ArticleFEMS microbiology ecology2024
A metagenomic alpha-diversity index for microbial functional biodiversity.
Article in FEMS microbiology ecology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis 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.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut microbiota-dependent mechanisms and efficacy of natural polysaccharides in multitarget antidepressant therapy: a systematic review.Frontiers in psychiatry · 2026Pooled it
- Article
- High-throughput 16S rRNA sequencing reveals gut dysbiosis and linked hepatic toxicity in triflumezopyrim treated juvenile freshwater fish Labeo rohita.World journal of microbiology & biotechnology · 2026Article
- Global long-term agricultural experiments reveal consequences of mineral fertilization for soil microbiomes.Nature communications · 2026Article
- Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.Environmental microbiology reports · 2026Article
- Metagenomic analysis of fecal microbial communities in dairy goats from different farms.Protoplasma · 2026Article
- Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.Nutrients · 2026Article
- Gut phages are linked to off-target antimicrobial resistance genes in orthopedic patients receiving peri-surgical antibiotics.Frontiers in microbiology · 2026Article
- Gut microbiota and intestinal polyps: a systematic review and meta-analysis based on 16S rRNA gene sequencing.Gut pathogens · 2025Review
- Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Identifying the location-dependent adipose tissue bacterial DNA signatures in obese patients that predict body weight loss.Gut microbes · 2025Article
- Multi-Omics Decoding of Potential Microbial-Genetic Synergy Underlying Polysaccharide and Glycosidic Polymer Biosynthesis in Two Cultivars ofMetabolites · 2025Article
- Time-series metatranscriptomics reveals differential salinity effects on the methanogenic food web in paddy soil.mSystems · 2025Article
- Integrated multi-omics reveals the impact of ruminal keystone bacteria and microbial metabolites on average daily gain in Xuzhou cattle.Microbiology spectrum · 2025Article
- Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.Current microbiology · 2025Review
- The blueberry phyllosphere microbiota: tissue-specific core communities and their stability across cultivars and years.BMC plant biology · 2025Article
- Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.Scientific reports · 2025Article
- Bacterial colonization contributes to pathological scar formation via the regulation of inflammatory response.Journal of translational medicine · 2025Article
- Marine-DerivedFoods (Basel, Switzerland) · 2025Article
- Maternal consumption of glycerol monolaurate optimizes milk fatty acid profile and enhances piglet gut health in association with G protein-coupled receptor 84 (GPR84) activation.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2025Article
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Funding
Abstract
Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.
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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.