Jonathan B Clayton

• Doctor of Philosophy
• Professor (Assistant) at University of Nebraska at Omaha

Gut microbial essential amino acid (EAA) provisioning to mammalian hosts remains a critical yet poorly understood aspect of host-microbe nutritional interactions, with significant implications for human and animal health. To investigate microbial EAA contributions in mice with reconstituted gut microbiomes, we analyzed stable carbon isotopes (¹³C)...

Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas f...

Emerging evidence indicates that antibiotic-induced dysbiosis can play an etiological role in the pathogenesis of neuropsychiatric disorders. However, most of this evidence comes from rodent models. The objective of this study was to evaluate if antibiotic-induced gut dysbiosis can elicit changes in gut metabolites and behavior indicative of gut-br...

Understanding and mediating health conditions in endangered species under human care is important to optimize welfare and ex-situ breeding, as animals experience novel stressors inherent to a captive environment. Some species are able to adapt to their new environment with little consequence, while others respond with behavioral changes and experie...

Background: Alouatta palliata palliata are an ecologically flexible howler monkey subspecies that has recently been relisted as Endangered. Populations are declining through much of the subspecies' range, including at our study site at La Pacifica, Costa Rica. Our objectives were to screen blood hematology and biochemistry samples collected from t...

There are previous epidemiological studies reporting associations between antibiotic use and psychiatric symptoms. Antibiotic-induced gut dysbiosis and alteration of microbiota-gut-brain axis communication has been proposed to play a role in this association. In this systematic review and meta-analysis, we reviewed published articles that have pres...

Background: A significant portion of individuals in the United States and worldwide experience diseases related to or driven by diet. As research surrounding user-centered design and the microbiome grows, movement of the spectrum of translational science from bench to bedside for improvement of human health through nutrition becomes more accessible...

Chlamydia trachomatis (CT) causes the most prevalent sexually transmitted bacterial disease in the United States. The lack of drug selectivity is one of the main challenges of the current antichlamydial pharmacotherapy. The metabolic needs of CT are controlled, among others, by cylindrical proteases and their chaperones (e.g., ClpX). It has been sh...

Vast numbers of microorganisms inhabit the mammalian gastrointestinal tract in a complex community referred to as the gut microbiome. An individual’s microbiome may be impacted by genetics, diet, and various environmental factors, and has been associated with many health states and diseases, though specific explanations are lacking. While these com...

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...

The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition-the bacteriome and have commonly overlooked the fungal fraction-the mycobiome. To further understand the factors that shape the gut mycobiome...

The Colobines are a group of Afroeurasian monkeys that exhibit extraordinary behavioural and ecological diversity. With long tails and diverse colourations, they are medium-sized primates, mostly arboreal, that are found in many different habitats, from rain forests and mountain forests to mangroves and savannah. Over the last two decades, our unde...

The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the “normal” state of the GI microbiome composition across multiple host species has gained in...

The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology across species and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterize the transcriptional response of human...

The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity...

Upregulated in inflammation, calprotectin (complexed S100A8 and S100A9; S100A8/A9) functions as an innate immune effector molecule, promoting inflammation, and as an antimicrobial protein. We hypothesized that antimicrobial S100A8/A9 would mitigate change to the local microbial community and promote resistance to experimental periodontitis in vivo....

Folivory evolved independently at least three times over the last 40 million years among Madagascar's lemurs. Many extant lemuriform folivores exist in sympatry in Madagascar's remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota d...

Childhood obesity is a serious public health problem worldwide. Perturbations in the gut microbiota composition have been associated with the development of obesity in both children and adults. Probiotics, on the other hand, are proven to restore the composition of the gut microbiome which helps reduce the development of obesity. However, data on t...

Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance we...

The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology, and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterized the transcriptional response of colonic epithelial...

Background The gut microbiome harbors trillions of bacteria that play a major role in dietary nutrient extraction and host metabolism. Metabolic diseases such as obesity and diabetes are associated with shifts in microbiome composition and have been on the rise in Westernized or highly industrialized countries. At the same time, Westernized diets l...

Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior to pairing and for 8 weeks fol...

Alternative approaches are greatly needed to reduce the need for antibiotic use in food animal production. This study utilized a pipeline for the development of a host-tailored probiotic to enhance performance in commercial turkeys and modulate their microbiota, similar to the effects of low-dose antibiotic administration. We determined that a host...

Both host phylogenetic placement and feeding strategy influence the structure of the gut microbiome (GMB); however, parsing their relative contributions presents a challenge. To meet this challenge, we compared GMB structure in two genera of lemurs characterized by different dietary specializations, the frugivorous brown lemurs ( Eulemur spp.) and...

The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communi...

Environment and diet are key factors which shape the microbiome of organisms. There is also a disparity between captive and wild animals of the same species, presumably because of the change in diet. Being able to reverse the microbiome to the wild type is thus particularly important for the reintroduction efforts of Critically Endangered animals....

A recent surge of microbiome research has characterized gastrointestinal microbiome (GIM) composition and diversity among mammalian species with the aim to use GIM analyses as a clinical tool. However, a basic understanding of the “normal variation” for GIMs in non-human primates is lacking. All gorilla species are critically endangered; thus, gori...

Background The aim of this study was to longitudinally investigate the prevalence and characterization of Campylobacter spp. from non‐human primates primate (NHP) with a history of endemic diarrhea housed at Como Park Zoo. Methods Fecal samples from 33 symptom‐free NHP belonging to eight different species were collected weekly for 9 weeks. Species...

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 underst...

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). He...

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about mi...

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 dietary habits including consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric...

The intestinal microbiota plays a major role in host development, metabolism, and health. To date, few longitudinal studies have investigated the causes and consequences of microbiota variation in wildlife, although such studies provide a comparative context for interpreting the adaptive significance of findings from studies on humans or captive an...

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitati...

Significance Trillions of bacteria live in the primate gut, contributing to metabolism, immune system development, and pathogen resistance. Perturbations to these bacteria are associated with metabolic and autoimmune human diseases that are prevalent in Westernized societies. Herein, we measured gut microbial communities and diet in multiple primat...

Amplicon-based marker gene surveys form the basis of most microbiome and other microbial community studies. Such PCR-based methods have multiple steps, each of which is susceptible to error and bias. Variance in results has also arisen through the use of multiple methods of next-generation sequencing (NGS) amplicon library preparation. Here we form...

Primates of the Colobinae subfamily are highly folivorous. They possess a sacculated foregut and are believed to rely on a specialized gut microbiota to extract sufficient energy from their hard-to-digest diet. Although many colobines are endangered and would benefit from captive breeding programs, maintaining healthy captive populations of colobin...

Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associ...

The gastrointestinal (GI) tracts of non-human primates (NHPs) are well known to harbor Escherichia coli, a known commensal of human beings and animals. While E. coli is a normal inhabitant of the mammalian gut, it also exists in a number of pathogenic forms or pathotypes, including those with predisposition for the GI tract as well as the urogenita...

The red-shankeddouc (Pygathrixnemaeus) is rare and an endangered species of Asian colobine, which inhabits east-central Lao PDR, central Vietnam, and northeast Cambodia. It is listed as Endangered on the IUCN Red List (IUCN 2007) and is also on Appendix 1 of CITES and in Vietnam’s Red Data Book (2007) and classified into IB according the Viet Nam G...

The catacomb of Saints Peter and Marcellinus located in the south-east of Rome approximately contains 25 000 graves dated from the 3rd to the 5th century AD. Seven newly discovered rooms having an unusual organization in the heart of the catacomb were investigated in 2003. Excavations of these rooms revealed a mass grave, where 3000 corpses were la...

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...

The study of endocranial asymmetries of hominids is a central topic in paleoneurology. However, our knowledge about the emergence of these asymmetries during human evolution is still limited. This is partly due to the fact that, so far, these 3D asymmetries have been mostly analyzed using landmarks-based methods. Such methods are limited as they on...