ArticleFEMS microbiology letters2020
Expanding Tiny Earth to genomics: a bioinformatics approach for an undergraduate class to characterize antagonistic strains.
Article in FEMS microbiology letters, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 14 citations in OpenAlex.
- Optimization of Screening Media to Improve Antimicrobial Biodiscovery from Soils in Undergraduate/Citizen Science Research-Engaged Initiatives.Antibiotics (Basel, Switzerland) · 2024Article
- Draft Genome Sequences of Three Antibiotic-Producing Soil Bacteria, Staphylococcus pasteuri WAM01, Peribacillus butanolivorans WAM04, and Micrococcus yunnanensis WAM06, with Growth-Inhibiting Effects against CommensalMicrobiology resource announcements · 2022Article
- Article
- Characterizing Staphylococcus aureus from Healthy Individuals: an Authentic Research Experience for Undergraduates.Journal of microbiology & biology education · 2022Article
- Real-World Ethical Dilemmas in Laboratory Safety for Microbiology Under-Resourced and Outreach Teaching.Frontiers in microbiology · 2021Article
- Bridging Trade-Offs between Traditional and Course-Based Undergraduate Research Experiences by Building Student Communication Skills, Identity, and Interest.Journal of microbiology & biology education · 2021Article
- Is Community Relevance Enough? Civic and Science Identity Impact of Microbiology CUREs Focused on Community Environmental Justice.Frontiers in microbiology · 2020Article
- Bringing Real-World Microbiology Experiences to Undergraduate Students in Resource-Limited Environments.Frontiers in microbiology · 2020Article
- Microbiomes for All.Frontiers in microbiology · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The evolution of multidrug resistant pathogens and the diminishing supply of effective antibiotics are global crisis. Tiny Earth (TE) is undergraduate curriculum that encourage students to pursue science careers by engagement in authentic drug discovery research. Through the TE program, students identify environmental strains that inhibit other bacteria. Although these isolates may produce antibiotics based on the antagonistic phenotype, understanding the activity in regard to genome content remains elusive. Previously, we developed a transposon mutagenesis module for use with TE to identify genes involved in antibiotic production. Here, we extend this approach to a second semester undergraduate course to understand the origin of antagonism and genome diversity. Using a bioinformatics strategy, we identified gene clusters involved in activity, and with annotated genomes in hand, students were able to characterize strain diversity. Genomes were analyzed using different computational tools, including average nucleotide identity for species identification and whole genome comparisons. Because the focus of TE involves the evolution of drug resistance, predicted products in strains were identified and verified using a drug susceptibility assay. An application of this curriculum by TE members would assist in efforts with antibiotic discovery.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.