Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery

Amanda Hurley¹, Marc G Chevrette¹, Deepa D Acharya¹, Gabriel L Lozano^{1

2}, Manuel Garavito¹, Jen Heinritz¹, Luis Balderrama^{1

3}, Mara Beebe¹, Martel L DenHartog¹, Kamiyah Corinaldi^{4

5}, Renee Engels¹, Alyssa Gutierrez^{4

6}, Orli Jona¹, Josephine H I Putnam¹, Brody Rhodes^{4

7}, Tiffany Tsang⁸, Simon Hernandez⁹, Carol Bascom-Slack¹⁰, Jessamina E Blum¹¹, Paul A Price¹², Debra Davis¹³, Joanna Klein¹⁴, Joshua Pultorak¹, Nora L Sullivan¹⁵, Nigel J Mouncey¹⁶, Pieter C Dorrestein¹⁷, Sarah Miller⁴, Nichole A Broderick^{18

19}, Jo Handelsman²⁰

Affiliations

¹ Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
² Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
³ Hamline University, Minneapolis, Minnesota, USA.
⁴ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁵ Colorado State University, Fort Collins, Colorado, USA.
⁶ University of Alabama, Tuscaloosa, Alabama, USA.
⁷ University of West Alabama, Livingston, Alabama, USA.
⁸ Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.
⁹ University of Rochester Medical Center, Rochester, New York, USA.
¹⁰ Department of Medical Education, Tufts University, Boston, Massachusetts, USA.
¹¹ University of Minnesota Medical School, Minneapolis, Minnesota, USA.
¹² Department of Biology, Eastern Michigan University, Ypsilanti, Michigan, USA.
¹³ Department of Biology, Wingate University, Wingate, North Carolina, USA.
¹⁴ Department of Biology and Biochemistry, University of Northwestern-St. Paul, Saint Paul, Minnesota, USA.
¹⁵ Biology Department, Citrus College, Glendora, California, USA.
¹⁶ Joint Genome Institute, Berkeley, California, USA.
¹⁷ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
¹⁸ Department of Molecular and Cell Biology, University of Connecticut, Mansfield, Connecticut, USA nbroder1@jhu.edu jo.handelsman@wisc.edu.
¹⁹ Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
²⁰ Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA nbroder1@jhu.edu jo.handelsman@wisc.edu.

PMID: 33593964
PMCID: PMC8545114
DOI: 10.1128/mBio.03432-20

Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery

Amanda Hurley et al. mBio. 2021.

. 2021 Feb 16;12(1):e03432-20.

doi: 10.1128/mBio.03432-20.

Authors

Affiliations

¹ Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
² Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
³ Hamline University, Minneapolis, Minnesota, USA.
⁴ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA.
⁵ Colorado State University, Fort Collins, Colorado, USA.
⁶ University of Alabama, Tuscaloosa, Alabama, USA.
⁷ University of West Alabama, Livingston, Alabama, USA.
⁸ Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.
⁹ University of Rochester Medical Center, Rochester, New York, USA.
¹⁰ Department of Medical Education, Tufts University, Boston, Massachusetts, USA.
¹¹ University of Minnesota Medical School, Minneapolis, Minnesota, USA.
¹² Department of Biology, Eastern Michigan University, Ypsilanti, Michigan, USA.
¹³ Department of Biology, Wingate University, Wingate, North Carolina, USA.
¹⁴ Department of Biology and Biochemistry, University of Northwestern-St. Paul, Saint Paul, Minnesota, USA.
¹⁵ Biology Department, Citrus College, Glendora, California, USA.
¹⁶ Joint Genome Institute, Berkeley, California, USA.
¹⁷ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
¹⁸ Department of Molecular and Cell Biology, University of Connecticut, Mansfield, Connecticut, USA nbroder1@jhu.edu jo.handelsman@wisc.edu.
¹⁹ Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
²⁰ Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA nbroder1@jhu.edu jo.handelsman@wisc.edu.

PMID: 33593964
PMCID: PMC8545114
DOI: 10.1128/mBio.03432-20

Abstract

The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

Keywords: antimicrobial activity; crowdsourcing; multiomics.

PubMed Disclaimer

Figures

**FIG 1**
Tiny Earth Chemistry Hub pipeline. (A) Heat map of global Tiny Earth partner institutions. (B) Strains are catalogued and stored at the Chemistry Hub where each strain is then tested against the safe relatives of ESKAPE pathogens to verify activity profile. Molecules from active strains are extracted in organic solvents. (C, left) Phylum affiliations of strains submitted to the Chemistry Hub as determined by 16S rRNA gene sequencing. NCBI (National Center for Biotechnology Information) catalogues all known sequenced organisms. (C, right) Growth medium differentially affects discovery rate of antibiotic-producing bacteria based on target bacteria. Tryptic soy agar (TSA) enhances isolation of bacteria that inhibit Erwinia carotovora, while potato dextrose agar (PDA) favors inhibition of Acinetobacter baylyi and Pseudomonas putida. Results shown for the three target bacteria are from three separate soils, suggesting soil origin influences media specificity. (D, left) DNA is extracted for whole-genome sequencing and chemical compounds are harvested for mass determination to search for novel patterns. Putative biosynthetic pathways for potential antibiotics are organized in clusters by similarity, with green circles representing similarity to pathways of known function and purple indicating those of unknown function. (D, right) Families of molecules produced by sequenced strains with the same color legend as the left panel. (E) Using both genomic and metabolomic data, strains with potentially novel chemistry are prioritized to purify molecules and determine the structure and activity of a new antibiotic; the structure of soil-derived zwittermicin (37) is shown as an example.

See this image and copyright information in PMC

References

1. National Academies of Science, Engineering, and Medicine. 2016. Barriers and opportunities for 2-year and 4-year STEM degrees: systemic change to support students’ diverse pathways. Malcolm S, Feder M (ed), National Academies Press, Washington, DC. - PubMed
1. President’s Council of Advisors on Science and Technology. 2012. Report to the president, engage to excel: producing one million additional college graduates with degrees in science, technology, engineering, and mathematics. https://aaas-arise.org/resource/engage-to-excel-producing-one-million-ad....
1. Seymour E., Hunter A.-B., ed, 2019. Talking about leaving revisited: persistence, relocation, and loss in undergraduate STEM education. Springer Nature, Cham Switzerland.
1. Theobald EJ, Hill MJ, Tran E, Agrawal S, Arroyo EN, Behling S, Chambwe N, Cintrón DL, Cooper JD, Dunster G, Grummer JA, Hennessey K, Hsiao J, Iranon N, Jones L, Jordt H, Keller M, Lacey ME, Littlefield CE, Lowe A, Newman S, Okolo V, Olroyd S, Peecook BR, Pickett SB, Slager DL, Caviedes-Solis IW, Stanchak KE, Sundaravardan V, Valdebenito C, Williams CR, Zinsli K, Freeman S. 2020. Active learning narrows achievement gaps for underrepresented students in undergraduate science, technology, engineering, and math. Proc Natl Acad Sci U S A 117:6476–6483. doi:10.1073/pnas.1916903117. - DOI - PMC - PubMed
1. Miller S, Pfund C, Pribbenow CM, Handelsman J. 2008. The pipeline. Scientific teaching in practice. Science 322:1329–1330. doi:10.1126/science.1166032. - DOI - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

LinkOut - more resources

Full Text Sources
- Atypon
Medical
- MedlinePlus Health Information

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery

Affiliations

Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery

Authors

Affiliations

Abstract

Figures

References

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Medical