Analysis of Bacterial DNA Sequences in Genomics and Metagenomics
Emily Longo ’21, Minjun Choung ’21 and Professor Funmilola Ayeni (Biology)
The global importance of microbes as beneficial and pathogenic organisms cannot be overemphasized. A variety of modern tools are available for characterizing communities of microorganisms and their genomes through genomics and metagenomics. In genomics, whole genome sequencing, genome assembly, and downstream analysis can be used to characterize pathogenicity, while the metagenomics QIIME2 pipeline can be used to characterize entire microbial communities. The aim of the current study is to learn and apply the practical assembly of bacterial genomes and the QIIME2 pipeline. Whole genome assembly and analysis were learned and applied through a case study of 18 Salmonella strains isolated from 138 fecal samples of Sokoto Gudali cattle at the University of Ibadan in Ibadan, Nigeria. The DNA was sequenced using Illumina MiSeq, assembled de novo using FastQC, Trimmomatic, SPAdes and Quast, and subjected to downstream analysis by Pathogenwatch, MLST, ABRicate, CGE, FigTree, Microreact, PATRIC, and BAGEL4. The metagenomics pipeline QIIME2 (v. 2020.6) was studied through the online “Moving Pictures” tutorial. The 18 Salmonella strains were of the species Salmonella enterica ssp. enterica belonging to five different sequence types ST5332, ST473, ST519, ST5330 and ST3961 and serovars Banalia/Tounouma, Hadar, Koketime, Hermannswerder, and Chomedey/Glostrup, respectively. There was an absence of virulence genes in all strains and 83.3% of the strains carried only one antibiotic-resistant gene, aac(6’)-laa, which suggests that these Salmonella strains pose minimal health risks. Genome assembly and analysis, as well as the QIIME2 pipeline, were learned successfully based on the same results obtained from two different operating systems. These two techniques provide insight into bacterial genomes and communities that proves valuable in an age of increasing concern about infection and disease.