ReviewFrontiers in genetics2019
Advances and Challenges in Metatranscriptomic Analysis.
Review in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 186 papers, 3 of them syntheses that pooled it.
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
186 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- Microbiome in Eosinophilic Esophagitis-Metagenomic, Metatranscriptomic, and Metabolomic Changes: A Systematic Review.Frontiers in physiology · 2021Pooled it
- Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities.Frontiers in bioengineering and biotechnology · 2021Pooled it
- Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications.World journal of microbiology & biotechnology · 2026Review
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- The Role of the Oral Microbiome in the Development and Treatment of Periodontal Disease: Functional Meta-Omics Evidence.Current microbiology · 2026Review
- Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy.Molecules (Basel, Switzerland) · 2026Review
- Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.FEMS microbiology ecology · 2026Article
- Zooplankton Metabolism Shapes Molecular Composition of Dissolved Organic Matter in Coastal Waters.Environmental science & technology · 2026Article
- An Exponential Scale Mixture Model for Metatranscriptomics Data with Application to Inflammatory Bowel Disease.bioRxiv : the preprint server for biology · 2026Article
- Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.Foods (Basel, Switzerland) · 2026Review
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways.Microbiome · 2026Article
- From soil to sequences: mechanisms and tools unravelling plant-rhizomicrobiome interactions.World journal of microbiology & biotechnology · 2026Review
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Article
- Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.Applied and environmental microbiology · 2026Article
- Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.Frontiers in microbiology · 2026Review
- A Multi-omics Approach for Microbiome Data Analysis in Legumes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Revealing the Physiological Patterns of Dinoflagellates in North-Eastern Adriatic Phytoplankton.Ecology and evolution · 2026Article
126 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.
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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.