Comparison of bacterial diversity from goat farm and sewage treatment plant effluent using metagenomic analysis

Abstract

The need for clean water is challenging when the effectiveness of monitoring the source of pollution is still in question. Water pollution due to fecal contamination has been linked with the entry of sewage from animal husbandry through non-point sources. Due to the inherent limitations of conventional fecal indicator bacteria, microbial source tracking is more appropriate to resolve fecal pollution from non-point sources. Microbial community analysis is the current interest of microbial source tracking. Thus, this project aimed to study the metagenomic microbial community of goat farm effluent to determine its unique microbe for source tracking of goat fecal pollution. Effluents from Osman Goat Farm and sewage treatment plant (STP) in UTM were collected. The STP sample functioned as a reference for comparison. Total DNA from both samples was extracted using the phenol-chloroform method. 16 S rDNA sequencing analysis was done to determine their microbial community. Sequencing results showed 316 Operational Taxonomic Units (OTU) represented the goat farm effluent sample, yielding 93 bacterial genera whereas 523 OTUs were in the STP and assigned to 295 bacterial genera. Twenty four genera from the STP effluent sample were associated with human microbes. Proteobacteria such as Alphaproteobacteria and Gammaproteobacteria were observed as dominant in the STP (44.3%) and associated with the human gut. In the goat farm effluent sample, Bacteroidetes (28.6%) and Firmicutes (49.5%) phyla were dominant. Comparing both samples at the genus level found Saccharofermentans uncultured rumen bacterium and Bacteroidales RF16 uncultured bacterium were genera specific to and differentiate goat farm effluent from the human STP effluent, although both genera were common in other ruminants. In conclusion, 16S rDNA metagenomic sequencing successfully distinguished goat farm effluent from human STP effluent. Suggestions were proposed that the genera be best identified to species level for better association with the goat farm. Their persistence in withstanding artificial external environments must be confirmed before they can be used as goat farm-specific microbial community markers.