16S rRNA Sequencing Using the Oxford Nanopore Minion

There has been some interest in our recent preprint describing Oxford Nanopore MinIONTM sequencing for 16S rRNA microbiome characterization and I was asked to write a post for microbenet on this technology. Disclaimers – this paper is a work in progress – our paper has not yet been peer-reviewed and we are continuing to revise …

The Importance of Microbial Eukaryotes in Premise Plumbing Systems

The environmental engineering research community now recognizes that it is important to understand the bacterial ecology of premise (building) plumbing systems to control opportunistic pathogens (OP). Many investigations, including those supported by the Sloan Foundation MoBE program, have begun to shed light on the factors driving bacterial ecology in drinking water systems. While the bacterial …

Careful Consideration of Bioinformatic Pipeline Choices Based on Study Goals

Sequencing of PCR-amplified marker regions (e.g. 16S, ITS) for characterization of sample microbial ecology is a widely-used tool in Microbiology of the Built Environmenta (MoBE) investigations. Due to the large amount of data produced by these methods, sequences are typically clustered into operational taxonomic units (OTUs) based on sequence similarity to simplify downstream processing. However, …

Moving Public Perception from Abiotic to Probiotic

The two greatest scientific breakthroughs of twentieth century, if we measure by increased life expectancy, were improvements in our ability to kill microorganisms (drinking water disinfection and the invention of antibiotics). Perhaps as a remnant of these advances, it seems to me that the average citizen has a largely abiotic mindset, seeing microorganisms as agents …