ReviewProtein & cell2021
A practical guide to amplicon and metagenomic analysis of microbiome data.
Review in Protein & cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 395 papers, 2 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
395 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.Journal of translational medicine · 2025Pooled it
- Gut microbiota translocation and dissemination in health: can it be beneficial and purposeful?Gut microbes · 2026Review
- Article
- Accounting for Variability Across Years, Depths, and Non-Target Reads Improves Quantification of Root Community Composition in Plant Mixtures.Molecular ecology resources · 2026Article
- Article
- Intratumoral microbiota in the growth of CRC and lung cancer: Comprehensive insights from etiology to therapy.iScience · 2026Review
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.Pest management science · 2026Article
- Endophytes Across the Plant Life Cycle: Potential Roles in Plant Protection, Litter Decomposition, and Nutrient Cycling.Plants (Basel, Switzerland) · 2026Review
- Quantifying the Contributions of Food, Glucose, Sleep, and Microbiome Data to Personalized Glycemic Response Prediction.Current developments in nutrition · 2026Article
- Review
- A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.Brain, behavior, & immunity - health · 2026Article
- Article
- Non-invasive Vagal Nerve Stimulation as a Potential Treatment for Repetitive Blast Trauma.bioRxiv : the preprint server for biology · 2026Article
- Salt/alkali‑tolerant Streptomyces luteus TRM 45540 improves pepper growth and soil quality in acidic and alkaline soils.BMC plant biology · 2026Article
- Article
- Host-microbial co-regulation mediates rumen volatile fatty acid production and utilization in dairy cows.Science China. Life sciences · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- Article
335 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
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.
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.