Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

2014 ◽  
Vol 12 (9) ◽  
pp. 635-645 ◽  
Author(s):  
Pablo Yarza ◽  
Pelin Yilmaz ◽  
Elmar Pruesse ◽  
Frank Oliver Glöckner ◽  
Wolfgang Ludwig ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Uncultured Bacteria

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 Metagenomic approach for the isolation and cultivation of cellulose-degrading myxobacteria

2020 ◽  
Vol 14 (1) ◽  
Keyword(s):  
New Species ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Cellulose Degradation ◽  
Rrna Gene ◽  
Fruiting Bodies ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Uncultured Bacteria ◽  
Molecular Phylogenetic

Cellulose-degrading myxobacteria are common soil microorganisms with unique morphologies and are united forming the distinct Sorangium and Byssovorax clades in the Polyangiaceae family, order Myxococcales. Cells of these fascinating bacteria can glide, form fruiting bodies and degrade agar and cellulose. However, phenotypic studies based on the swarm, fruiting bodies and cellulose degradation pattern have shown many dissimilarities among strains suggesting more potential to identify new species in Sorangium clade. Currently, nine validly described species are recognized capable of decomposing cellulose in myxobacteria, of which eight species belong to the genus Sorangium and one species to Byssovorax. With the increasing number of species recently validated in Sorangium, likely there will also be more species of Byssovorax that can be found in the environment. BLAST search analysis of Byssovorax 16S rRNA gene sequences in NCBI public database (GenBank) revealed 97-98.8 % similarity with sequences derived from clones of uncultured bacteria. In Sorangium, six 16S rRNA gene sequences derived from clones of uncultured bacteria were identified occupying novel branches and exhibiting 96.9% – 98.6% similarities with type strains. Molecular phylogenetic analysis confirmed the affiliations of these clones within Sorangium and Byssovorax clades, indicating potentially new species within these genera. Surprisingly, one sequence derived from a clone (DEN_SIP_103) may potentially represent a novel genus only if this strain can be successfully cultured in the future.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

Sign in / Sign up

Export Citation Format

Share Document