“Shovel-ready” Sequences as a Stimulus for the Next Generation of Life Scientists

Abstract

Genomics and bioinformatics are dynamic fields well-suited for capturing the imagination of undergraduates in both research laboratories and classrooms. Currently, raw nucleotide sequence is being provided, as part of several genomics research initiatives, for undergraduate research and teaching. These initiatives could be easily extended and much more effective if the source of the sequenced material and the subsequent focus of the data analysis were aligned with the research interests of individual faculty at undergraduate institutions. By judicious use of surplus capacity in existing nucleotide sequencing cores, raw sequence data could be generated to support ongoing research efforts involving undergraduates. This would allow these students to participate actively in discovery research, with a goal of making novel contributions to their field through original research while nurturing the next generation of talented research scientists.

Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome

“…The described activity also possesses the capacity to directly integrate bioinformatics exercises, where students could be provided with hands-on opportunities to familiarize themselves with bioinformatics software such as Acacia, the QIIME analysis pipeline, and reference databases used to generate the microbiome data. Students can learn to use these and other software packages by visualizing and measuring the degree of compositional similarity across bacteria taxa, as well as potentially incorporating elements of whole-genome sequencing and microbial genome annotation from previously described classroom exercises ( 6 , 11 ).…”

Microbiomes for All

“…Nearly 90% of the successfully classified sequences from the student Annotathons were bacteria, with an additional small percentage from Archaea and viruses. The student Annotathon process involves supervision and iteration to work toward a reliable sequence annotation, and is similar to models for student analysis of genomes and other biological data sets that had been developed earlier ( Goodner et al, 2001 ; Hatfull et al, 2006 ; Slawson et al, 2006 ; Pico et al, 2008 ; Boyle, 2010 ; Ditty et al, 2010 ). Beyond sequence analysis, an ambitious ecological metagenomics course was developed for upper-level undergraduates and graduate students to contribute to on-going research of California sea lions and included surface marine water and kelp forest microbiome samples ( Edwards et al, 2013 ).…”

“…Microbiome research projects are ideal for teaching microbiology in a real-world context. Importantly, large microbiome data sets can be generated and analyzed in a massively parallel fashion by students working individually or in small groups ( Hingamp et al, 2008 ; Boyle, 2010 ; Buonaccorsi et al, 2011 ; Bolyen et al, 2019 ). Students are excited by work on unanswered questions and take ownership of research projects that make use of samples they have collected in their communities and local environments ( Lopatto, 2010 ; Hanauer and Dolan, 2014 ; Weber et al, 2015 ; Cooper et al, 2019a ).…”

GCAT-SEEKquence: Genome Consortium for Active Teaching of Undergraduates through Increased Faculty Access to Next-Generation Sequencing Data

“…This was one of the key reasons for adopting a model in which an investigator requested the raw sequence data related to their research expertise and passion. (For a detailed discussion of these considerations, see Boyle [2010] .) The GCAT-SEEK network will periodically request proposals using its listserv.…”