Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.

Rock pigeon (Columba livia), are domesticated birds, commonly found in urban areas worldwide. Apart from being a nuisance, pigeons are associated with 110 pathogens, with most studies focused on the bacterial and fungal diversity due to its zoonotic potential. Previously, culture-dependent technique...

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Main Author:	Vaenessa, Noni @ Boni
Format:	Thesis
Language:	English
Published:	2024
Subjects:	Q Science (General) QR Microbiology
Online Access:	http://ir.unimas.my/id/eprint/46413/3/Thesis%20Master_Vaenessa%20anak%20Noni.pdf
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id	my-unimas-ir.46413
record_format	uketd_dc
spelling	my-unimas-ir.464132024-10-23T04:35:02Z Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo. 2024-10-18 Vaenessa, Noni @ Boni Q Science (General) QR Microbiology Rock pigeon (Columba livia), are domesticated birds, commonly found in urban areas worldwide. Apart from being a nuisance, pigeons are associated with 110 pathogens, with most studies focused on the bacterial and fungal diversity due to its zoonotic potential. Previously, culture-dependent techniques in diversity studies were preferred, including bacterial and fungal studies of pigeon stool. However, the technique underestimates presence of unculturable bacteria and fungi, ultimately inaccurately reporting the actual diversity. To this day, only one study respectively has described on the bacterial and fungal diversity using culture-independent techniques worldwide. Additionally, any microbiome data on pigeon stool has not been reported in Malaysia previously. Thus, to fill this knowledge gap, this study aims to characterise the bacterial and fungal diversity and to identify potentially pathogenic bacteria and fungi in pigeon stool found in towns of Sarawak using high- throughput amplicon sequencing and to identify potentially pathogenic bacterial and fungal genera. Six samples consisting of fresh and dry stool samples were collected from four towns in Sarawak, and its microbial composition was identified through sequencing of the V3 – V4 16S rRNA and ITS2 rRNA regions. A total of 1381 and 481 bacterial and fungal amplicon sequence variants (ASVs), respectively, were identified in pigeon stool, with dry pigeon stool having higher bacterial and fungal ASVs than fresh pigeon stool. Firmicutes was the dominating bacterial pigeon stool contributed by the presence of probiotic bacteria such as Sporosarcina, Clostridium sensu stricto 1, Romboutsia, Lactobacillus and Anerosporobacter, reflecting the pigeon gut microbiome. Whereas, the dominance of Proteobacteria in dry pigeon stool was attributed to the presence of enteric bacteria such as Escherichia-Shigella and Enterococcus, which have been found to proliferate upon the excrement from the gastrointestinal tract. On the other hand, dominance of Ascomycota is contributed by the presence of Kazachstania and Neocucurbutaria. However, environmental fungal genera including Aspergillus, Trichosporon, Penicillium, Iodophanus, and Cephaliophora contributed to the dominance of Ascomycota in dry pigeon stool. Additionally, 18 bacterial and fungal genera, respectively, were flagged as potentially pathogenic. Of these, four and six bacterial and fungal genera, respectively, were not previously associated with pigeon stool. This study gives insight into the importance of utilising high-throughput amplicon sequencing for bacterial and fungal diversity characterisation, depicting the important role of fresh and dry pigeon stool in the environment. Additionally, the detection of additional pigeon-related potentially pathogenic pathogens in study shows that geographical location and immune status of the bird plays a role in the prevalence of microbes. Universiti Malaysia Sarawak 2024-10 Thesis http://ir.unimas.my/id/eprint/46413/ http://ir.unimas.my/id/eprint/46413/3/Thesis%20Master_Vaenessa%20anak%20Noni.pdf text en validuser masters Faculty of Medicine and Health Sciences Department of Paraclinical Sciences
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	Q Science (General) QR Microbiology
spellingShingle	Q Science (General) QR Microbiology Vaenessa, Noni @ Boni Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
description	Rock pigeon (Columba livia), are domesticated birds, commonly found in urban areas worldwide. Apart from being a nuisance, pigeons are associated with 110 pathogens, with most studies focused on the bacterial and fungal diversity due to its zoonotic potential. Previously, culture-dependent techniques in diversity studies were preferred, including bacterial and fungal studies of pigeon stool. However, the technique underestimates presence of unculturable bacteria and fungi, ultimately inaccurately reporting the actual diversity. To this day, only one study respectively has described on the bacterial and fungal diversity using culture-independent techniques worldwide. Additionally, any microbiome data on pigeon stool has not been reported in Malaysia previously. Thus, to fill this knowledge gap, this study aims to characterise the bacterial and fungal diversity and to identify potentially pathogenic bacteria and fungi in pigeon stool found in towns of Sarawak using high- throughput amplicon sequencing and to identify potentially pathogenic bacterial and fungal genera. Six samples consisting of fresh and dry stool samples were collected from four towns in Sarawak, and its microbial composition was identified through sequencing of the V3 – V4 16S rRNA and ITS2 rRNA regions. A total of 1381 and 481 bacterial and fungal amplicon sequence variants (ASVs), respectively, were identified in pigeon stool, with dry pigeon stool having higher bacterial and fungal ASVs than fresh pigeon stool. Firmicutes was the dominating bacterial pigeon stool contributed by the presence of probiotic bacteria such as Sporosarcina, Clostridium sensu stricto 1, Romboutsia, Lactobacillus and Anerosporobacter, reflecting the pigeon gut microbiome. Whereas, the dominance of Proteobacteria in dry pigeon stool was attributed to the presence of enteric bacteria such as Escherichia-Shigella and Enterococcus, which have been found to proliferate upon the excrement from the gastrointestinal tract. On the other hand, dominance of Ascomycota is contributed by the presence of Kazachstania and Neocucurbutaria. However, environmental fungal genera including Aspergillus, Trichosporon, Penicillium, Iodophanus, and Cephaliophora contributed to the dominance of Ascomycota in dry pigeon stool. Additionally, 18 bacterial and fungal genera, respectively, were flagged as potentially pathogenic. Of these, four and six bacterial and fungal genera, respectively, were not previously associated with pigeon stool. This study gives insight into the importance of utilising high-throughput amplicon sequencing for bacterial and fungal diversity characterisation, depicting the important role of fresh and dry pigeon stool in the environment. Additionally, the detection of additional pigeon-related potentially pathogenic pathogens in study shows that geographical location and immune status of the bird plays a role in the prevalence of microbes.
format	Thesis
qualification_level	Master's degree
author	Vaenessa, Noni @ Boni
author_facet	Vaenessa, Noni @ Boni
author_sort	Vaenessa, Noni @ Boni
title	Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
title_short	Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
title_full	Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
title_fullStr	Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
title_full_unstemmed	Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
title_sort	investigating the diversity of bacteria and fungi in rock pigeon (columba livia) stool using metagenomics in sarawak, malaysian borneo.
granting_institution	Faculty of Medicine and Health Sciences
granting_department	Department of Paraclinical Sciences
publishDate	2024
url	http://ir.unimas.my/id/eprint/46413/3/Thesis%20Master_Vaenessa%20anak%20Noni.pdf
_version_	1818611696766287872

Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.

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