IDENTIFICATION OF Bacteroides spp. FROM DUCKS USING 16S rRNA GENE PCR ASSAY: PRELUDE TO ITS APPLICATION IN MICROBIAL SOURCE TRACKING

Abstract

Fecal pollution monitoring using fecal indicator bacteria has many limitations. Alternatively, using 16S rRNA gene Bacteroides-based polymerase chain reaction (PCR) showed promise because Bacteroides spp. are a major part of the gut microbiota. In the Philippines, duck backyard farming waste management is unmonitored. Hence, the objective of this study was to isolate Bacteroides DNA from duck feces and to establish genetic relatedness that can be used to develop new microbial source tracking markers. Fifty (50) duck fecal samples were collected. Of the 50, 20 were subjected to total DNA extraction and the remaining 30 were used for the isolation of Bacteroides. A total of 32 Bacteroides were isolated that included 6 B. nordii and 26 B. ovatus. A phylogenetic tree showing the host sources of Bacteroides generated five clusters. Four clusters came from this study, while the fifth cluster was composed of sequences from a study in Japan. This shows an intraspecies difference between Bacteroides species in the Philippines and Japan. This difference is a result of variations in the gut microbiome such as host species, diet, and geography. Results of this study will expand the present sequence database of Bacteroides from ducks that can be used in identifying sources of fecal pollution in the environment.