The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity

Malukiewicz, Joanna; Cartwright, Reed A.; Dergam, Jorge Abdala; Igayara, Claudia S; Kessler, Sharon E; Moreira, Sílvia Bahadian; Nash, Leanne T.; Nicola, Patrícia Avello; Pereira, Luiz Cézar Machado; Pissinatti, Alcides; Ruiz‐Miranda, Carlos R.; Ozga, Andrew T.; Quirino, Adriana A.; Roos, Christian; Silva, Daniel L.; Stone, Anne C.; Grativol, Adriana D.

doi:10.1101/708255

Cited by 13 publications

(20 citation statements)

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“…We hypothesize that increased environmental exposure and enrichment promotes a wild-like microbiome, rich in bifidobacteria that help metabolize oligosaccharide-rich tree gums, a common food source for wild marmosets 45,47 . High abundances of Actinobacteria are observed in wild callitrichids, but not in captive and semi-captive marmosets 24 . Unexpectedly, Ross et al also reported high Bifidobacterium levels in marmosets housed within a specific-pathogen free (SPF) barrier facility and at the Southwest National Primate Resource Center (SNPRC) 30 .…”

Section: Discussionmentioning

confidence: 82%

“…However, Megasphaera has been known to produce butyrate under specific conditions 33,44 . Inter-institutional differences greatly affect marmoset microbiomes, as previous studies report marmoset gut microbiota dominated by Actinobacteria 29,30 , Firmicutes 33,34 , Proteobacteria 24,45,46 and Bacteroidetes 31,32,46 . At the Biomedical Primate Research Centre (BPRC) (Rijswijk, the Netherlands), Actinobacteria , represented by Bifidobacterium and Collinsella , was the most abundant phylum (66%), while Bacteroides and Prevotella represented <5% of the microbiome each 29 .…”

Section: Discussionmentioning

confidence: 97%

“…As the microbiome has been associated to human GI diseases, factors affecting the microbiome in non-human primates (NHP) are being explored, such as species, social structure, environment and diet 23–26 . Captivity and captive diets have been associated with microbial diversity loss, shifts in the Firmicutes : Bacteroidetes ratio, and increased GI disease and mortality 23,26,27 . Dietary specialists, such as marmosets, are more susceptible to captivity-associated dietary changes 26 .…”

Section: Introductionmentioning

confidence: 99%

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Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

Sheh

Artim

Burns

et al. 2020

Preprint

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Chronic gastrointestinal (GI) diseases are the most common diseases in captive marmosets. The gut microbiome of healthy (n=91), inflammatory bowel disease (IBD) (n=59), and duodenal ulcer/stricture (n=23) captive marmosets was characterized. Healthy marmosets exhibited a “humanized,” Bacteroidetes-dominant microbiome. Despite standardized conditions, cohorts subdivided into Prevotella- and Bacteroides-dominant groups based on marmoset source. IBD was highest in a Prevotella-dominant cohort while strictures were highest in a Bacteroides-dominant cohort. Stricture-associated dysbiosis was characterized by Anaerobiospirillum loss and Clostridium perfringens increases. Stricture tissue presented upregulation of lipid metabolism genes and increased abundance of C. perfringens, a causative agent of GI diseases and intestinal strictures in humans. IBD was associated with a lower Bacteroides:P. copri ratio within each source. Consistent with Prevotella-linked diseases, pro-inflammatory genes were upregulated. This report highlights the humanization of the captive marmoset microbiome and its potential as a “humanized” animal model of C. perfringens-induced enteritis/strictures and P. copri-associated IBD.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

Sheh

Artim

Burns

et al. 2020

Preprint

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“…Greater likelihood of genetic similarity between DPG and HHG populations is unlikely to explain these results; previous studies in nonhuman primates have found that environmentdiet in particularappears to be much more important than host genetics in predicting the composition of the gut microbiota. 2,24 390 d after importation, bacterial community composition remained distinct between the imported population groups (DPG, HHG) and the stable population group (JHU). These results suggest a level of long-term stability of the gut microbiota in captive marmosets when moved between institutions and subjected to diet change.…”

Section: Discussionmentioning

confidence: 96%

“…In one study of the gut bacterial microbiota in multiple marmoset species and hybrid types, the degree of captivitycaptive-born vs. wild-born captive vs. wildhad a stronger overall effect on the microbial composition than did host genetics. 2 Importantly, there is reason to believe that even conditions of captivity that are relatively similar between colonies can yield significantly differential gut microbial community composition. In inbred mice populations originating from different vendors, or arriving at different facilities with standardized husbandry practices, significant gut microbial variation exists and has been shown to impact research outcomes and disease phenotype.…”

Section: Introductionmentioning

confidence: 99%

Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration

Cooper

Mangus

Lynch

et al. 2020

Preprint

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Characterization of the gut microbiome may aid understanding and management of natural and experimental disease states in research animals, thereby promoting reproducibility. In this study, the rectal bacterial communities of three separate common marmoset (Callithrix jacchus) breeding colonies were defined using 16S rRNA sequencing of rectal swab samples. Study animals originated from two German colonies and a United States colony (JHU). The two German cohorts, previously fed the same diet, were imported into the JHU facility; they were then isolated, transitioned onto JHU diet, and then moved into rooms housing JHU animals. To dissect the contributions of diet and integration in shaping the rectal bacterial community, samples were collected from German origin marmosets upon JHU arrival (baseline), following diet transition (100 d), and following cohousing (390 d). Baseline and 390 d samples were collected from stably maintained JHU marmosets. Bacterial community composition was distinct between all three cohorts at baseline, suggesting that factors other than primary diet confer significant differences between captive populations. Beta-diversity of the animals from the two German colonies converged by 100 d but remained distinct from JHU sample beta-diversity throughout the 390-d study, indicating that diet had greater influence on bacterial community composition than did housing animals within the same room. Our results demonstrate substantial differences in gut bacteria between different captive marmoset colonies, with persistence of these differences following husbandry standardization and housing integration. Goals of rigor and reproducibility in research underscore the need to consider microbial differences between marmosets of diverse origin.ImportanceCharacterizing gut microbial populations is expected to promote health and enhance research reproducibility in animal studies. As use of common marmosets as animal models of human diseases expands, evaluating the marmoset gut bacterial community will be critical for interpreting research findings, especially as marmosets are prone to gastrointestinal inflammation. In this study, using 16S rRNA sequencing of rectal swab samples, we compared bacterial community among three captive colonies of marmosets at baseline and following importation of cohorts from two of the colonies into the third colony. Diet history had sustained influence on bacterial community composition, while housing the animals within the same room over a period of eight months did not appear to be a major factor. These persistent differences in marmoset gut bacterial community highlight the need for careful consideration of animal origin as a variable in marmoset research studies.

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Evolutionary and biomedical insights from a marmoset diploid genome assembly

Yang

Zhou

Marcus

et al. 2021

Nature

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The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes, and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an important primate model system widely used in biomedical research2,3. The full heterozygosity spectrum between the two haplotypes involves 1.36% of the genome, much higher than the 0.13% indicated by the standard single nucleotide heterozygosity estimation alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, where the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex differentiated region and unique evolutionary changes in the marmoset Y chromosome. Additionally, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain related genes were highly conserved between marmosets and humans, though several genes experienced lineage-specific copy number variations or diversifying selection, providing important implications for the application of marmosets as a model system.

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The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity

Cited by 13 publications

References 123 publications

Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration

Evolutionary and biomedical insights from a marmoset diploid genome assembly

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