The Effects of Methodological, Intrinsic, and Extrinsic Factors on the Host-associated Microbiota of Birds and Ticks

• Other Authors: Gil, Joshua (Creator), Hird, Sarah (Major Advisor), Klassen, Jonathan (Associate Advisor), Knutie, Sarah (Associate Advisor), University of Connecticut (Degree grantor)
• Format: Text
• Language: unknown
• Published: University of Connecticut 2022
• Subjects: Canada; Branta canadensis; Canada Goose
• Online Access: http://hdl.handle.net/11134/20002:860707556; https://digitalcollections.ctstatelibrary.org/islandora/object/20002%3A860707556/datastream/TN/view/Effects%20of%20Methodological,%20Intrinsic,%20and%20Extrinsic%20Factors%20on%20the%20Host-associated%20Microbiota%20of%20Birds%20and%20Ticks.jpg

The collection of microbes in or on a host, or microbiome, confers numerous benefits, directly and indirectly, to the host. The microbiome is an ecological community shaped by many factors deriving from the host, environment, and constituents within the microbiome. This dissertation explores the intrinsic and extrinsic factors that affect the microbiomes in multiple species. One of the many methods used to study microbiomes is “Amplicon sequencing”, which amplifies a conserved marker gene and is predominantly used to identify the taxa present in a microbiome, but amplicons contain no information on the microbiome's functioning. Shotgun metagenomic or metatranscriptomic sequencing, provide data on microbiome function; however, multi-omics analyses can be cost-prohibitive. Simulated metagenomes can be generated from amplicons at a fraction of the price, but the accuracy in non-model organisms is poorly known. In chapter 2, I collected Canada goose (Branta canadensis) fecal samples, generated empirical -omics data, and compared those with simulated metagenomes derived from 16S rRNA amplicon sequences. Simulated metagenomes did not accurately represent the microbiome in totality. Traditional sequencing methods should not be replaced by these predictive tools without verification. Microbiomes are influenced by the host’s environment. In Chapters 3 and 4, we performed range-wide sampling of two bird species, Canada geese and saltmarsh sparrows (Ammospiza caudacuta), to understand the relationship between geography and microbiomes. In both species, as individuals become more distant geographically, their microbiomes become more dissimilar. The extrinsic environment was more important than the intrinsic factors like age and sex in shaping their microbiomes. Blacklegged ticks (Ixodes scapularis) are vectors for many human pathogens. Some of these pathogens can alter the microbiomes of the tick they colonize in controlled environments. We acquired wild ticks carrying zero to three human pathogens. Using 16S rRNA amplicon ...