Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes
Abstract The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal o...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12866-023-03037-y |
| _version_ | 1797453688530272256 |
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| author | Asako Tan Senthil Murugapiran Alaya Mikalauskas Jeff Koble Drew Kennedy Fred Hyde Victor Ruotti Emily Law Jordan Jensen Gary P. Schroth Jean M. Macklaim Scott Kuersten Brice LeFrançois Daryl M. Gohl |
| author_facet | Asako Tan Senthil Murugapiran Alaya Mikalauskas Jeff Koble Drew Kennedy Fred Hyde Victor Ruotti Emily Law Jordan Jensen Gary P. Schroth Jean M. Macklaim Scott Kuersten Brice LeFrançois Daryl M. Gohl |
| author_sort | Asako Tan |
| collection | DOAJ |
| description | Abstract The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome. |
| first_indexed | 2024-03-09T15:26:14Z |
| format | Article |
| id | doaj.art-4eb70698f25f4d8a8f6a55e39aaa7355 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-03-09T15:26:14Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-4eb70698f25f4d8a8f6a55e39aaa73552023-11-26T12:30:33ZengBMCBMC Microbiology1471-21802023-10-0123111710.1186/s12866-023-03037-yRational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomesAsako Tan0Senthil Murugapiran1Alaya Mikalauskas2Jeff Koble3Drew Kennedy4Fred Hyde5Victor Ruotti6Emily Law7Jordan Jensen8Gary P. Schroth9Jean M. Macklaim10Scott Kuersten11Brice LeFrançois12Daryl M. Gohl13Illumina, IncDiversigen, IncDNA Genotek, IncIllumina, IncIllumina, IncIllumina, IncIllumina, IncDiversigen, IncDiversigen, IncIllumina, IncDNA Genotek, IncIllumina, IncDNA Genotek, IncDiversigen, IncAbstract The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome.https://doi.org/10.1186/s12866-023-03037-yNext-generation sequencingMicrobiomeMetatranscriptomicsrRNA depletion |
| spellingShingle | Asako Tan Senthil Murugapiran Alaya Mikalauskas Jeff Koble Drew Kennedy Fred Hyde Victor Ruotti Emily Law Jordan Jensen Gary P. Schroth Jean M. Macklaim Scott Kuersten Brice LeFrançois Daryl M. Gohl Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes BMC Microbiology Next-generation sequencing Microbiome Metatranscriptomics rRNA depletion |
| title | Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes |
| title_full | Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes |
| title_fullStr | Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes |
| title_full_unstemmed | Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes |
| title_short | Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes |
| title_sort | rational probe design for efficient rrna depletion and improved metatranscriptomic analysis of human microbiomes |
| topic | Next-generation sequencing Microbiome Metatranscriptomics rRNA depletion |
| url | https://doi.org/10.1186/s12866-023-03037-y |
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