ReviewFrontiers in microbiology2017
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.
Review in Frontiers in microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 4 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
132 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Fungal backpackers-the mycobiome ofFrontiers in microbiology · 2025Pooled it
- A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease.Molecular psychiatry · 2023Pooled it
- The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis.Scientific reports · 2022Pooled it
- The Application of High-Throughput Technologies for the Study of Microbiome and Cancer.Frontiers in genetics · 2021Pooled it
- Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses.Translational psychiatry · 2021Trial
- Signatures of oral microbiome in HIV-infected individuals with oral Kaposi's sarcoma and cell-associated KSHV DNA.PLoS pathogens · 2020Trial
- Soil microbial growth rate, trophic strategy, and the oligotroph-copiotroph continuum.Applied and environmental microbiology · 2026Article
- Low determinism in community assembly of transient and resident pelagic fungi across climate zones in Scandinavian lakes.mSystems · 2026Article
- Ecology of protection: probiotic biogeography and sepsis prevention in the neonatal intestine.mBio · 2026Article
- RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2.Bioinformatics (Oxford, England) · 2026Article
- Enhancing the understanding of environmental microbiomes through topic modeling: a quantitative and qualitative analysis.Environmental microbiome · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Helicoverpa armigera (Lepidoptera, Noctuidae) as a reservoir of potential polystyrene-degrading fungi.BMC microbiology · 2026Article
- Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods and a Vagina-Specific 16S rRNA Gene Database.Microorganisms · 2026Article
- Ammonia fumigation combined with nitrogen inhibitor reduces root-knot nematode populations and NFrontiers in microbiology · 2026Article
- Bayesian inference captures metabolite-bacteria interactions in a microbial community.ISME communications · 2026Article
- Harnessing the gut microbiome to combat tuberculosis: a technological and clinical review.Frontiers in cellular and infection microbiology · 2026Review
- Dependence of Bacterial OTUs on Selected Features of Beaver Ponds.Ecology and evolution · 2025Article
- Changes in Microbial Communities in Industrial Anaerobic Digestion of Dairy Manure Caused byBiotech (Basel (Switzerland)) · 2025Article
- The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.Scientific reports · 2025Article
72 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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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.