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Complete Genome Sequences of Four Isolated Bacteria from an Undergraduate Microbiology Course Using a Hybrid Assembly Approach.

ABSTRACT: Three Gram-negative bacteria and one Gram-positive bacterium were isolated from environmental samples in an undergraduate microbiology class on the basis of antibiotic resistance. Isolate DNA was purified, sequenced, and assembled using a hybrid approach. Here, we report the genomes of Acinetobacter johnsonii CSUSB1, Aeromonas hydrophila CSUSB2, Bacillus velezensis CSUSB3, and Comamonas thiooxydans CSUSB4.

SUBMITTER: Sanders CI

PROVIDER: S-EPMC8830300 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Complete Genome Sequences of Four Isolated Bacteria from an Undergraduate Microbiology Course Using a Hybrid Assembly Approach.

Sanders Ciara I CI Ne Ville Christopher J CJ Orwin Paul M PM

Microbiology resource announcements 20220210 2

Three Gram-negative bacteria and one Gram-positive bacterium were isolated from environmental samples in an undergraduate microbiology class on the basis of antibiotic resistance. Isolate DNA was purified, sequenced, and assembled using a hybrid approach. Here, we report the genomes of Acinetobacter johnsonii CSUSB1, Aeromonas hydrophila CSUSB2, Bacillus velezensis CSUSB3, and Comamonas thiooxydans CSUSB4. ...[more]

PMID: 35142546

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Project description:Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

Dataset Information

Complete Genome Sequences of Four Isolated Bacteria from an Undergraduate Microbiology Course Using a Hybrid Assembly Approach.

Publications

Complete Genome Sequences of Four Isolated Bacteria from an Undergraduate Microbiology Course Using a Hybrid Assembly Approach.

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