Fecal Bacterial community and potential pathogens from Sunda Porcupine (Hystrix javanica) based on nanopore 16S rRNA amplicon sequencing

Sunda porcupine (Hystrix javanica) is an endemic rodent species to Indonesia. Potential zoonoses from this bushmeat is poorly studied although it has become a popular bushmeat in several regions Java Island. The aims of this preliminary study were to assess bacterial community and to observe any potential pathogenic bacteria in Sunda porcupine. A freshly defecated feces from a healthy Sunda porcupine was collected aseptically and then subjected for DNA extraction and 16S rRNA amplification before further process for DNA sequencing in the Nanopore MinION Mk1b. After analysis using EPI2ME Labs. A total 34 phyla were detected, dominated by Firmicutes (77.32%) followed by Bacteroidetes (14.23%), and Proteobacteria (3.26%). Meanwhile, more than 760 genera were observed, dominated by Bacteroides (5.88%), Romboutsia (4.64%) and Clostridium (3.99%). Nonpathogenic bacteria were dominantly observed in the sample but several potential pathogenic bacteria were also detected, including Shigella (0.01%), Plesiomonas shigelloides (0.01%), Prevotella loescheii (0.02%), Salmonella (0.002%) and Vibrio cholera (<0.001%). Although the pathogenic bacteria were detected in a very low proportion, their presence may raise a concern when fecal contamination occurred during meat processing. Proper hygiene and sanitation are critical parts of to prevent food borne pathogens transmission to humans.