The gut microbiome of exudivorous marmosets in the wild and captivity

Gut microbiota of the critically endangered Saiga antelope across two wild populations in a year without mass mortality

The Saiga are migratory antelopes inhabiting the grasslands of Eurasia. Over the last century, Saiga have been pushed to the brink of extinction by mass mortality events and intense poaching. Yet, despite the high profile of the Saiga as an animal of conservation concern, little is known of its biology. In particular, the gut microbiota of Saiga has not been studied, despite its potential importance in health. Here, we characterise the gut microbiota of Saiga from two geographically distinct populations in Kazakhstan and compare it with that of other antelope species. We identified a consistent gut microbial diversity and composition among individuals and across two Saiga populations during a year without die-offs, with over 85% of bacterial genera being common to both populations despite vast geographic separation. We further show that the Saiga gut microbiota resembled that of five other antelopes. The putative causative agent of Saiga mass die-offs, Pasteurella multocida, was not detected in the Saiga microbiota. Our findings provide the first description of the Saiga gut microbiota, generating a baseline for future work investigating the microbiota's role in health and mass die-offs, and supporting the conservation of this critically endangered species.

Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools

Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.

Review of Environmental and Health Factors Impacting Captive Common Marmoset Welfare in the Biomedical Research Setting

As a small-bodied neotropical nonhuman primate species, common marmosets have unique requirements for adequate husbandry and veterinary care to ensure proper maintenance and to promote good animal welfare in a biomedical research setting. Environmental conditions, as well as medical and research-related manipulations, can impact marmoset welfare. Research focus areas, including basic neuroscience, transgenics, and aging, involve additional implications for marmoset welfare. This manuscript provides a comprehensive review of factors that should be considered and mitigated as needed by clinical and research staff working with marmosets in biomedical research facilities to optimize the welfare of captive marmosets.

High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Pantheratigrisjacksoni) during fasting

The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.

Comparative Analysis of Gut Microbiota between Wild and Captive Golden Snub-Nosed Monkeys

Environmental shifts and dietary habits could directly affect the gut microbiota of animals. In this study, we investigated the gut microbiota of golden snub-nosed monkeys under two different conditions: captive and wild. Our study adopted a non-invasive sampling method, using full-length 16S rRNA Pacbio SMAT sequencing technology to compare the gut microbiota of wild and captive golden snub-nosed monkeys. The results showed that the captive populations had higher alpha diversity than the wild populations, and there were also significant differences in beta diversity. The linear discriminant analysis effect size (LEfSe) analysis showed 39 distinctly different taxonomic units. At the phylum level, the most dominant bacteria under captive and wild conditions were Bacteroidetes and Firmicutes. This study revealed that the different fiber intake between wild and captive populations might be the main reason for the difference in the gut microbiota. We found that captive golden snub-nosed monkeys had less beneficial bacteria and more potentially pathogenic bacteria than wild ones. Functional predictions showed that the most significant functional pathway at the second level between the captive and wild monkeys was carbohydrate metabolism. Therefore, our results indicate that diet changes caused by captivity could be the main reason impacting the gut microbiota of captive golden snub-nosed monkeys. We further highlight the potential impact of diet changes on the health of captive golden snub-nosed monkeys and offer some suggestions for the feeding of captive golden snub-nosed monkeys.

The common marmoset as a model of neurodegeneration

Human life expectancy has increased over the past few centuries, and the incidence of dementia in the older population is also projected to continue to rise. Neurodegenerative diseases are complex multifactorial conditions for which no effective treatments are currently available. Animal models are necessary to understand the causes and progression of neurodegeneration. Nonhuman primates (NHPs) offer significant advantages for the study of neurodegenerative disease. Among them, the common marmoset, Callithrix jacchus, stands out due to its easy handling, complex brain architecture, and occurrence of spontaneous beta-amyloid (Aβ) and phosphorylated tau aggregates with aging. Furthermore, marmosets present physiological adaptations and metabolic alterations associated with the increased risk of dementia in humans. In this review, we discuss the current literature on the use of marmosets as a model of aging and neurodegeneration. We highlight aspects of marmoset physiology associated with aging, such as metabolic alterations, which may help understand their vulnerability to developing a neurodegenerative phenotype that goes beyond normal aging.

Oral and fecal microbiome of confiscated Bengal slow lorises in response to confinement duration

Slow lorises are small arboreal and nocturnal primates. Due to the illegal trade, a large number of slow lorises were confiscated into wildlife sanctuaries or rescue centers. The re-release has been considered a preferable approach for alleviating the captive pressure, but inappropriate and long-term confinement make it difficult to achieve this goal. In this study, we investigated and compared the fecal and oral microbiome of Bengal slow lorises (Nycticebus bengalensis) under long-term captivity (LC) and short-term captivity (SC) groups based on 16s rRNA high-throughput gene sequencing. The oral microbiome displayed higher Chao1 richness but lower Shannon and Simpson indices than the fecal microbiome. The Bengal slow lorises under long-term captivity had abundant pathogenic genera in both gut and oral microbiomes, such as Desulfovibrio, Actinomyces, Capnocytophaga, Neisseria, and Fusobacterium, while some specific bacterial taxa associated with intestinal balance were more enriched in the SC group. Due to the plant gum scarcity in the diet, both groups had a low abundance of Bifidobacterium. Function profile prediction indicated that the LC group was enriched with genetic information processing and metabolism pathways due to the stable food intake. The increased membrane transport and xenobiotic metabolism and degradation functions in the SC group could be explained by the function of the host microbiome in facilitating adaptation to changing environments and diets. The results demonstrated that the oral microbiome had the potential to be used as a regular surveillance tool. Also, current captive management should be improved to ensure reintroduction success.