The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
Open accessAbstract
Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.
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Cited by
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493
Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
Prodan, A., Tremaroli, V., Brolin, H., Zwinderman, A. H., Nieuwdorp, M., & Levin, E. (2020) · PLOS ONE · doi:10.1371/journal.pone.0227434 · Cited by 462
The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth
Stinson, L. F., Boyce, M. C., Payne, M. S., & Keelan, J. A. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01124 · Cited by 389
Nearing, J. T., Douglas, G. M., Comeau, A. M., & Langille, M. G. I. (2018) · PeerJ · doi:10.7717/peerj.5364 · Cited by 355
Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet
Bisanz, J. E., Upadhyay, V., Turnbaugh, J. A., Ly, K., & Turnbaugh, P. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.06.013 · Cited by 333
Metadata
- Authors
- Edgar, R. C.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2017-10-04
- Volume
- 5
- Pages
- e3889
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W2762260969
- Cited by
- 225
- References
- 7
- FWCI
- 10.48
- Type
- journal article
- Language
- en
- Open access
- gold
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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