Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples
Summary: 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 r...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722006529 |
| _version_ | 1811292312149426176 |
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| author | Chloe J. Love Carolina Gubert Saritha Kodikara Geraldine Kong Kim-Anh Lê Cao Anthony J. Hannan |
| author_facet | Chloe J. Love Carolina Gubert Saritha Kodikara Geraldine Kong Kim-Anh Lê Cao Anthony J. Hannan |
| author_sort | Chloe J. Love |
| collection | DOAJ |
| description | Summary: 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). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T04:43:32Z |
| format | Article |
| id | doaj.art-994b64d8645941f88e9791e8ca8abd11 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T04:43:32Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-994b64d8645941f88e9791e8ca8abd112022-12-22T03:01:55ZengElsevierSTAR Protocols2666-16672022-12-0134101772Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samplesChloe J. Love0Carolina Gubert1Saritha Kodikara2Geraldine Kong3Kim-Anh Lê Cao4Anthony J. Hannan5The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, AustraliaThe Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia; Corresponding authorDepartment of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia; Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville VIC, 3010, AustraliaThe Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, AustraliaDepartment of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, AustraliaThe Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia; Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia; Corresponding authorSummary: 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). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722006529BioinformaticsSingle CellCancerHealth SciencesGeneticsGenomics |
| spellingShingle | Chloe J. Love Carolina Gubert Saritha Kodikara Geraldine Kong Kim-Anh Lê Cao Anthony J. Hannan Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples STAR Protocols Bioinformatics Single Cell Cancer Health Sciences Genetics Genomics |
| 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 | Bioinformatics Single Cell Cancer Health Sciences Genetics Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722006529 |
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