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Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis
Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this stud...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8973471/ https://www.ncbi.nlm.nih.gov/pubmed/35368336 http://dx.doi.org/10.7717/peerj.12970 |
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author | Mohd Salleh, Mohd Hairul Esa, Yuzine Ngalimat, Mohamad Syazwan Chen, Pelf Nyok |
author_facet | Mohd Salleh, Mohd Hairul Esa, Yuzine Ngalimat, Mohamad Syazwan Chen, Pelf Nyok |
author_sort | Mohd Salleh, Mohd Hairul |
collection | PubMed |
description | Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3–V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis. |
format | Online Article Text |
id | pubmed-8973471 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-89734712022-04-02 Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis Mohd Salleh, Mohd Hairul Esa, Yuzine Ngalimat, Mohamad Syazwan Chen, Pelf Nyok PeerJ Conservation Biology Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3–V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis. PeerJ Inc. 2022-03-29 /pmc/articles/PMC8973471/ /pubmed/35368336 http://dx.doi.org/10.7717/peerj.12970 Text en ©2022 Mohd Salleh et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Conservation Biology Mohd Salleh, Mohd Hairul Esa, Yuzine Ngalimat, Mohamad Syazwan Chen, Pelf Nyok Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title | Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title_full | Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title_fullStr | Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title_full_unstemmed | Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title_short | Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis |
title_sort | faecal dna metabarcoding reveals novel bacterial community patterns of critically endangered southern river terrapin, batagur affinis |
topic | Conservation Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8973471/ https://www.ncbi.nlm.nih.gov/pubmed/35368336 http://dx.doi.org/10.7717/peerj.12970 |
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