ArticleGene2016
PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.
Article in Gene, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units.Scientific reports · 2018Pooled it
- Weather parameters and biotic factors synergistically shape the phyllosphere microbiome of pomelo (Frontiers in plant science · 2025Article
- Dynamic nesting ofEcology and evolution · 2024Article
- Untangling the complex interactions between turtle ants and their microbial partners.Animal microbiome · 2023Article
- Comparison of salivary gland and midgut microbiome in the soft ticksFrontiers in microbiology · 2023Article
- Rickettsia helvetica infection is associated with microbiome modulation in Ixodes ricinus collected from humans in Serbia.Scientific reports · 2022Article
- Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner.Frontiers in immunology · 2021Article
- Anti-Tick Microbiota Vaccine ImpactsVaccines · 2020Article
- Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota.AMB Express · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundIdentifying core microbiota is an important step for understanding the key components of microbial communities. Traditional approach that identifies core taxa at the OTU level ignores potential ecological coherence of higher rank taxa. There is a need to develop software that can systematically identify core taxa at and above the species level.
resultsHere we developed PhyloCore, an application that uses a phylogeny-based algorithm to identify core taxa at the proper taxonomic levels. It incorporates a number of features that users can set according to their needs. Using multiple gut microbiota as test cases, we demonstrate that PhyloCore is more powerful and flexible than OTU-based approaches.
conclusionsPhyloCore is a flexible and fast application that identifies core taxa at proper taxonomic levels, making it useful to sequence-based microbial ecology studies. The software is freely available at http://wolbachia.biology.virginia.edu/WuLab/Software.html.
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Registered trials
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