Summary
This systematic review synthesised evidence from 100 papers on functional inference tools that predict microbial ecosystem functions from DNA metabarcoding data, a cost-effective alternative to shotgun sequencing. The authors benchmarked tool performance and identified major limitations, particularly inadequate reference genome databases for soil and other complex ecosystems compared with human microbiota. Whilst these tools show promise for ecosystem diagnosis, the review concludes that standardised indicators and repositories are needed to translate functional predictions into operational practice.
UK applicability
The findings are directly relevant to UK soil science and agricultural research, where DNA metabarcoding is increasingly adopted for monitoring soil health and function. The identified gaps in reference databases and standardisation protocols represent priorities for UK research infrastructure and policy development in precision agriculture and soil management.
Key measures
Modularity, portability, and robustness of functional prediction tools; reference genome availability; tool applicability to bacterial versus fungal functions
Outcomes reported
The authors reviewed 100 scientific papers to evaluate functional inference tools and ecological trait assignment methods based on DNA metabarcoding data. The review benchmarked advantages, specificities, and drawbacks of these bioinformatic tools for predicting microbiota functions in ecosystems.
Topic tags
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