ArticlemSystems2021
Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 2 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
23 citing papers in PubMed, 2 syntheses or guidelines pooled 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
- Evaluating 16S metagenomics data analysis pipelines using an Ion Torrent sequencer for human gut microbiome research.BMC microbiology · 2026Article
- Higher-dimensional ordination analysis teases out impacts ofMicrobiology spectrum · 2026Article
- Distinct Gut Microbiome Characteristics Associated with Mental Health Symptoms of Healthy Adults.Brain sciences · 2026Article
- TAGINE: fast taxonomy-based feature engineering for microbiome analysis.Bioinformatics advances · 2026Article
- Gum Arabic modulates the microbiota-gut-brain axis and affects general fitness in zebrafish.Scientific reports · 2025Article
- The Impact of Endocrine Disruptors on the Female Genital Tract Microbiome: A Narrative Review.Life (Basel, Switzerland) · 2025Review
- Accurate prediction of absolute prokaryotic abundance from DNA concentration.Cell reports methods · 2025Article
- Association between gut microbiota and short-chain fatty acids in children with obesity.Scientific reports · 2025Article
- Comparative metagenomic analysis on COPD and health control samples reveals taxonomic and functional motifs.Frontiers in microbiology · 2025Article
- Airway Microbiota Profiles in Children With and Without Asthma: A Comparative Study.Journal of asthma and allergy · 2025Article
- Article
- A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.Genome biology · 2024Article
- Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis.International journal of molecular sciences · 2024Article
- Gut microbiota signatures in inflammatory bowel disease.United European gastroenterology journal · 2024Article
- Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.Animal microbiome · 2023Article
- Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.Nature communications · 2023Article
- TaxaHFE: a machine learning approach to collapse microbiome datasets using taxonomic structure.Bioinformatics advances · 2023Article
- Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples.International journal of environmental research and public health · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reproducibility is a major issue in microbiome studies, which is partly caused by missing consensus about data analysis strategies. The complex nature of microbiome data, which are high-dimensional, zero-inflated, and compositional, makes them challenging to analyze, as they often violate assumptions of classic statistical methods. With advances in human microbiome research, research questions and study designs increase in complexity so that more sophisticated data analysis concepts are applied. To improve current practice of the analysis of microbiome studies, it is important to understand what kind of research questions are asked and which tools are used to answer these questions. We conducted a systematic literature review considering all publications focusing on the analysis of human microbiome data from June 2018 to June 2019. Of 1,444 studies screened, 419 fulfilled the inclusion criteria. Information about research questions, study designs, and analysis strategies were extracted. The results confirmed the expected shift to more advanced research questions, as one-third of the studies analyzed clustered data. Although heterogeneity in the methods used was found at any stage of the analysis process, it was largest for differential abundance testing. Especially if the underlying data structure was clustered, we identified a lack of use of methods that appropriately addressed the underlying data structure while taking into account additional dependencies in the data. Our results confirm considerable heterogeneity in analysis strategies among microbiome studies; increasingly complex research questions require better guidance for analysis strategies.
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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.