Bird Feeders in the City

In January 2021, I discovered a deceased Pine Siskin (Spinus pinus), a small songbird common to central California, in my backyard. At the time, there was an outbreak of Salmonella affecting this species and causing illness in humans, primarily along the U.S. West Coast. After consulting with my colleague from Fresno State, Dr. Joel Slade, I collected a sample and confirmed that it was indeed infected with Salmonella enterica serovar Typhimurium, the same strain causing illness in birds and humans.

In collaboration with Dr. Slade, we sequenced the genome of the bacterium and published our findings in 2022. As part of our ongoing research, we set out to understand why some songbird species, such as the Lesser Goldfinch and American Goldfinch (both members of the Spinus genus), and the more distantly related House Finch (Haemorhous mexicanus), were not succumbing to the infection, despite the fact that the Pine Siskin was.

Laboratory experiments conducted by Dr. Slade revealed that the Pine Siskin and the Lesser and American Goldfinches were unable to effectively eliminate Salmonella using bacterial killing assays (a metric of the effectiveness of the innate immune response), while the House Finch was. This unexpected finding led us to hypothesize that the Pine Siskin may have a distinct gut microbiome or variations in immune-related genes compared to the other species.

With funding from the National Science Foundation (NSF), our research team is now investigating these hypotheses. Dr. Slade will examine the immunogenetics of the birds, focusing on genes involved in immune system function. Simultaneously, my research group will conduct metagenomic analyses to identify and compare the gut microbial communities of the four species and determine if any of the microbes carry genes that encode antibiotic resistance.

Additionally, we are conducting whole genome sequencing and comparative genomic analyses of all four bird species. By identifying genetic differences between species, we hope to uncover potential factors contributing to their differential susceptibility to Salmonella enterica serovar Typhimurium.

Our research aims to shed light on the mechanisms that enable certain songbird species to resist infection with this pathogenic bacteria. This knowledge will not only contribute to our understanding of the interactions between birds and bacteria but may also have implications for human health and the management of zoonotic diseases.

Personnel involved: Jair