ArticleGenes & diseases2021
Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations.
Article in Genes & diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Association of gut microbiota and inflammatory markers with enteral nutrition intolerance in patients with early-stage moderate-to-severe intracerebral hemorrhage.Microbiology spectrum · 2026Article
- Association of multi-site microbial features with malignancy risk in pulmonary ground-glass nodules and identification of predictive biomarkers: a prospective multicenter cohort study.Journal of translational medicine · 2025Article
- Rhizospheric microbiomes differ between dormant and active Potaninia mongolica in the Gobi desert of Mongolia.Scientific reports · 2025Article
- Host Genetic Effects and Phenotypic Landscapes of Rumen Bacterial Enterotypes in a Large Sheep Population.Animals : an open access journal from MDPI · 2025Article
- Evaluating the prognostic value of microbial communities in predicting recurrence of laryngeal carcinoma: a multicenter case-control study.NPJ biofilms and microbiomes · 2025Article
- Differences in Intestinal Microbiota Between White and Common Cranes in the Yellow River Delta During Winter.Biology · 2025Article
- Differential impact of spotted fever groupFrontiers in microbiology · 2025Article
- Effects of forages on the microbiota of crossed sheep on cold Plateau.Animal biotechnology · 2024Article
- Influence ofFoods (Basel, Switzerland) · 2024Article
- Gut Roseburia is a protective marker for peritoneal metastasis of gastric cancer.Cancer medicine · 2024Article
- Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation.Microorganisms · 2024Article
- A syrup containing L-arabinose and D-xylose appears superior to PEG-4000 as a bowel cleansing agent.AMB Express · 2024Article
- Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering.Microorganisms · 2024Article
- Effect ofFrontiers in veterinary science · 2024Article
- Succession of Fungal Community during Outdoor Deterioration of Round Bamboo.Journal of fungi (Basel, Switzerland) · 2023Article
- Gut microbiota and its metabolites in non-small cell lung cancer and brain metastasis: from alteration to potential microbial markers and drug targets.Frontiers in cellular and infection microbiology · 2023Article
- GutFrontiers in microbiology · 2023Article
- Analysis of bacterial community structure of Fuzhuan tea with different processing techniques.Open life sciences · 2023Article
- Correlation between microbial community and flavour formation in dry-cured squid analysed by next-generation sequencing and molecular sensory analysis.Food chemistry: X · 2022Article
- Bringing pharmacomicrobiomics to the clinic through well-designed studies.Clinical and translational science · 2022Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data analysis. While many articles have demonstrated the use of QIIME2 with suitable datasets, the application to pre-clinical data has rarely been talked about. The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis. In addition, there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find. Running the program without knowing the logic behind it is extremely risky. In this article, we first provide a guideline for analyzing 16S rRNA data using QIIME2. Then we will talk about issues in pre-clinical data, and how they could impact the outcome. Finally, we provide brief explanations of statistical methods such as group significance tests and sample size calculation.
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