scholarly journals Benchmark taxonomic classification of chicken gut bacteria based on 16S rRNA gene profiling in correlation with various feeding strategies

2020 ◽  
Vol 32 (1) ◽  
pp. 1034-1041
Author(s):  
Zubia Rashid ◽  
Syed Muddassar Hussain Gilani ◽  
Asma Ashraf ◽  
Sitwat Zehra ◽  
Abid Azhar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Bacteria ◽  
Taxonomic Classification ◽  
Gene Profiling ◽  
Feeding Strategies ◽  
Rrna Gene

scholarly journals C16S — A Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences

Genomics ◽  
2012 ◽  
Vol 99 (4) ◽  
pp. 195-201 ◽  
Author(s):  
Tarini Shankar Ghosh ◽  
Purnachander Gajjalla ◽  
Monzoorul Haque Mohammed ◽  
Sharmila S Mande
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Taxonomic Classification ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

scholarly journals Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

2021 ◽  
Vol 12 ◽  
Author(s):  
Michal Ziemski ◽  
Treepop Wisanwanichthan ◽  
Nicholas A. Bokulich ◽  
Benjamin D. Kaehler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
Taxonomic Classification ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Neural Network Classifiers

Naive Bayes classifiers (NBC) have dominated the field of taxonomic classification of amplicon sequences for over a decade. Apart from having runtime requirements that allow them to be trained and used on modest laptops, they have persistently provided class-topping classification accuracy. In this work we compare NBC with random forest classifiers, neural network classifiers, and a perfect classifier that can only fail when different species have identical sequences, and find that in some practical scenarios there is little scope for improving on NBC for taxonomic classification of 16S rRNA gene sequences. Further improvements in taxonomy classification are unlikely to come from novel algorithms alone, and will need to leverage other technological innovations, such as ecological frequency information.

scholarly journals Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

2012 ◽  
Vol 6 (7) ◽  
pp. 1440-1444 ◽  
Author(s):  
David A W Soergel ◽  
Neelendu Dey ◽  
Rob Knight ◽  
Steven E Brenner
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Taxonomic Classification ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Selection Of

scholarly journals ZetaHunter: a reproducible taxonomic classification tool for tracking the ecology of the Zetaproteobacteria and other poorly-resolved taxa

2018 ◽  
Author(s):  
Sean M. McAllister ◽  
Ryan M. Moore ◽  
Clara S Chan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Taxonomic Classification ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Classification Tool

AbstractLike many taxa, the Zetaproteobacteria lack well-defined taxonomic divisions, 32 making it difficult to compare between studies. We designed ZetaHunter to reproducibly 33 assign 16S rRNA gene sequences to previously-described OTUs based on a curated 34 database. While ZetaHunter can use any given database, we include a curated 35 classification of publically-available Zetaproteobacteria.

scholarly journals Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore

2010 ◽  
Vol 60 (12) ◽  
pp. 2719-2723 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sung-Ran Moon ◽  
Young-Hyun Park ◽  
Jung-Ho Kim ◽  
Hoon Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Crude Oil ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Low Levels

A novel Gram-negative, aerobic, motile, short rod-shaped bacterium, designated MS-3T, was isolated from a crude oil-contaminated seashore in Taean, Korea. Strain MS-3T grew at 4–30 °C, at pH 6.0–9.5 and with 0–5 % NaCl and was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MS-3T was most similar to Pseudomonas marincola KMM 3042T (97.9 % 16S rRNA gene sequence similarity), P. cuatrocienegasensis 1NT (97.8 %), P. borbori R-20821T (97.3 %) and P. lundensis ATCC 49968T (97.1 %). Relatively low levels of DNA–DNA relatedness were found between strain MS-3T and P. cuatrocienegasensis LMG 24676T (57.2 %), P. borbori LMG 23199T (39.7 %), P. marincola KMM 3042T (32.2 %) and P. lundensis KACC 10832T (32.1 %), which support the classification of strain MS-3T within a novel species of the genus Pseudomonas. The G+C content of the genomic DNA of strain MS-3T was 57.6 mol% and the major isoprenoid quinone was Q-9. Strain MS-3T contained summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 38.0 %), C16 : 0 (24.4 %), C18 : 1 ω7c (12.8 %), C12 : 0 (9.6 %) and C10 : 0 3-OH (4.9 %) as the major cellular fatty acids. On the basis of the phenotypic, genotypic and phylogenetic data, strain MS-3T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas taeanensis sp. nov. is proposed. The type strain is MS-3T (=KCTC 22612T =KACC 14032T =JCM 16046T =NBRL 105641T).

scholarly journals Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

2006 ◽  
Vol 72 (7) ◽  
pp. 5069-5072 ◽  
Author(s):  
T. Z. DeSantis ◽  
P. Hugenholtz ◽  
N. Larsen ◽  
M. Rojas ◽  
E. L. Brodie ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Taxonomic Classification ◽  
Rrna Gene ◽  
Link Type ◽  
Gene Database ◽  
Public Repositories ◽  
Environmental Sequences ◽  
Standard Alignment

ABSTRACT A 16S rRNA gene database (http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

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