ReviewProceedings of the National Academy of Sciences of the United States of America2021
Defining and quantifying the core microbiome: Challenges and prospects.
Review in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 297 papers, 3 of them syntheses 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
297 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Salivary microbial meta-analysis reveals gender differences in oral microbiota, core microbiota, and molecular markers.Frontiers in cellular and infection microbiology · 2026Pooled it
- [Advances in the Application of Forensic Microbiome Analysis in Tissue Source Inference].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2025Pooled it
- Metaproteomic portrait of the healthy human gut microbiota.NPJ biofilms and microbiomes · 2024Pooled it
- Gut microbiomes of tribal communities in India vary with dairy and grain consumption.Gut microbes · 2026Article
- The core taxa connectivity in leaf microbiomes in ash trees stands is modulated by host-related and environmental factors.Environmental microbiome · 2026Article
- Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients.Environmental microbiology reports · 2026Article
- The role of phages in plant-associated microbial communities.Essays in biochemistry · 2026Review
- Genetic dissection of the eggplant rhizosphere microbiome enables microbiome-assisted breeding.Horticulture research · 2026Article
- Host-Associated Differentiation of Gut Microbiota Among Four Crane Species Wintering in Rice Paddies Around Poyang Lake.Ecology and evolution · 2026Article
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- Microbial community structure in the firn associated with a ∼1000 km transect of the Eastern Antarctic Ice Sheet.FEMS microbiology ecology · 2026Article
- Effects of Dietary Protein and Starch Digestion Rates on Jejunal and Cecal Microbial Community States and Feed Efficiency in Raccoon Dogs.Animals : an open access journal from MDPI · 2026Article
- Bacterial Community Dynamics and Ecological Characteristics in Temporary Holding Water of Live Seafood Tanks.Biology · 2026Article
- Exploring the Development of Wild Microbiomes in the Eastern Fence Lizard.Environmental microbiology reports · 2026Article
- Salinity-adapted and core microbiota along the soil salinity gradients encircling the Tarim Basin.Environmental microbiome · 2026Article
- Exploring local and regional drivers of microbial biodiversity across freshwater ponds.FEMS microbiology ecology · 2026Article
- Multiscale Structuring of Mycorrhizal Fungal Communities of Tropical Epiphytic Orchids.Microbial ecology · 2026Article
- Social organization and habitat use shape the gut microbiome of a marine fish.The Journal of animal ecology · 2026Article
- Article
237 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
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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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.