High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling Article Swipe
YOU?
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· 2022
· Open Access
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· DOI: https://doi.org/10.1038/s41598-022-23943-x
Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41598-022-23943-x
- https://www.nature.com/articles/s41598-022-23943-x.pdf
- OA Status
- gold
- Cited By
- 14
- References
- 58
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4309181911
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4309181911Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s41598-022-23943-xDigital Object Identifier
- Title
-
High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profilingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-11-11Full publication date if available
- Authors
-
Kie Kumaishi, Erika Usui, Kenta Suzuki, Shungo Kobori, Takumi Sato, Yusuke Toda, Hideki Takanashi, Satoshi Shinozaki, Munehiro Noda, Akiko Takakura, Kayoko Matsumoto, Yuji Yamasaki, Hisashi Tsujimoto, Hiroyoshi Iwata, Yasunori IchihashiList of authors in order
- Landing page
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https://doi.org/10.1038/s41598-022-23943-xPublisher landing page
- PDF URL
-
https://www.nature.com/articles/s41598-022-23943-x.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.nature.com/articles/s41598-022-23943-x.pdfDirect OA link when available
- Concepts
-
DNA extraction, Biology, Metagenomics, 16S ribosomal RNA, Microbiome, Polymerase chain reaction, Microbial population biology, DNA sequencing, Bacteria, Computational biology, DNA, Gene, GeneticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
14Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 7, 2024: 2, 2023: 5Per-year citation counts (last 5 years)
- References (count)
-
58Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.profiling. | 219 |
| abstract_inverted_index.sequencing | 30, 73 |
| abstract_inverted_index.technology | 31 |
| abstract_inverted_index.exonuclease | 133 |
| abstract_inverted_index.maintaining | 211 |
| abstract_inverted_index.microbiota, | 9, 77 |
| abstract_inverted_index.significant | 21 |
| abstract_inverted_index.agriculture. | 55 |
| abstract_inverted_index.commercially | 185 |
| abstract_inverted_index.demonstrated | 129 |
| abstract_inverted_index.exonuclease. | 90 |
| abstract_inverted_index.purification | 88, 131, 159 |
| abstract_inverted_index.amplification | 67 |
| abstract_inverted_index.modifications | 92 |
| abstract_inverted_index.agroecosystems. | 7 |
| abstract_inverted_index.high-throughput | 208 |
| abstract_inverted_index.next-generation | 29 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 94 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 15 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/2 |
| sustainable_development_goals[0].score | 0.7099999785423279 |
| sustainable_development_goals[0].display_name | Zero hunger |
| citation_normalized_percentile.value | 0.90886499 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |