ReviewGigaScience2022
Inferring microbiota functions from taxonomic genes: a review.
Review in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
67 citing papers in PubMed, 139 citations in OpenAlex.
- Pangenome analysis reveals both niche-specific "specialists" and microbial "side hustlers" in colorectal cancer microbiomes.Gut microbes · 2026Article
- The Chaetocerosphere: Chaetoceros Species and Associated Prokaryotes in a Coastal Area.Environmental microbiology reports · 2026Article
- Metabolite-Resolved Validation of Bacterial Organophosphate Transformation in Soil: A Critical Review of Selected Organophosphate Case Studies.Microorganisms · 2026Review
- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- From functional annotation to functional meaning in microbiome research.Environmental microbiome · 2026Review
- Climate-induced shifts in ectomycorrhizal explorations from long to short strategies along an elevation gradient.The New phytologist · 2026Article
- Soil Bacterial Community Structure and Functional Potential in the Caspian Drylands of Western Kazakhstan.Biology · 2026Article
- Egg microbiome of the yellow-spotted Amazon river turtle (Podocnemis unifilis) modulates fusariosis fungal infection and hatching success.Communications biology · 2026Article
- Selective survival of anaerobic digester microbes afterWater science and technology : a journal of the International Association on Water Pollution Research · 2026Article
- Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.Environmental microbiome · 2026Article
- Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.Environmental microbiology reports · 2026Article
- NativePathogens (Basel, Switzerland) · 2026Article
- BactoTraits: a trait database for exploring functional diversity of bacterial communities.Scientific data · 2026Article
- Microbiota and horizontal microbial transmission dynamics associated with bramble (Rubus spp.) flowers.Environmental microbiome · 2026Article
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- SIPdb: a stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using reverse ecology.ISME communications · 2026Article
- Effects of different intercropping patterns on tea rhizosphere environment and leaf quality.Frontiers in plant science · 2026Article
- Functional Specialisation and Diversity Shape the Rhizosphere Microbiota of Cacao and Coffee in the Amazonas Region, Peru.Environmental microbiology reports · 2025Article
- Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.Environmental microbiome · 2025Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.