16S rRNA sequence of UMCf Bioreactor
16S Metagenomic Sequencing and qPCR. Samples were shipped to Microbial Insights, Inc. (Knoxville, TN) for molecular analysis. DNA extractions were performed, and 16S metagenomic sequencing was conducted using bacterial primers designed for the high throughput Illumina MiSeq platform. Taxonomic classification of 16S rRNA amplicon reads was performed with the Illumina 16S Metagenomics application which utilizes a curated version of the Green Genes taxonomic database and a high-performance implementation of the Ribosomal Database Project (RDP) Classifier algorithm (Wang et al. 2007). Phylogenetic operational taxonomic unit (OTU) assignment and analyses of community alpha and beta diversity was analyzed according to the Quantitative Insights Into Microbial Ecology (QIIME2) bioinformatics pipeline (Caporaso et al. 2010). Quantitative polymerase chain reaction (qPCR) was performed on QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems, Grand Island, NY). All qPCR experiments included appropriate negative (no DNA) and positive control reactions. No amplification was detected in negative controls (Ct > total cycles).