ArticlePeerJ2016
A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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
24 citing papers in PubMed.
- Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.Biotech (Basel (Switzerland)) · 2026Article
- Gradient inflammation in the pancreatic stump after pancreaticoduodenectomy: Two case reports and review of literature.World journal of clinical cases · 2024Article
- Article
- Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations.Frontiers in microbiology · 2023Review
- Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.Frontiers in microbiology · 2021Article
- Serum metabolites reflecting gut microbiome alpha diversity predict type 2 diabetes.Gut microbes · 2020Article
- Chemical composition and pharmacological mechanism of Qingfei Paidu Decoction and Ma Xing Shi Gan Decoction against Coronavirus Disease 2019 (COVID-19): In silico and experimental study.Pharmacological research · 2020Article
- Consumption of Stilbenes and Flavonoids is Linked to Reduced Risk of Obesity Independently of Fiber Intake.Nutrients · 2020Article
- Phyllosphere bacterial assembly in citrus crop under conventional and ecological management.PeerJ · 2020Article
- The Relationships Between the Free-Living and Particle-Attached Bacterial Communities in Response to Elevated Eutrophication.Frontiers in microbiology · 2020Article
- ThePathogens (Basel, Switzerland) · 2019Article
- 'RA and the microbiome: do host genetic factors provide the link?Journal of autoimmunity · 2019Review
- Circulating levels of the anti-oxidant indoleproprionic acid are associated with higher gut microbiome diversity.Gut microbes · 2019Article
- GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach.BMC bioinformatics · 2018Article
- Gut microbiota associations with common diseases and prescription medications in a population-based cohort.Nature communications · 2018Article
- Gut microbial diversity is associated with lower arterial stiffness in women.European heart journal · 2018Article
- The fecal metabolome as a functional readout of the gut microbiome.Nature genetics · 2018Article
- Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning-interplay between nanoflagellates and bacterioplankton.The ISME journal · 2018Article
- Article
- Heritable components of the human fecal microbiome are associated with visceral fat.Gut microbes · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods' ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts' properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.
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