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A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia
BACKGROUND AND AIM: Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Veterinary World
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9394126/ https://www.ncbi.nlm.nih.gov/pubmed/36185528 http://dx.doi.org/10.14202/vetworld.2022.1798-1803 |
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author | Widiyani, Platika Sudarwanto, Mirnawati B. Latif, Hadri Lukman, Denny Widaya Thong, Daniel Rahayu, Puji |
author_facet | Widiyani, Platika Sudarwanto, Mirnawati B. Latif, Hadri Lukman, Denny Widaya Thong, Daniel Rahayu, Puji |
author_sort | Widiyani, Platika |
collection | PubMed |
description | BACKGROUND AND AIM: Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird’s nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island. MATERIALS AND METHODS: In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software. RESULTS: Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were Aeromonas, Escherichia, Acinetobacter, Arcobacter, and Acetoanaerobium. Those in Group B (nitrite levels <30 ppm) were Aeromonas, Pseudomonas, Shewanella, Escherichia, and Acinetobacter. There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively. CONCLUSION: This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. Aeromonas was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs. |
format | Online Article Text |
id | pubmed-9394126 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Veterinary World |
record_format | MEDLINE/PubMed |
spelling | pubmed-93941262022-09-30 A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia Widiyani, Platika Sudarwanto, Mirnawati B. Latif, Hadri Lukman, Denny Widaya Thong, Daniel Rahayu, Puji Vet World Research Article BACKGROUND AND AIM: Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird’s nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island. MATERIALS AND METHODS: In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software. RESULTS: Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were Aeromonas, Escherichia, Acinetobacter, Arcobacter, and Acetoanaerobium. Those in Group B (nitrite levels <30 ppm) were Aeromonas, Pseudomonas, Shewanella, Escherichia, and Acinetobacter. There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively. CONCLUSION: This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. Aeromonas was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs. Veterinary World 2022-07 2022-07-26 /pmc/articles/PMC9394126/ /pubmed/36185528 http://dx.doi.org/10.14202/vetworld.2022.1798-1803 Text en Copyright: © Widiyani, et al. https://creativecommons.org/licenses/by/4.0/Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Widiyani, Platika Sudarwanto, Mirnawati B. Latif, Hadri Lukman, Denny Widaya Thong, Daniel Rahayu, Puji A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title | A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title_full | A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title_fullStr | A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title_full_unstemmed | A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title_short | A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird’s nest on Sumatera Island, Indonesia |
title_sort | preliminary metagenomics study of bacteria present in the dirt of swiftlet farmhouses based on nitrite levels in edible bird’s nest on sumatera island, indonesia |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9394126/ https://www.ncbi.nlm.nih.gov/pubmed/36185528 http://dx.doi.org/10.14202/vetworld.2022.1798-1803 |
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