Microbial Source Tracking for Monitoring Pest Bird Contamination in Dairy Farm Settings

Chengzhe He^1, and Laura A. Onyango¹

¹Department of Biology, Faculty of Natural and Applied Sciences, Trinity Western University Langley, British Columbia, Canada

Cite this paper:
Chengzhe He and Laura A. Onyango. Microbial Source Tracking for Monitoring Pest Bird Contamination in Dairy Farm Settings. Journal of Applied & Environmental Microbiology. 2026; 14(2):30-37. doi: 10.12691/jaem-14-2-1

Abstract

Pest bird intrusion into British Columbia (BC) dairy farms has become increasingly problematic in recent years due to changes in agricultural land use practices and habitat disruption. These birds are reservoirs of diverse microbial agents that can contribute to the transmission of zoonotic and livestock diseases, including avian influenza and Salmonellosis. In addition to health impacts on both humans and livestock, pest bird fecal contamination of livestock feed results in substantial economic losses, with estimates exceeding US$14.7 million annually across the Pacific Northwest (PNW) dairy industry. Given the direct implications for animal, environmental, and human health, as well as subsequent economic impacts, accessible microbial monitoring strategies are needed to support a One-Health approach to farm biosecurity. This study employed an in-silico method for microbial identification and source tracking to assess pest bird fecal contamination in a dairy farm in Agassiz, BC. Water trough, bedding, and cattle feed samples were collected, and DNA extracted. High-purity DNA was sequenced using the Oxford Nanopore MinION^® platform, followed by metagenomic analysis to identify microbial taxa and assess contamination sources. Bacterial taxa consistent with avian fecal microbiomes such as Escherichia, Salmonella, and Pseudomonas spp. were detected in dairy farm samples. Comparative microbial profiling revealed strong similarity between goose fecal samples and cattle feed, suggesting shared microbial signatures. The avian‑specific GFD genetic marker further confirmed the presence of avian fecal DNA in cattle feed and select water samples, indicating avian-origin contamination within the farm environment. Overall, these findings demonstrate that combined metagenomic and MST approaches provide an effective framework for rapidly identifying avian fecal contamination in dairy farm settings. This integrated workflow supports proactive biosecurity measures, reduces risks of pathogen transmission, and contributes to sustainable livestock management under a One-Health paradigm.

Keywords:
pest birds dairy farm avian fecal contamination microbial source tracking metagenomics One-Health

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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