ReviewFrontiers in plant science2014
An introduction to the analysis of shotgun metagenomic data.
Review in Frontiers in plant science, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 252 papers, 4 of them syntheses that pooled it.
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
252 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- The mosquito gut microbiome andFrontiers in cellular and infection microbiology · 2026Pooled it
- The association between early-life gut microbiota and childhood respiratory diseases: a systematic review.The Lancet. Microbe · 2022Pooled it
- Shotgun Metagenomics and Volatilome Profile of the Microbiota of Fermented Sausages.Applied and environmental microbiology · 2018Pooled it
- Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.Journal of the International Society of Sports Nutrition · 2026Article
- Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.International journal of molecular sciences · 2026Article
- RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.Bioinformatics (Oxford, England) · 2026Article
- Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.Microbial ecology · 2026Article
- Gut check: Exploring tools, techniques, and future directions in microbiome research.Poultry science · 2026Article
- Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.bioRxiv : the preprint server for biology · 2026Article
- Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.Environmental microbiome · 2026Article
- Gut-kidney axis: Dysbiosis and renal disease.World journal of nephrology · 2026Review
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.Scientific reports · 2026Article
- A comprehensive database for biological data derived from sewage in five European cities.Database : the journal of biological databases and curation · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- DeepIMB: Imputation of non-biological zero counts in microbiome data.Genes & genomics · 2026Article
- Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.Journal of oral microbiology · 2026Article
- Review
- Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.Frontiers in microbiology · 2026Article
192 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
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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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.