ArticleMethods in enzymology2013
Advancing our understanding of the human microbiome using QIIME.
Article in Methods in enzymology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 331 papers, 1 of them a synthesis 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
331 citing papers in PubMed, 1 synthesis or guideline pooled it, 620 citations in OpenAlex.
- Qiita: rapid, web-enabled microbiome meta-analysis.Nature methods · 2018Pooled it
- Fecal microbiota transplantation in the treatment of irritable bowel syndrome: a single-center prospective study in Japan.BMC gastroenterology · 2022Trial
- Ulmus macrocarpa Hance extract modulates intestinal microbiota in healthy adults: a randomized, placebo-controlled clinical trial.Journal of microbiology (Seoul, Korea) · 2021Trial
- Clinical utility of subgingival plaque-specific bacteria in salivary microbiota for detecting periodontitis.PloS one · 2021Trial
- Rosuvastatin alters the genetic composition of the human gut microbiome.Scientific reports · 2020Trial
- Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage.Scientific reports · 2019Trial
- Article
- Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- Impact of carbapenem-resistantMicrobiology spectrum · 2026Article
- Effect of a fructooligosaccharides fraction fromBioscience of microbiota, food and health · 2026Article
- Decoding the reproductive microbiome: enabling clinical and biological insights through machine and deep learning.Frontiers in endocrinology · 2026Review
- Impact of data compositionality on the detection of microbiota responses.Gut microbes · 2025Article
- Article
- Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study.Journal of family medicine and primary care · 2025Article
- Gut microbiota dysbiosis and systemic immune dysfunction in critical ill patients with multidrug-resistant bacterial colonization and infection.Journal of translational medicine · 2025Article
- Probiotic and Vitamin D Ameliorate TNBS-Induced Colitis by Targeting Mucosal Barrier and Neutrophil Infiltration.Nutrients · 2025Article
- Review
- The Impact of the Skin Microbiome and Oxidative Stress on the Initiation and Development of Cutaneous Chronic Wounds.Antioxidants (Basel, Switzerland) · 2025Review
- Oral microbiota related to allergy in Norwegian adults.The journal of allergy and clinical immunology. Global · 2025Article
- Association of Intratumoral Microbiota with Prognosis in Patients with Lacrimal Gland Tumor.Biomedicines · 2025Article
271 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
16 authors at 6 institutions in 2 countries.
Funding
Abstract
High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.
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.