ReviewMicrobiome2017
Optimizing methods and dodging pitfalls in microbiome research.
Review in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 307 papers, 7 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
307 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- A network-based meta-analysis of the honeybee gut microbiome: geographic, seasonal, and pesticide-associated shifts.Scientific reports · 2026Pooled it
- Pooled it
- Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series.Brain and behavior · 2024Pooled it
- Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review.Viruses · 2024Pooled it
- Pooled it
- Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research.Microbiome · 2021Pooled it
- Gut Microbiota in Psychiatric Disorders: A Systematic Review.Psychosomatic medicine · 2021Pooled it
- Trial
- Trial
- Trial
- Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.PloS one · 2021Trial
- Gut dysbiosis, blood pressure regulation, and cardiometabolic risk in polyendocrine metabolic ovarian syndrome (PMOS).Reviews in endocrine & metabolic disorders · 2026Review
- Exploring the Possible Role of Endometriosis-Associated Dysbiosis in Endometrial Carcinogenesis.Medicina (Kaunas, Lithuania) · 2026Review
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.Microorganisms · 2026Review
- Article
- Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.bioRxiv : the preprint server for biology · 2026Article
- Depression of tryptophan may contribute to adverse effects of naproxen.Nature communications · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
247 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
15 authors.
Funding
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
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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.