Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples

Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene...

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Autores principales: Love, Chloe J., Gubert, Carolina, Kodikara, Saritha, Kong, Geraldine, Lê Cao, Kim-Anh, Hannan, Anthony J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9597187/
https://www.ncbi.nlm.nih.gov/pubmed/36313541
http://dx.doi.org/10.1016/j.xpro.2022.101772
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author Love, Chloe J.
Gubert, Carolina
Kodikara, Saritha
Kong, Geraldine
Lê Cao, Kim-Anh
Hannan, Anthony J.
author_facet Love, Chloe J.
Gubert, Carolina
Kodikara, Saritha
Kong, Geraldine
Lê Cao, Kim-Anh
Hannan, Anthony J.
author_sort Love, Chloe J.
collection PubMed
description Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene V4 region sequencing, and bioinformatic analyses. This protocol includes detailed instructions and example outputs to ensure accurate, reproducible results and data visualization. Comprehensive troubleshooting and limitation sections address technical and statistical issues that may arise when profiling microbiota. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2022).
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spelling pubmed-95971872022-10-27 Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples Love, Chloe J. Gubert, Carolina Kodikara, Saritha Kong, Geraldine Lê Cao, Kim-Anh Hannan, Anthony J. STAR Protoc Protocol Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene V4 region sequencing, and bioinformatic analyses. This protocol includes detailed instructions and example outputs to ensure accurate, reproducible results and data visualization. Comprehensive troubleshooting and limitation sections address technical and statistical issues that may arise when profiling microbiota. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2022). Elsevier 2022-10-21 /pmc/articles/PMC9597187/ /pubmed/36313541 http://dx.doi.org/10.1016/j.xpro.2022.101772 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Love, Chloe J.
Gubert, Carolina
Kodikara, Saritha
Kong, Geraldine
Lê Cao, Kim-Anh
Hannan, Anthony J.
Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title_full Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title_fullStr Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title_full_unstemmed Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title_short Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
title_sort microbiota dna isolation, 16s rrna amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9597187/
https://www.ncbi.nlm.nih.gov/pubmed/36313541
http://dx.doi.org/10.1016/j.xpro.2022.101772
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