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Cited by 13Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyEnvironmental DNA in Biodiversity Studies

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

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Arikawa, Koji, Hosokawa, Masahito·2023·Computational and Structural Biotechnology Journal
DOI 10.1016/j.csbj.2023.09.010PMC PMC10523443
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Abstract

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.

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Cited by

Sorted by citations

Authors
Arikawa, K., & Hosokawa, M.
Affiliations
Waseda University (JP)
Corresponding author
Hosokawa, Masahito
ORCID
Hosokawa, Masahito
Venue
Computational and Structural Biotechnology Journal
Publisher
American Association for the Advancement of Science (AAAS)
Published
2023-01
Volume
21
Pages
4508-4518
ISSN
2001-0370 (ISSN-L)
DOI
10.1016/j.csbj.2023.09.010
PMC
PMC10523443
OpenAlex
W4386690165
Cited by
13
References
6
Citations by year
2026: 3 · 2025: 8 · 2024: 2
FWCI
0.34
Type
journal article
Language
en
Open access
Licence
Locations
  • Computational and Structural Biotechnology Journal (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology
  • Japan Society for the Promotion of Science (21H01733)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords
metagenomics, single-cell genomics, microbial dark matter, reference genome database, soil microbial diversity, contig assembly, mobile genetic elements, long-read sequencing

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