbiome of nonhuman primates: Lessons in ecology and evolution.
(American journal of primatology, 2018-06-04) Clayton, Jonathan B; Gomez, Andres; Amato, Katherine; Knights, Dan; Travis, Dominic A; Blekhman, Ran; Knight, Rob; Leigh, Steven; Stumpf, Rebecca; Wolf, Tiffany; Glander, Kenneth E; Cabana, Francis; Johnson, Timothy J
The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.