The Human Microbiome Project: An Opportunity to Engage Undergraduates in Research

Abstract The Human Microbiome Project (HMP) aims to characterize the diversity of microbial species found at several different sites on the human body. The HMP has sequenced hundreds of microbial reference genomes from multiple body sites and provides a wealth of primary genomic sequence data for analysis. Existing open source bioinformatics applications and resources allow for functional analysis of genomic data. Even budding scientists can quickly learn the tools necessary for functional gene annotation and comparative genomics analysis. These analyses in turn can provide the bases for hypothesis generation and testing at the laboratory bench. We are making use of these data and tools for student research in our NSF-sponsored project, Genome Solver. Our project has two parts: (1) development of workshops for faculty training in use of these tools, incorporated into a framework of sound pedagogy and (2) generation of a web site that will serve as an online community of practice for students, faculty, and bioinformatics experts to share work and ideas.

[1]  D. Lopatto.  Survey of Undergraduate Research Experiences (SURE): first findings. , 2004, Cell biology education.

[2]  W. Wood,et al.  Innovations in teaching undergraduate biology and why we need them. , 2009, Annual review of cell and developmental biology.

[3]  R. Kahn.  ARF Family GTPases , 2003, Proteins and Cell Regulation.

[4]  Krister Wennerberg,et al.  The Ras superfamily at a glance , 2005, Journal of Cell Science.

[5]  J. Wen,et al.  Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs. , 2007, Gene.

[6]  B. Haas,et al.  A Catalog of Reference Genomes from the Human Microbiome , 2010, Science.

[7]  J Otlewski,et al.  Structure of small G proteins and their regulators. , 2001, Acta biochimica Polonica.

[8]  Elizabeth A. Grice,et al.  The skin microbiome , 2020, Nature.

[9]  Jason M. Link,et al.  MglA, a small GTPase, interacts with a tyrosine kinase to control type IV pili‐mediated motility and development of Myxococcus xanthus , 2002, Molecular microbiology.

[10]  James Versalovic,et al.  Human microbiome in health and disease. , 2012, Annual review of pathology.

[11]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[12]  C. E. Caldon,et al.  Function of the universally conserved bacterial GTPases. , 2003, Current opinion in microbiology.

[13]  David Lopatto,et al.  Undergraduate research experiences support science career decisions and active learning. , 2007, CBE life sciences education.

[14]  Milton Glaser,et al.  Reinventing Undergraduate Education: Three Years After the Boyer Report. , 2001 .

[15]  M. Cormican,et al.  A multi-country outbreak of Salmonella Agona, February - August 2008. , 2008, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[16]  J. Walter,et al.  The human gut microbiome: ecology and recent evolutionary changes. , 2011, Annual review of microbiology.

[17]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[18]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[19]  N. Bergman,et al.  Genomic fluidity: an integrative view of gene diversity within microbial populations , 2011, BMC Genomics.

[20]  D. Allen,et al.  Approaches to biology teaching and learning: science teaching and learning across the school--university divide--cultivating conversations through scientist-teacher partnerships. , 2003, Cell biology education.

[21]  Linking Student Interests to Science Curricula , 2007, Science.

[22]  Andrew L. Zydney,et al.  Impact of Undergraduate Research Experience in Engineering , 2002 .

[23]  D. Kaiser,et al.  Function of MglA, a 22-kilodalton protein essential for gliding in Myxococcus xanthus , 1991, Journal of bacteriology.

[24]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[25]  M. Wiedmann,et al.  Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica , 2011, BMC Genomics.

[26]  C. E. Caldon,et al.  Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function , 2001, Molecular microbiology.

[27]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.