Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis

PeerJ

article

Mohd Hairul Mohd Salleh¹  Yuzine Esa¹  Mohamad Syazwan Ngalimat⁴  Pelf Nyok Chen⁵ 

[1] Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia;Royal Malaysian Customs Department;International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia;Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia;Turtle Conservation Society of Malaysia

关键词: Freshwater turtle;    16s rRNA;    Peninsular Malaysia;    V3–V4 region;    Captive and wild;    Taxonomic profile;    Gut microbiota;   

DOI  :  10.7717/peerj.12970

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY