Multiple levels of the unknown in microbiome research
Open accessAbstract
Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered using metagenomics, but different kinds of "unknowns" still remain in a microbiome experiment. We discuss here whether and how it is possible to deal with them.
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20%-50% of shotgun metagenomic reads cannot be mapped.
“Based on what is known and what is feasible, 20%-50% of shotgun metagenomic reads cannot be mapped, 30%-50% of identified genes are of unknown function, and most strikingly, 80%-90% of metabolites cannot be identified. 135,147”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [147]
Complete characterization of stool composition is so far impossible to achieve, even with the most recent multiomic approaches.
“However, the complete characterization of stool composition is so far impossible to achieve, even with the most recent multiomic approaches.”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [147]
80%-90% of metabolites cannot be identified.
“Based on what is known and what is feasible, 20%-50% of shotgun metagenomic reads cannot be mapped, 30%-50% of identified genes are of unknown function, and most strikingly, 80%-90% of metabolites cannot be identified. 135,147”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [147]
30%-50% of identified genes are of unknown function.
“Based on what is known and what is feasible, 20%-50% of shotgun metagenomic reads cannot be mapped, 30%-50% of identified genes are of unknown function, and most strikingly, 80%-90% of metabolites cannot be identified. 135,147”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [147]
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- Authors
- Thomas, A. M., & Segata, N.
- Affiliations
- University of Trento (IT)
- Corresponding author
- Segata, Nicola
- Venue
- BMC Biology
- Published
- 2019-06-12
- Volume
- 17
- Issue
- 1
- Pages
- 48-48
- ISSN
- 1741-7007 (ISSN-L)
- PMC
- PMC6560723
- OpenAlex
- W2950447040
- Cited by
- 176
- References
- 13
- Citations by year
- 2026: 14 · 2025: 20 · 2024: 25 · 2023: 23 · 2022: 29 · 2021: 36 · 2020: 25 · 2019: 4
- FWCI
- 8.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by)
- Funders
- Ministero dell’Istruzione, dell’Università e della Ricerca (H2020, RBFR13EWWI_001)
- LEO Pharma
- Horizon 2020 Framework Programme (MASTER-818368, OncoBiome 825410, 818368, ONCOBIOME-825410 project, MASTER-818368 project, 825410)
- H2020 European Research Council (716575)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- microbiome research, metagenomics, microbial communities, unculturable microorganisms, unknown genes, microbial diversity, experimental design
- MeSH terms
- Archaea, Bacteria, Bacterial Physiological Phenomena, Metagenome, Metagenomics, Microbiota
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