Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow
Creators: name: Rohrer, Sage
name: Robertson, Briana
name: Chubiz, Lon
name: Parker, Patricia
Publisher: name: Zenodo
Year: 2023
Subjects: Avian microbiome
Gut microbiome
Plasmodium
blood parasites
Sparrows

description: Recent expansion of microbiome research has uncovered connections between resident microbial communities and blood parasite risk, establishing the potential for microbial disease treatments such as probiotics in the future. However, this field has largely focused on humans and model organisms, leaving much unknown about how microbial communities might directly or indirectly impact parasite infection in wild populations and non-mammals. To contribute to this knowledge base in wild birds, we collected fecal and blood samples from wild Eurasian tree sparrows (<em>Passer montanus</em>) in the United States to test for associations between blood parasite infection and the gut microbiome. We used a widespread molecular approach to test 81 samples from peripheral blood for <em>Plasmodium</em> and <em>Haemoproteus</em>, and we characterized the gut microbiome using fecal samples as a proxy. Neither alpha nor beta diversity significantly varied with detected <em>Plasmodium</em> infection. However, differential abundance analysis highlighted a number of significantly varying bacteria, with the greatest representation within the phyla <em>Proteobacteria</em> and <em>Firmicutes</em> in <em>Plasmodium</em>-infected birds. These differentially abundant taxa offer a starting point for experimental work establishing the relationship between microbial abundance and <em>Plasmodium</em> infection.
description: R (https://www.r-project.org/) may be used to run all of the scripts included in the Dada2_plasmodium.html file. The parasite lineages may be examined using a tool such as Gear-Genomics (https://www.gear-genomics.com/). Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100008982<br>Award Number: GRF1945995Funding provided by: Harris World Ecology Center<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100011416<br>Award Number: Funding provided by: Sigma Xia<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100011084<br>Award Number: G2020100193156089Funding provided by: National Institutes of Health<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002<br>Award Number: AI137984Funding provided by: Des Lee Collaborative Vision*<br>Crossref Funder Registry ID: <br>Award Number:
description: Eurasian tree sparrows were sampled in Missouri, USA during 2020 and 2021. Fecal and blood samples were collected from each individual, birds were tagged with numbered color bands, and basic body measurements were taken. DNA was extracted from fecal and blood samples. Blood sample DNA was tested for haemosporidian parasites, and the positive amplicons were sequenced. Parasite sequence files are included here. Parasite lineage results are included in the metadata files. Fecal sample DNA was sequenced using 16S rRNA gene sequencing and the sequence files are uploaded on the NCBI SRA under the project number PRJNA825312. R code is uploaded here as an HTML file. Metadata files are included for 2020 and 2021 as excel sheets.