Shotgun metagenomic approach to the influence of industrialization and social behavior on fecal microbiomes

Yarlagadda, Karthik

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https://hdl.handle.net/2142/113269 Copy

Description

Title

Shotgun metagenomic approach to the influence of industrialization and social behavior on fecal microbiomes

Author(s)

Yarlagadda, Karthik

Issue Date

2021-07-06

Director of Research (if dissertation) or Advisor (if thesis)

Malhi, Ripan S

Doctoral Committee Chair(s)

Malhi, Ripan S

Committee Member(s)

• Swanson, Kelly
• Carter, Gerald
• Roseman, Charles

Department of Study

Anthropology

Discipline

Anthropology

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• ancient DNA
• canine
• diet
• industrialization
• metagenomics
• microbiome
• social behavior
• vampire bat

Abstract

The microbiome is a complex, rapidly evolving field of study dedicated to understanding the multitudes of micro-organisms that we live with, and that engage in reciprocal interactions with our own biology for both ill and good. These collections of microbes are susceptible to numerous influences derived from their hosts, ranging from diet, to industrialization, to social behavior. When considering these factors, it is to our advantage that these systems that alter microbiomes are uniform across species, which allows us to take advantage of suitable animal models, like dogs and vampire bats, to better recapitulate the effects of specific interventions that shape and alter microbiomes. In the following studies, we analyze a breadth of samples to understand how the previously aforementioned factors, diet, industrialization, and social behavior, alter the fecal microbiomes and identify the importance of those changes. First, we present microbial sequence data from canine coprolites, fossilized fecal samples, that preserve some amount of microbial DNA from the individual’s fecal microbiome. We contextualize these results within the scope of existing data in the literature, identifying a well-preserved coprolite and finding evidence for a high-protein diet based on microbial remains. To expound upon these results, we gathered and provide further sequence data from more diverse canine populations than are currently represented in the literature. We find evidence to support the hypothesis of a gradient of industrialization that highlights a decrease in taxonomic diversity with increasing industrialization. We also find evidence to support the hypothesis of functional redundancy, showing that across populations, similar functional and metabolic pathways can exist across this taxonomic diversity. These results demonstrate the importance of population diversity, as we highlight greater similarity between the microbial profiles of the ancient dogs that produced the coprolites and modern dogs engaged in a similar lifestyle as the ancient dogs. Finally, we present results of a longitudinal study in vampire bats, tracking changes in fecal microbiome over time from their capture in the wild through captivity. With the context of additional samples provided by zoo and wild populations, we identify overall low levels of taxonomic diversity across individuals, functional constraints consistent with other obligate sanguivores, and increased microbial similarity between individuals engaged in more social behavior. Together, these results highlight gaps in the existing literature, and demonstrate the utility of animal models in understanding microbiome variation along known factors.

Graduation Semester

2021-08

Type of Resource

Thesis

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http://hdl.handle.net/2142/113269

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Copyright 2021 Karthik Yarlagadda

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