Mission: Help Document & Publish Novel bacteria

After first learning about the “uncultivated majority”, then teaching about it, we started identifying environmental unknowns in the Lycoming College Bio321 Microbiology Lab. The discovery of so many unnamed microbes led to a new appreciation for the difference between uncultured and unculturable.

• In 1998, while the regular professor was on sabbatical, we did manual 16S sequencing and found an organism whose (very clean) sequence did not match anything in the database so we stored it in the freezer.

• In 2004, when transitioning to take over the Microbiology and Biochemistry courses after the other professor retired, the centerpiece of the Microbiology Lab became a 10 week course-based undergraduate research experience (CURE) to characterize and identify unknown environmental isolates. By then, we sent our 16S rRNA gene PCR products out for sequencing, and every year we found organisms whose sequence did not match database entries very well. Some students wanted to do more research on their organisms as independent study and honors projects, which led us into the field of taxonomy and systematics.

• In 2009, we applied for and received an NSF Major Research Instrumentation (MRI) grant funded by the stimulus package passed by President Obama and Congress to help recover from the Great Recession. With this grant, we purchased an Omnilog system from Biolog to perform medium scale phenotyping with their GenIII 96 well plates and large scale phenotyping with their phenotype microarray plates. We purchased the Sherlock system from Microbial ID Inc (MIDI) for Fatty Acid Methyl Ester (FAME) analysis. Lastly, we purchased an Agilent 1200 HPLC with a Diode Array Detector that is used for Respiratory Quinone and Pigment Analysis. This instrument is becoming the front end of an LC-MS Q-TOF instrument during summer 2019, further enhancing our capabilities. We have continued to learn and refine our approaches and standard operating procedures for characterizing the novel microbes discovered in our undergraduate microbiology lab, and have expanded to include collaboration with faculty at Oak Ridge National Lab, Penn State University, University of New Hampshire, Susquehanna University, SUNY Cortland and several others.

• In 2013, through the NSF and HHMI-funded Research Collaboration Network: The Genome Consortium for Active Teaching-Next Generation Sequencing Group (RCN GCAT-SEEK), we developed skills and tools for bacterial genome sequencing and analysis. The combination of genomics, cutting edge phenotyping and chemotaxonomic capabilities has led to our current pipeline outlined here to document and publish novel species.

• In 2019, NovelMicrobe.com represents the next step in the evolution of our lab to provide services and support to other researchers who have discovered novel bacteria and would like to name and publish them, but may not have the expertise or instrumentation meet the requirements of the International Committee on the Systematics of Prokaryotes (ICSP).