ReviewmSystems2023
Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis.
Review in mSystems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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.
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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
40 citing papers in PubMed.
- Ectoparasitism and the gut microbiota: a cross-fostering experiment in a wild passerine.FEMS microbiology ecology · 2026Article
- Host Species Mediate Distinct Seed Microbiome Responses to Restoration.Microbial ecology · 2026Article
- Microbial fingerprinting of marine water masses in an Antarctic and hydrographically complex area.BMC biology · 2026Article
- Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.Scientific reports · 2026Article
- Barking up the right tree: ecological insights into the microbiome of bald cypress tree bark.Environmental microbiome · 2026Article
- Article
- Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.NPJ biofilms and microbiomes · 2026Article
- Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities.Microorganisms · 2026Article
- The influence of breast milk microbiota from HIV-infected women on infant gut microbiota colonization within the first two weeks of life.Frontiers in microbiomes · 2026Article
- Diatoms vs dinoflagellates: a temporal network analysis of bloom impacts on phytoplankton diversity and community structure in French coastal waters.ISME communications · 2026Article
- The stone-degrading metabolic potential of the urinary microbiome: Sexual dimorphism and dysbiosis in urolithiasis.AIMS microbiology · 2026Article
- A duo of fungi and complex and dynamic bacterial community networks contribute to shape the Ascophyllum nodosum holobiont.Environmental microbiome · 2025Article
- Global Distribution Patterns of Dark Matter Fungi in Cold Seep: A Metagenomic Meta-Analysis.Journal of fungi (Basel, Switzerland) · 2025Article
- Positive Interactions Under Ocean Warming and Acidification: Crustose Coralline Algae Holobionts Enhance Gorgonian Larval Settlement Under Climate Change.Environmental microbiology · 2025Article
- Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.Microbial ecology · 2025Article
- Article
- Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species,Ecology and evolution · 2025Article
- Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.Microbiome · 2025Article
- The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.Communications biology · 2025Article
- Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.Nature communications · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The concept of a core microbiome has been broadly used to refer to the consistent presence of a set of taxa across multiple samples within a given habitat. The assignment of taxa to core microbiomes can be performed by several methods based on the abundance and occupancy (i.e., detection across samples) of individual taxa. These approaches have led to methodological inconsistencies, with direct implications for ecological interpretation. Here, we reviewed a set of methods most commonly used to infer core microbiomes in divergent systems. We applied these methods using large data sets and analyzed simulations to determine their accuracy in core microbiome assignments. Our results show that core taxa assignments vary significantly across methods and data set types, with occupancy-based methods most accurately defining true core membership. We also found the ability of these methods to accurately capture core assignments to be contingent on the distribution of taxon abundance and occupancy in the data set. Finally, we provide specific recommendations for further studies using core taxa assignments and discuss the need for unifying methodical approaches toward data processing to advance ecological synthesis.
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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.