doi: 10.1016/j.mimet.2014.05.006.
Epub 2014 May 21.
Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR
Affiliations
- PMID: 24858450
- DOI: 10.1016/j.mimet.2014.05.006
Item in Clipboard
Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR
J Microbiol Methods.
2014 Aug.
Abstract
The functional mcrA gene of methanogens can generate phylogeny as congruent as the 16S rRNA gene phylogeny. For the mcrA sequences amplified by mlas/mcrA-rev primers, we created a database for taxonomical classification and propose cut-off values for OTU clustering and further analysis of α- and β-diversity with the MOTHUR software.
Keywords: Cut-off; MOTHUR; Methanogens; Taxonomic database; mcrA gene.
Copyright © 2014 Elsevier B.V. All rights reserved.
Similar articles
-
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.J Biotechnol. 2009 Jun 1;142(1):38-49. doi: 10.1016/j.jbiotec.2009.02.010. Epub 2009 Feb 27. J Biotechnol. 2009. PMID: 19480946
-
New primers, taxonomic database and cut-off value for processing nxrB gene high-throughput sequencing data by MOTHUR.J Microbiol Methods. 2020 Jun;173:105939. doi: 10.1016/j.mimet.2020.105939. Epub 2020 Apr 29. J Microbiol Methods. 2020. PMID: 32360381
-
[Analysis of methanogenic community of anaerobic granular sludge based on mcrA gene].Huan Jing Ke Xue. 2011 Apr;32(4):1114-9. Huan Jing Ke Xue. 2011. PMID: 21717756 Chinese.
-
25 years of serving the community with ribosomal RNA gene reference databases and tools.J Biotechnol. 2017 Nov 10;261:169-176. doi: 10.1016/j.jbiotec.2017.06.1198. Epub 2017 Jun 23. J Biotechnol. 2017. PMID: 28648396 Review.
-
Experimental and analytical tools for studying the human microbiome.Nat Rev Genet. 2011 Dec 16;13(1):47-58. doi: 10.1038/nrg3129. Nat Rev Genet. 2011. PMID: 22179717 Free PMC article. Review.
Cited by
-
Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill.Appl Environ Microbiol. 2022 May 10;88(9):e0243821. doi: 10.1128/aem.02438-21. Epub 2022 Apr 11. Appl Environ Microbiol. 2022. PMID: 35404071 Free PMC article.
-
Rates and Microbial Players of Iron-Driven Anaerobic Oxidation of Methane in Methanic Marine Sediments.Front Microbiol. 2020 Jan 17;10:3041. doi: 10.3389/fmicb.2019.03041. eCollection 2019. Front Microbiol. 2020. PMID: 32010098 Free PMC article.
-
Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period.PLoS One. 2017 Nov 8;12(11):e0187858. doi: 10.1371/journal.pone.0187858. eCollection 2017. PLoS One. 2017. PMID: 29117259 Free PMC article.
-
Impact of Saccharomyces cerevisiae on the intestinal microbiota of dogs with antibiotic-induced dysbiosis.Front Vet Sci. 2025 Feb 6;12:1462287. doi: 10.3389/fvets.2025.1462287. eCollection 2025. Front Vet Sci. 2025. PMID: 39981313 Free PMC article.
-
Ex Situ Culturing Experiments Revealed Psychrophilic Hydrogentrophic Methanogenesis Being the Potential Dominant Methane-Producing Pathway in Subglacial Sediment in Larsemann Hills, Antarctic.Front Microbiol. 2018 Feb 21;9:237. doi: 10.3389/fmicb.2018.00237. eCollection 2018. Front Microbiol. 2018. PMID: 29515536 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
