ArticlePloS one2015
Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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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
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meat Consumption and Gut Microbiota: a Scoping Review of Literature and Systematic Review of Randomized Controlled Trials in Adults.Advances in nutrition (Bethesda, Md.) · 2023Pooled it
- Host Species Mediate Distinct Seed Microbiome Responses to Restoration.Microbial ecology · 2026Article
- Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.Frontiers in microbiology · 2024Article
- Supragingival microbiome alternations as a consequence of smoking different tobacco types and its relation to dental caries.Scientific reports · 2022Article
- Microbiota in Periodontitis: Advances in the Omic Era.Advances in experimental medicine and biology · 2022Review
- Microbial Diversity Profiling of Gut Microbiota ofMicroorganisms · 2021Article
- Evaluating tannery wastewater treatment performance based on physicochemical and microbiological characteristics: An Ethiopian case study.Water environment research : a research publication of the Water Environment Federation · 2021Article
- Analysis of T-cell receptor repertoire in peripheral blood of patients with pancreatic cancer and other pancreatic diseases.Journal of cellular and molecular medicine · 2021Article
- Restricted TcR β chain CDR3 clonotype is associated with resolved acute hepatitis B subjects.BMC infectious diseases · 2021Article
- Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues.Parasites & vectors · 2020Article
- The Penile Microbiota in Uncircumcised and Circumcised Men: Relationships With HIV and Human Papillomavirus Infections and Cervicovaginal Microbiota.Frontiers in medicine · 2020Review
- Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma.Scientific reports · 2019Article
- Considerations When Designing a Microbiome Study: Implications for Nursing Science.Biological research for nursing · 2019Article
- Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction.Journal of translational medicine · 2019Article
- Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing.PloS one · 2019Article
- The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean).Ecology and evolution · 2019Article
- T Cell Receptor Immune Repertoires Are Promptly Reconstituted After Methicillin-ResistantFrontiers in microbiology · 2019Article
- Phenotypic and Genotypic Identification of Bacteria Isolated From Traditionally Prepared Dry Starters of the Eastern Himalayas.Frontiers in microbiology · 2019Article
- Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- An adaptive microbiome α-diversity-based association analysis method.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5). Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques.
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