ArticleScientific reports2025
Key features and guidelines for the application of microbial alpha diversity metrics.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 5 of them syntheses that pooled it.
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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.
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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.
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Who cites it
100 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Gut Microbiota Alterations Associated With Colonization by Multidrug-Resistant Organisms in ICU Patients: First Systematic Review and Meta-Analysis.MicrobiologyOpen · 2026Pooled it
- Impacts of Lifestyle and Microbiota-Targeted Interventions for Overweight and Obesity on the Human Gut Microbiome: A Systematic Review.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2026Pooled it
- The composition alteration of gut microbiota in lung cancer: a systematic review and meta-analysis.Frontiers in microbiology · 2026Pooled it
- Gut microbiota composition in responders vs. non-responders with hepatocellular carcinoma under ICI therapy: a systematic review and meta-analysis.Frontiers in medicine · 2026Pooled it
- Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.Medicina (Kaunas, Lithuania) · 2025Pooled it
- Sex-specific differences in salivary microbiota composition and their associations with metabolic health in adults with excess body weight: a secondary cross-sectional analysis.Clinical oral investigations · 2026Trial
- Association between dental flossing frequency and oral microbiome in U.S. adults.Annals of medicine · 2026Article
- Humanizing Zophobas morio larvae microbiota for rapid screening of emerging decolonization strategies against multidrug-resistant bacteria.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Airborne Bacterial and Eukaryotic Communities in Temuco, Chile, a City Dominated by Residential Wood Combustion.Life (Basel, Switzerland) · 2026Article
- Exploring the Relationship Between Sleep Disturbances, Gut Microbiota, and Cognition in Patients with Heart Failure: A Cross-Sectional Study.Medicina (Kaunas, Lithuania) · 2026Article
- Article
- Intermittent Fasting and the Gut Microbiota: Mechanisms Linking Microbial Remodeling to Metabolic and Immune Regulation.Nutrients · 2026Review
- An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.Advances in therapy · 2026Review
- Multidimensional Profiles of Microbial Contamination and Hygiene Risk Across Functional Areas in Family Hotels.Life (Basel, Switzerland) · 2026Article
- Antihypertensive effect of acupuncture involve reshaping gut microbiota and alleviating gut inflammation in spontaneously hypertensive rats.Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan · 2026Article
- Article
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- The effect of SSRI/SNRI antidepressant treatment on the gut microbiota of patients with major depressive disorder.Communications medicine · 2026Article
- Microbial Contamination of Gym Equipment: Diversity Patterns, Temporal Dynamics, Staphylococcus Hotspots, and Device-Level Risk Indices.Pathogens (Basel, Switzerland) · 2026Observational
- DNA and RNA metabarcoding reveal shared dominant seed-borne fungi.Environmental microbiome · 2026Article
40 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Studies of microbial communities vary widely in terms of analysis methods. In this growing field, the wide variety of diversity measures and lack of consistency make it harder to compare different studies. Most existing alpha diversity metrics are inherited from other disciplines and their assumptions are not always directly meaningful or true for microbiome data. Many existing microbiome studies apply one or some alpha diversity metrics with no fundamentals but also an unclear results interpretation. This work focuses on a theoretical, empirical, and comparative analysis of 19 frequently and less-frequently used microbial alpha diversity metrics grouped into 4 proposed categories, including key features of every analyzed metric with their mathematical assumptions, to provide a deeper understanding of the existing metrics and a practical implementation guide for future studies. Key metrics that should be required in microbiome analysis include richness, phylogenetic diversity, entropy, dominance of a few microbes over others, and an estimate of unobserved microbes. Collectively, these metrics contribute to a comprehensive set of analyses characterizing samples, allowing the determination of key aspects that might be otherwise obscured by partial or biased information. These guidelines enable further detailed analysis by each author according to their specific interests and clinical trials. Several practical examples are provided to illustrate how these recommendations improve the quality and depth of information obtained, facilitating better interpretation when working with microbiome data. These guidelines can be applied to both existing and future research studies, enhancing the standardization, consistency, and robustness of the analyses conducted. This approach aims to improve the capture of biological diversity, leading to better interpretations and insights.
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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.