Detection and identification of pathogenic microorganisms in native pigeons’ fresh faecal samples within Universiti Tunku Abdul Rahman (UTAR) Kampar campus using shotgun metagenomic sequencing

Fong, Gui Ying (2026) Detection and identification of pathogenic microorganisms in native pigeons’ fresh faecal samples within Universiti Tunku Abdul Rahman (UTAR) Kampar campus using shotgun metagenomic sequencing. Master dissertation/thesis, UTAR.

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Abstract

Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. The faecal microbiota of native pigeons remains uncharacterised. This study utilised shotgun metagenomic sequencing to comprehensively analyse rock pigeon faecal microbiota and identify potential pathogens, within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. The collected fresh faecal samples were subjected to total DNA and viral genome extractions, and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. Microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, suggesting potential enteric-like issues in pigeon populations. Approximately 5.11% of the bacterial community (38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected. The presence of AMR genes and potential co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.

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