High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia
Sea cucumbers are soft-bodied marine organisms found in the benthic environment which are known as trepang, gamat or timun laut by locals. Sea cucumbers are commercially exploited for their body extracts due to their therapeutic properties and as culinary demands. Moreover, sea cucumbers are host to...
| Main Authors: | , , , , |
|---|---|
| Format: | Conference or Workshop Item |
| Language: | English |
| Published: |
AIP Publishing
2023
|
| Subjects: | |
| Online Access: | http://umpir.ump.edu.my/id/eprint/39709/ http://umpir.ump.edu.my/id/eprint/39709/1/High-throughput%20amplicon%20sequencing%20of%20gut%20microbiome%20sea%20cucumber%20in%20Pahang.pdf |
| _version_ | 1848825843573325824 |
|---|---|
| author | Choo, Mei-Yen Muhammad Fitri, Yusof Shamrulazhar Shamzir, Kamal Nielsen, Dennis Sandris Hajar Fauzan, Ahmad |
| author_facet | Choo, Mei-Yen Muhammad Fitri, Yusof Shamrulazhar Shamzir, Kamal Nielsen, Dennis Sandris Hajar Fauzan, Ahmad |
| author_sort | Choo, Mei-Yen |
| building | UMP Institutional Repository |
| collection | Online Access |
| description | Sea cucumbers are soft-bodied marine organisms found in the benthic environment which are known as trepang, gamat or timun laut by locals. Sea cucumbers are commercially exploited for their body extracts due to their therapeutic properties and as culinary demands. Moreover, sea cucumbers are host to complex community of microbes. However, less efforts were documented on the identification of these microbial communities using high-throughput sequencing approach. The purpose of this study is to identify the gut microbiome of the sea cucumber from Stichopus ocellatus species. For this study, the sea cucumbers were collected from a coastal area in Pahang, Malaysia. The gut contents were sampled and processed fresh upon collection and maintained on ice prior delivery to the storage facility. The DNA was extracted prior two steps Polymerase Chain Reaction (PCR) for amplicon library preparation by targeting the V4 region of 16S rRNA. The prepared libraries were sequenced using the Illumina iSeq 100 system. The raw data were analysed using QIIME2 and other bioinformatics software. Here, we observed that the gut of Stichopus ocellatus is home for the genera of Vibrio, Tropicibacter, Desulfopila and Halioglobus. Remarkably, the bacteria from the genus Vibrio are the most abundant bacteria colonising the gut microenvironment. This study suggests baseline microbial community that inhibit the gut of sea cucumber that may confer biotechnological important bacteria for pharmaceutical applications and drug development. |
| first_indexed | 2025-11-15T03:35:22Z |
| format | Conference or Workshop Item |
| id | ump-39709 |
| institution | Universiti Malaysia Pahang |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T03:35:22Z |
| publishDate | 2023 |
| publisher | AIP Publishing |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | ump-397092023-12-21T03:12:51Z http://umpir.ump.edu.my/id/eprint/39709/ High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia Choo, Mei-Yen Muhammad Fitri, Yusof Shamrulazhar Shamzir, Kamal Nielsen, Dennis Sandris Hajar Fauzan, Ahmad Q Science (General) RM Therapeutics. Pharmacology TP Chemical technology Sea cucumbers are soft-bodied marine organisms found in the benthic environment which are known as trepang, gamat or timun laut by locals. Sea cucumbers are commercially exploited for their body extracts due to their therapeutic properties and as culinary demands. Moreover, sea cucumbers are host to complex community of microbes. However, less efforts were documented on the identification of these microbial communities using high-throughput sequencing approach. The purpose of this study is to identify the gut microbiome of the sea cucumber from Stichopus ocellatus species. For this study, the sea cucumbers were collected from a coastal area in Pahang, Malaysia. The gut contents were sampled and processed fresh upon collection and maintained on ice prior delivery to the storage facility. The DNA was extracted prior two steps Polymerase Chain Reaction (PCR) for amplicon library preparation by targeting the V4 region of 16S rRNA. The prepared libraries were sequenced using the Illumina iSeq 100 system. The raw data were analysed using QIIME2 and other bioinformatics software. Here, we observed that the gut of Stichopus ocellatus is home for the genera of Vibrio, Tropicibacter, Desulfopila and Halioglobus. Remarkably, the bacteria from the genus Vibrio are the most abundant bacteria colonising the gut microenvironment. This study suggests baseline microbial community that inhibit the gut of sea cucumber that may confer biotechnological important bacteria for pharmaceutical applications and drug development. AIP Publishing 2023-02 Conference or Workshop Item PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/39709/1/High-throughput%20amplicon%20sequencing%20of%20gut%20microbiome%20sea%20cucumber%20in%20Pahang.pdf Choo, Mei-Yen and Muhammad Fitri, Yusof and Shamrulazhar Shamzir, Kamal and Nielsen, Dennis Sandris and Hajar Fauzan, Ahmad (2023) High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia. In: AIP Conference Proceedings. AIP Conference Proceedings; 3rd Symposium on Industrial Science and Technology, SISTEC 2021 , 25 - 26 August 2021 , Pahang, Virtual. pp. 1-2., 2682 (050009). ISSN 0094-243X ISBN 978-073544326-6 (Published) https://doi.org/10.1063/5.0114373 |
| spellingShingle | Q Science (General) RM Therapeutics. Pharmacology TP Chemical technology Choo, Mei-Yen Muhammad Fitri, Yusof Shamrulazhar Shamzir, Kamal Nielsen, Dennis Sandris Hajar Fauzan, Ahmad High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title | High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title_full | High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title_fullStr | High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title_full_unstemmed | High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title_short | High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia |
| title_sort | high-throughput amplicon sequencing of gut microbiome sea cucumber in pahang, malaysia |
| topic | Q Science (General) RM Therapeutics. Pharmacology TP Chemical technology |
| url | http://umpir.ump.edu.my/id/eprint/39709/ http://umpir.ump.edu.my/id/eprint/39709/ http://umpir.ump.edu.my/id/eprint/39709/1/High-throughput%20amplicon%20sequencing%20of%20gut%20microbiome%20sea%20cucumber%20in%20Pahang.pdf |