Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on t...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023003227 |
| _version_ | 1797384094065098752 |
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| author | Koji Arikawa Masahito Hosokawa |
| author_facet | Koji Arikawa Masahito Hosokawa |
| author_sort | Koji Arikawa |
| collection | DOAJ |
| description | Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications. |
| first_indexed | 2024-03-08T21:30:32Z |
| format | Article |
| id | doaj.art-c9d16088ff9148948c5bb078e36d7100 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:32Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-c9d16088ff9148948c5bb078e36d71002023-12-21T07:32:06ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012145084518Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomicsKoji Arikawa0Masahito Hosokawa1Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, JapanDepartment of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Corresponding author at: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, JapanOwing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.http://www.sciencedirect.com/science/article/pii/S2001037023003227MetagenomicsSingle-cell genomicsMicrobiomeDatabaseMetagenome-assembled genomeSingle amplified genome |
| spellingShingle | Koji Arikawa Masahito Hosokawa Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics Computational and Structural Biotechnology Journal Metagenomics Single-cell genomics Microbiome Database Metagenome-assembled genome Single amplified genome |
| title | Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics |
| title_full | Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics |
| title_fullStr | Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics |
| title_full_unstemmed | Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics |
| title_short | Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics |
| title_sort | uncultured prokaryotic genomes in the spotlight an examination of publicly available data from metagenomics and single cell genomics |
| topic | Metagenomics Single-cell genomics Microbiome Database Metagenome-assembled genome Single amplified genome |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023003227 |
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