Browsing by Author "Leigh, Steven R."

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Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)
(2016-11) Vickova, Klara; Gomez, Andres; Whittier, Christopher A.; Todd, Angelique F.; Yeoman, Carl J.; Nelson, Karen E.; Wilson, Brenda A.; Stumpf, Rebecca M.; Modry, David; White, Bryan A.; Leigh, Steven R.
The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas (Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates.
Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns
(2016-03) Gomez, Andres; Petrzelkova, Klara J.; Burns, Michael B.; Yeoman, Carl J.; Amato, Katherine R.; Vlckova, Klara; Modry, David; Todd, Angelique F.; Jost Robinson, Carolyn A.; Remis, Melissa J.; Torralba, Manolito G.; Morton, Elise; Umaña, Juan D.; Carbonero, Franck; Gaskins, H. Rex; Nelson, Karen E.; Wilson, Brenda A.; Stumpf, Rebecca M.; White, Bryan A.; Leigh, Steven R.; Blekhman, Ran
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications
(2016-07) Stumpf, Rebecca M.; Gomez, Andres; Amato, Katherine R.; Yeoman, Carl J.; Polk, J. D.; Wilson, Brenda A.; Nelson, Karen E.; White, B. A.; Leigh, Steven R.
Conservation strategies require multifaceted approaches to monitor and protect primate populations, many of which are rapidly declining around the world. We propose that microbial ecology and next-generation microbiome analyses offer valuable perspectives and tools for investigating and monitoring primate health and improving conservation efforts. The microbial communities inhabiting primates and other taxa profoundly affect host health, nutrition, physiology, and immune systems, through relationships that range from commensal and mutualistic to pathogenic. Recent advances in DNA sequencing now make it feasible and economically viable to identify microbiomes among and within hosts. Herein, we highlight several examples in which microbial analyses of primates can aid conservation approaches that are broadly applicable across other taxa. First, we highlight evidence for clear spatial variation (e.g. biogeographic niche specificity, both within the anatomical regions of the host body, as well as in the geographic location of the host) and temporal (e.g. seasonal, ontogenetic) patterns in microbial distribution. We emphasize that microbial communities are sensitive to alterations in the external environment and that microbial diversity correlates with habitat quality, imposing direct health consequences. Incorporating microbial host and biogeographic variation holds great potential for forest corridor assessments and for reintroduction efforts. Finally, microbial pathogens transmitted between humans and wild primate populations carry both direct and indirect conservation implications. Principally, we argue that phylogenetic analyses of infectious pathogens (e.g., Ebola, dengue, Borellia, and Treponema) can aid our understanding of modes of disease transmission and aid conservation disease abatement efforts. The application of microbial analyses to conservation is currently in its infancy but holds enormous potential. To date, no conservation policy or legislation includes microbiome assessments. Integrating new understanding of the patterns of microbial diversity and early signs of impending microbial disruption offer valuable tools for informing conservation strategies and monitoring and promoting primate (including human) health.
Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints
(2019-07-19) Gomez, Andres; Sharma, Ashok Kumar; Mallott, Elizabeth K.; Petrzelkova, Klara J.; Jost Robinson, Carolyn A.; Yeoman, Carl J.; Carbonero, Franck; Pafco, Barbora; Rothman, Jessica M.; Ulanov, Alexander; Vlckova, Klara; Amato, Katherine R.; Schnorr, Stephanie L.; Dominy, Nathaniel J.; Modry, David; Todd, Angelique F.; Torralba, Manolito; Nelson, Karen E.; Burns, Michael B.; Blekhman, Ran; Remis, Melissa; Stumpf, Rebecca M.; Wilson, Brenda A.; Gaskins, H. Rex; Garber, Paul A.; White, Bryan A.; Leigh, Steven R.
The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.
Variable responses of human & non-human primate gut microbiomes to a Western diet
(2015-11) Amato, Katherine R.; Yeoman, Carl J.; Cerda, Gabriela; Schmitt, Christopher A.; Danzy Cramer, Jennifer; Berg Miller, Margret E.; Gomez, Andres; Turner, Trudy R.; Wilson, Brenda A.; Stumpf, Rebecca M.; Nelson, Karen E.; White, Bryan A.; Knight, Rob; Leigh, Steven R.
Background: Brachylophosaurini is a clade of hadrosaurine dinosaurs currently known from the Campanian (Late Cretaceous) of North America. Its members include: Acristavus gagslarsoni, which lacks a nasal crest; Brachylophosaurus canadensis, which possesses a flat paddle-shaped nasal crest projecting posteriorly over the dorsal skull roof; and Maiasaura peeblesorum, which possesses a dorsally-projecting nasofrontal crest. Acristavus, from the lower Two Medicine Formation of Montana (~81–80 Ma), is hypothesized to be the ancestral member of the clade. Brachylophosaurus specimens are from the middle Oldman Formation of Alberta and equivalent beds in the Judith River Formation of Montana; the upper Oldman Formation is dated 77.8 Ma. Methodology/Principal Findings: A new brachylophosaurin hadrosaur, Probrachylophosaurus bergei (gen. et sp. nov.) is described and phylogenetically analyzed based on the skull and postcranium of a large individual from the Judith River Formation of northcentral Montana (79.8–79.5 Ma); the horizon is equivalent to the lower Oldman Formation of Alberta. Cranial morphology of Probrachylophosaurus, most notably the nasal crest, is intermediate between Acristavus and Brachylophosaurus. In Brachylophosaurus, the nasal crest lengthens and flattens ontogenetically, covering the supratemporal fenestrae in large adults. The smaller nasal crest of Probrachylophosaurus is strongly triangular in cross section and only minimally overhangs the supratemporal fenestrae, similar to an ontogenetically earlier stage of Brachylophosaurus. Sutural fusion and tibial osteohistology reveal that the holotype of Probrachylophosaurus was relatively more mature than a similarly large Brachylophosaurus specimen; thus, Probrachylophosaurus is not simply an immature Brachylophosaurus. Conclusions/Significance: The small triangular posteriorly oriented nasal crest of Probrachylophosaurus is proposed to represent a transitional nasal morphology between that of a non-crested ancestor such as Acristavus and the large flat posteriorly oriented nasal crest of adult Brachylophosaurus. Because Probrachylophosaurus is stratigraphically and morphologically intermediate between these taxa, Probrachylophosaurus is hypothesized to be an intermediate member of the Acristavus-Brachylophosaurus evolutionary lineage.