ArticleiMeta2022
Are short-read amplicons suitable for the prediction of microbiome functional potential? A critical perspective.
Article in iMeta, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- TwoInternational journal of molecular sciences · 2026Article
- Bacterial and fungal communities and network dynamics in Otitis media patients upon 1,8-Cineol treatment.NPJ systems biology and applications · 2026Article
- Holistic genome assembly and analysis of theIMA fungus · 2026Article
- Analysis of soil microbial community structure changes in the drainage field of the Shengli coalfield based on high-throughput sequencing.BMC microbiology · 2025Article
- The ecology and plasticity of fish skin and gill microbiomes: seeking what matters in health and disease.FEMS microbiology reviews · 2025Review
- Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.Frontiers in microbiology · 2024Article
- Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave.Frontiers in microbiology · 2023Article
- Article
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Authors and funding
2 authors.
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Abstract
Taxonomic marker gene analysis allows uncovering taxonomic profiles of microbial communities at low cost, making it omnipresent in microbiome research. There is an ever-expanding set of tools to extract further biological information from this kind of data. In this perspective, we enunciate several concerns regarding the biological validity of predicting functional potential from taxonomic profiles, especially when they are generated by short-read sequencing. The taxonomic resolution of marker genes, intragenomic variability of marker genes, and the compositional nature of microbiome data are discussed. Combining actual measurements of microbiome functions with predicted functional potentials is proposed as a powerful approach to better understand microbiome functioning. In this context, the significance of predicted functional potentials for generating and testing hypotheses is highlighted. We argue that functions of microbiomes predicted from microbiome DNA read count data generated by short-read amplicon sequencing should not serve as the only basis to draw biological inferences.
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Registered trials
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