ReviewEnvironmental microbiome2022
Ecosystem-specific microbiota and microbiome databases in the era of big data.
Review in Environmental microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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
15 citing papers in PubMed, 31 citations in OpenAlex.
- VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.Nature communications · 2025Article
- A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.Scientific reports · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Genomically-selected antifungal Bacillaceae strains improve wheat yield and baking quality.Applied microbiology and biotechnology · 2025Article
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.BMC bioinformatics · 2024Article
- A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5.Foods (Basel, Switzerland) · 2024Article
- SpeciateIT and vSpeciateDB: Novel, fast and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.bioRxiv : the preprint server for biology · 2024Article
- Review
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production.Biology · 2023Review
- Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes.Journal of the Indian Institute of Science · 2023Review
- The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms.International journal of molecular sciences · 2023Review
- MGnify: the microbiome sequence data analysis resource in 2023.Nucleic acids research · 2023Article
- Evolving approaches to profiling the microbiome in skin disease.Frontiers in immunology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.
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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.