The anthropogenic impact on tropical ecosystems has led to a significant loss of biological diversity, with non-human primates facing a high risk of extinction. According to the World Conservation Union (IUCN), almost one third of non-human primate species are classified as endangered, with the main driver being loss of preferred habitat and food resources. Habitat loss has inevitably affected the diet and gut microbiota of these species, leading to a loss of biological diversity at the microscopic level. The gut microbiota and its genome collection (gut microbiome) play an essential role in host health, performing functions such as digestion, fermentation of complex compounds, modulation of the immune system, and defense against external pathogens. Gut dysbiosis, due to the loss or acquisition of new microorganisms, is often associated with inflammation and disease. Research on the gut microbiota of wild animal species living in human-affected environments (e.g., deforestation) has shown losses in richness or changes in gut microbiota composition. However, deeper investigations into the functional significance of these losses are missing, and understanding the dynamics between host gut microorganisms and those of the surrounding environment would also elucidate the impact of human activities on host health. Using non-human primates as model species, this thesis aims to (i) describe the current understanding of gut symbiont dynamics and their consequences on host health; (ii) investigate the contribution of extrinsic and intrinsic factors to gut microbiota variation; and (iii) explore the impact of extrinsic factors on the microbiome and the resulting variations in host metabolic functions. Chapter 1: This review focuses on studies of the most abundant intestinal microorganisms (bacteria) in conjunction with other intestinal symbionts (fungi, archaea, helminths, and viruses) to understand their associations, interactions, and effects on host health. This chapter reviews the current understanding of interactions and associations between bacteria and various symbionts. It highlights how changes in some intestinal symbionts relative to others, as well as fluctuations among multiple symbionts due to intrinsic or extrinsic factors, can impact the host. These interactions and their effects are often complex and not easily understood. Chapter 2: Investigates the variation in gut microbiota (bacteria and fungi) of a population of yellow baboons (Papio cynocephalus) in relation to habitat type (extrinsic factor) and sex (intrinsic factor). The study observed that gut microbiota variations are affected by habitat type, with bacterial and fungal community diversity potentially mediated by sex, emphasizing the importance of combining biological and ecological factors in microbiota analyses. Chapter 3: Provides the first comprehensive identification of bacterial and fungal communities in the Sanje mangabey (Cercocebus sanjei), an endangered species endemic to the Udzungwa Mountains. The chapter explores the potential contamination of gut microorganisms by soil microorganisms, highlighting a significant transfer of soil saprotrophic fungal communities to the gut. This suggests an association between geophagy— a behavior of consuming soil observed in the Sanje mangabey—and its highly frugivorous diet. Geophagy is an adaptive behavior that may have various functions, such as relieving gastrointestinal stress. Our results suggest that these benefits may be partly determined by the presence of microorganisms in the soil and their interaction with the gut microbiome. Chapter 4: Investigates the diversity of metabolic functions of gut microorganisms in two non-human primate hosts, the Udzungwa red colobus (Piliocolobus gordonorum) and yellow baboons, using in-depth sequencing methods (metagenomics). The study found a strong association between observed metabolic functions and the distinct diets of the hosts. Differences in metabolic functions were also observed within the same host species living in contrasting habitat types, suggesting that specialized diets may be more affected by habitat differences than generalist diets. Overall, this thesis provides a comprehensive view of the complexity of gut microbial variations in terms of structure, composition, and metabolic functions. It emphasizes the importance of studying these variations in wild host species, which are often threatened by human activities. These findings can improve awareness in the field of conservation and aid in developing strategies to mitigate the effects of anthropogenic disturbance

BAMBI, MARINA (2024-09-27). Gut microbiome dynamics in primates across a tropical ecosystem. (Doctoral Thesis). Università degli studi di Parma, a.y. 2022/2023, Evolutionary Biology and Ecology XXXVI cycle. handle: https://hdl.handle.net/10449/88536

Gut microbiome dynamics in primates across a tropical ecosystem

BAMBI, MARINA
2024-09-27

Abstract

The anthropogenic impact on tropical ecosystems has led to a significant loss of biological diversity, with non-human primates facing a high risk of extinction. According to the World Conservation Union (IUCN), almost one third of non-human primate species are classified as endangered, with the main driver being loss of preferred habitat and food resources. Habitat loss has inevitably affected the diet and gut microbiota of these species, leading to a loss of biological diversity at the microscopic level. The gut microbiota and its genome collection (gut microbiome) play an essential role in host health, performing functions such as digestion, fermentation of complex compounds, modulation of the immune system, and defense against external pathogens. Gut dysbiosis, due to the loss or acquisition of new microorganisms, is often associated with inflammation and disease. Research on the gut microbiota of wild animal species living in human-affected environments (e.g., deforestation) has shown losses in richness or changes in gut microbiota composition. However, deeper investigations into the functional significance of these losses are missing, and understanding the dynamics between host gut microorganisms and those of the surrounding environment would also elucidate the impact of human activities on host health. Using non-human primates as model species, this thesis aims to (i) describe the current understanding of gut symbiont dynamics and their consequences on host health; (ii) investigate the contribution of extrinsic and intrinsic factors to gut microbiota variation; and (iii) explore the impact of extrinsic factors on the microbiome and the resulting variations in host metabolic functions. Chapter 1: This review focuses on studies of the most abundant intestinal microorganisms (bacteria) in conjunction with other intestinal symbionts (fungi, archaea, helminths, and viruses) to understand their associations, interactions, and effects on host health. This chapter reviews the current understanding of interactions and associations between bacteria and various symbionts. It highlights how changes in some intestinal symbionts relative to others, as well as fluctuations among multiple symbionts due to intrinsic or extrinsic factors, can impact the host. These interactions and their effects are often complex and not easily understood. Chapter 2: Investigates the variation in gut microbiota (bacteria and fungi) of a population of yellow baboons (Papio cynocephalus) in relation to habitat type (extrinsic factor) and sex (intrinsic factor). The study observed that gut microbiota variations are affected by habitat type, with bacterial and fungal community diversity potentially mediated by sex, emphasizing the importance of combining biological and ecological factors in microbiota analyses. Chapter 3: Provides the first comprehensive identification of bacterial and fungal communities in the Sanje mangabey (Cercocebus sanjei), an endangered species endemic to the Udzungwa Mountains. The chapter explores the potential contamination of gut microorganisms by soil microorganisms, highlighting a significant transfer of soil saprotrophic fungal communities to the gut. This suggests an association between geophagy— a behavior of consuming soil observed in the Sanje mangabey—and its highly frugivorous diet. Geophagy is an adaptive behavior that may have various functions, such as relieving gastrointestinal stress. Our results suggest that these benefits may be partly determined by the presence of microorganisms in the soil and their interaction with the gut microbiome. Chapter 4: Investigates the diversity of metabolic functions of gut microorganisms in two non-human primate hosts, the Udzungwa red colobus (Piliocolobus gordonorum) and yellow baboons, using in-depth sequencing methods (metagenomics). The study found a strong association between observed metabolic functions and the distinct diets of the hosts. Differences in metabolic functions were also observed within the same host species living in contrasting habitat types, suggesting that specialized diets may be more affected by habitat differences than generalist diets. Overall, this thesis provides a comprehensive view of the complexity of gut microbial variations in terms of structure, composition, and metabolic functions. It emphasizes the importance of studying these variations in wild host species, which are often threatened by human activities. These findings can improve awareness in the field of conservation and aid in developing strategies to mitigate the effects of anthropogenic disturbance
HAUFFE, HEIDI CHRISTINE
Settore BIOS-07/A - Biochimica
27-set-2024
2022/2023
Evolutionary Biology and Ecology XXXVI cycle
BAMBI, MARINA (2024-09-27). Gut microbiome dynamics in primates across a tropical ecosystem. (Doctoral Thesis). Università degli studi di Parma, a.y. 2022/2023, Evolutionary Biology and Ecology XXXVI cycle. handle: https://hdl.handle.net/10449/88536
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