Processes that shape the avian gut microbiome

Abstract/Contents

Abstract

Animals harbor and maintain a diverse assemblage of bacteria, viruses, fungi, and other eukaryotic organisms that reside and interact at a particular body site. The net effect of these interactions, most notably in the gut, is responsible for mediating host health. The gut community consistently demonstrates its importance in animal hosts. However, most studies focus on humans or model organisms. As such, I applied the techniques developed in microbiology to wildlife, particularly avian hosts. In my dissertation, I independently developed research questions, acquired funding for projects, and established collaborations with experts in various fields to investigate: (1) how land-use change influences Neotropical passerine birds, (2) how dietary guild affects the gut microbiome of a diverse group of bird species, (3) how captivity changes the Brown Kiwi (Apteryx mantelli) gut microbial communities, and (4) how the gut microbiome assembles and changes throughout Brown Kiwi development. In the first chapter, I quantified the impact of land-use change on six species of Neotropical passerines and their gut microbiomes (San Juan et al. 2020). I found bacterial communities responded more strongly to host species identity than to the habitat type, where sites ranged from primary forests to intensified coffee farms. However, the microbiomes of two out of the six bird species were modified, suggesting some bird species may be more vulnerable to land-use change than others. In chapter 2, I assessed how host species and family, dietary guild, habitat, and migratory status contribute to the gut bacteria of 79 bird species. I found host species identity to be the strongest predictor of the gut microbiome, followed by dietary guild. Migratory status had little influence on the gut microbiota. In chapter 3, I investigated how captive rearing, a practice crucial in the recovery of endangered species, impacts Brown Kiwi gut bacteria and fungi. I found a significant drop in alpha diversity and shifts in community composition between wild and captive kiwi (San Juan et al. 2021). To further elucidate captivity's influence on the gut microbiome, I performed a comprehensive longitudinal study on captive kiwi to explore the temporal dynamics of their gut microbes. I found that the gut microbiome fluctuates day-to-day, especially early on in life. Age was a stronger predictor of gut microbiome variation compared to a common disease (coccidiosis). Overall, my research considers host identity, life history traits, and environmental factors including their habitat as explanatory variables of wildlife gut microbiomes. I generated datasets that emphasize the importance of the gut microbiome, an often neglected aspect in conservation practices. Understanding the factors that contribute to avian gut microbial communities may highlight areas we have not considered in other host species.

Description

Type of resource	text
Form	electronic resource; remote; computer; online resource
Extent	1 online resource.
Place	California
Place	[Stanford, California]
Publisher	[Stanford University]
Copyright date	2022; ©2022
Publication date	2022; 2022
Issuance	monographic
Language	English

Creators/Contributors

Author	San Juan, Priscilla Ashley
Degree supervisor	Fukami, Tadashi, 1972-
Thesis advisor	Fukami, Tadashi, 1972-
Thesis advisor	Daily, Gretchen C
Thesis advisor	Peay, Kabir
Degree committee member	Daily, Gretchen C
Degree committee member	Peay, Kabir
Associated with	Stanford University, Department of Biology

Subjects

Genre	Theses
Genre	Text

Bibliographic information

Statement of responsibility	Priscilla Ashley San Juan.
Note	Submitted to the Department of Biology.
Thesis	Thesis Ph.D. Stanford University 2022.
Location	https://purl.stanford.edu/xy365xz8058

Access conditions

Copyright

© 2022 by Priscilla Ashley San Juan

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