ReviewBriefings in bioinformatics2021
Current challenges and best-practice protocols for microbiome analysis.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 291 papers, 6 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
291 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Standardized 16S Meta-Analysis Reveals Consistent Host-Associated Patterns in Laminariales Epiphytic Microbiomes.MicrobiologyOpen · 2026Pooled it
- Pooled it
- Breast cancer and microbiome: a systematic review highlighting challenges for clinical translation.BMC women's health · 2025Pooled it
- Guideline for designing microbiome studies in neoplastic diseases.GeroScience · 2024Guideline
- The Human Respiratory Microbiome: Current Understandings and Future Directions.American journal of respiratory cell and molecular biology · 2023Pooled it
- A systematic review on the effects of exercise on gut microbial diversity, taxonomic composition, and microbial metabolites: identifying research gaps and future directions.Frontiers in physiology · 2023Pooled it
- Consumption of yacon flour and energy-restricted diet increased the relative abundance of intestinal bacteria in obese adults.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Trial
- 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
- Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.Pest management science · 2026Article
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Coenocline Simulation of Microbiome Samples: A Biologically Mechanistic Framework for Generating Ecologically Realistic Synthetic Datasets to Support Classification Method Evaluation.Pathogens (Basel, Switzerland) · 2026Article
- Microbiome and resistome of the European bison (Bison bonasus).Scientific reports · 2026Article
- The role of the microbiota in hematological malignancies: A narrative review of mechanisms and therapeutic potential.New microbes and new infections · 2026Review
- Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications.Microorganisms · 2026Review
- Microbiome-guided cancer immunotherapy: immune mechanisms, resistance pathways, and translational opportunities for precision oncology.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- Mechanisms of Gut Microbiota-Derived Metabolites in Treating Hyperuricemia: Natural Products as Interventions.Molecules (Basel, Switzerland) · 2026Review
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Gut microbiota and cancer immunotherapy: from dysbiosis to personalized immune checkpoint blockade optimization.Folia microbiologica · 2026Review
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.Environmental microbiology reports · 2026Article
231 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
Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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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.