Summer Research: Urban Environmental Genomics Project
This summer, my students and I are working through analysis of wastewater microbiome sequencing data. The analysis includes 3 timepoints, 11 sampling points, 2 wastewater treatment streams, and 3 replicates of each sample. 198 samples in total. For each sample we have 16S ribosomal and whole genome metagenome sequence data, and mass spec analysis for 10 different antibiotics of interest. Samples were collected by students in areas made accessible to us by Charlotte Water, and sequenced at DHMRI.
We need to do several different types of sequence analysis here. QC of sequence reads, sorting 16S and whole genome metagenome sequence into OTUs using various methods, specific searches for matches to antibiotic resistance genes and pathways. Then at a level above that, statistical analyses across the microbiomes at various timepoints and locations, and integration of information from sequence and mass spec analyses.
I’ll be documenting each of the analysis steps as we go along. For those interesting in playing along at home on the metagenomics side, there is a similarly structured dataset from the PathoMap project available here.