Specificity and sensitivity of eubacterial primers utilized for molecular profiling of bacteria within complex microbial ecosystems
Abstract
Efficient profiling of eubacterial diversity within complex communities requires that primers are specific for eubacterial 16S rRNA. Specificity of published primers against eubacterial and archaeal 16S rRNA as well as protozoal and fungal 18S rRNA was assessed in silico. The specificity and sensitivity of the V3 and V6-V8 (F968gc and R1401) Denaturing Gradient Gel Electrophoresis (DGGE) primers was subsequently verified using rumen-derived samples. An assessment of the effects of employing touchdown PCR cycling conditions was also made. For DGGE profiling of eubacteria within rumen samples, primers F968gc and R1401 proved the most specific and sensitive providing that touchdown PCR is not used.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
For specific bacterial 16S rRNA, V6-V8 primers were more appropriate than V3 primers.
“However, Huws et al. (2007) concluded that for specific bacterial 16S rRNA V6-V8 primers were more appropriate.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Huws et al., 2007
V3 primers were non-specific to bacteria and could amplify plant chloroplastic DNA as well as archaeal 16S rDNA and protozoal 18S rDNA sequences.
“Huws et al. (2007) and Edwards et al. (2007), however showed that the V3 primers were non-specific to bacteria and could amplify plant chloroplastic DNA as well as archaeal 16S rDNA and protozoal 18S rDNA sequences.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Huws et al., 2007
The citation lists haven’t been fetched yet
References 25 · Cited by 150
- Authors
- Huws, S. A., Edwards, J. E., Kim, E. J., & Scollan, N. D.
- Affiliations
- Aberystwyth University (GB)
- Corresponding author
- Scollan, N.D.
- Venue
- Journal of Microbiological Methods
- Publisher
- Elsevier BV
- Published
- 2007-09
- Volume
- 70
- Issue
- 3
- Pages
- 565-569
- ISSN
- 0167-7012 (ISSN-L)
- OpenAlex
- W1981890438
- Cited by
- 150
- References
- 25
- Citations by year
- 2025: 5 · 2024: 7 · 2023: 18 · 2022: 17 · 2021: 9 · 2020: 12 · 2019: 11 · 2018: 10 · 2017: 5 · 2016: 2 · 2015: 9 · 2014: 7 · 2013: 6 · 2012: 10
- FWCI
- 4.62
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Microbiological Methods (publishedVersion)
- PubMed (publishedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BBS/E/G/00003008)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- primer specificity, primer sensitivity, rumen bacteria, microbial community analysis, 18S rRNA, touchdown PCR, V3 region, rumen microbiota
- MeSH terms
- Animals, Bacteria, Base Sequence, DNA, Ribosomal, Electrophoresis, Polyacrylamide Gel, Fungi, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S, Ruminants, Sensitivity and Specificity, Polymerase Chain Reaction, DNA Primers
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
