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Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

Thomas S. B. Schmidt, João F. Matias Rodrigues, Christian von Mering, Jonathan A. Eisen
2014 PLoS Computational Biology  
Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities  ...  Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency.  ...  Acknowledgments We thank Mark Robinson, University of Zürich, for insightful discussions on the Ecological Consistency Score, as well as Damian Szklarczyk and Alexander Roth for helpful discussions during  ... 
doi:10.1371/journal.pcbi.1003594 pmid:24763141 pmcid:PMC3998914 fatcat:p4gl2ywnn5h7zctxmi3thegzim

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Thorsten Stoeck, Anke Behnke, Richard Christen, Linda Amaral-Zettler, Maria J Rodriguez-Mora, Andrei Chistoserdov, William Orsi, Virginia P Edgcomb
2009 BMC Biology  
The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries  ...  (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large  ...  Acknowledgements The International Census of Marine Microbes and the W.M. Keck Foundation award to the Marine Biological Laboratory at Woods Hole (MA) supported the pyrosequencing part of this study.  ... 
doi:10.1186/1741-7007-7-72 pmid:19886985 pmcid:PMC2777867 fatcat:jps27wt34ran3gqrraey4ejixa

Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

H. E. O'Brien, J. L. Parrent, J. A. Jackson, J.-M. Moncalvo, R. Vilgalys
2005 Applied and Environmental Microbiology  
We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned  ...  Richness was consistently lowest in the deepest soil horizon samples.  ...  Operational taxonomic units (OTUs) were defined as a group of sequences sharing at least 97% pairwise similarity, which is within the range of intraspecific ITS sequence divergence.  ... 
doi:10.1128/aem.71.9.5544-5550.2005 pmid:16151147 pmcid:PMC1214672 fatcat:ktv2ndgdbnctxnw7chzcvkyjly

SSUnique: Detecting Sequence Novelty in Microbiome Surveys

Michael D. J. Lynch, Josh D. Neufeld, J. Gregory Caporaso
2016 mSystems  
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales.  ...  units (OTUs) from 16S rRNA gene sequence libraries by screening against consensus structural models for SSU rRNA.  ...  This clade-based approach results in a 2-fold benefit by highlighting reproducible unclassified diversity represented as monophyletic operational transcriptomic units (OTUs) and by establishing a putative  ... 
doi:10.1128/msystems.00133-16 pmid:28028549 pmcid:PMC5183599 fatcat:zkqziwwa5zbuzj6sadick6hudi

Molecular evidence for an active endogenous microbiome beneath glacial ice

Trinity L Hamilton, John W Peters, Mark L Skidmore, Eric S Boyd
2013 The ISME Journal  
The prevalence of SSU rRNA affiliated with lithoautotrophic bacteria, autotrophic methane producing archaea and heterotrophic eukarya in the subglacial environment is consistent with this hypothesis and  ...  Patterns in the phylogenetic structure and composition of subglacial sediment small subunit (SSU) ribosomal RNA (rRNA) assemblages indicate greater diversity and evenness than in glacial surface environments  ...  We thank the staff at the Biogeosciences Institute at the University of Calgary's Kananaskis Field Station for use of their laboratory facilities.  ... 
doi:10.1038/ismej.2013.31 pmid:23486249 pmcid:PMC3695297 fatcat:dfjeb5ztfbdjzh4ju3mib45huy

Policy, phylogeny, and the parasite

Grant D. Stentiford, Stephen W. Feist, David M. Stone, Edmund J. Peeler, David Bass
2014 Trends in Parasitology  
UK Natural Environment Research Council (NERC) grants NE/H009426/1 and NE/H000887/1, and a SynTax grant for completion of this review.  ...  Acknowledgements The opinions expressed herein represent those of the authors and not necessarily those of the OIE, the European Commission, or the UK Department for Environment, Food and Rural Affairs  ...  into operational taxonomic units (OTUs), usually based upon sequence similarity [6, 7] .  ... 
doi:10.1016/j.pt.2014.04.004 pmid:24780286 fatcat:sjmg6nqqxveo3a7sz5qc6fckum

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard, Oded Béjà
2011 PLoS Computational Biology  
Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs).  ...  Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a  ...  Acknowledgments We would like to thank the RDP for providing access to their curated SSU-rRNA multiple sequence alignments and CAMERA for enabling access to the Global Ocean Survey Data.  ... 
doi:10.1371/journal.pcbi.1001061 pmid:21283775 pmcid:PMC3024254 fatcat:x4ikfu56uzhw3ie6mrfuavjdpa

Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica

Yuan Xu, Trista Vick-Majors, Rachael Morgan-Kiss, John C. Priscu, Linda Amaral-Zettler
2014 The Biological Bulletin  
A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes.  ...  A new method for non-parametric multivariate analysis of variance. Austral. Ecol. 26: 32-46.  ...  We would also like to acknowledge the China Scholarship Council (No. [2012] 3013) for fellowship support to Yuan Xu enabling her to study at the Marine Biological Laboratory.  ... 
doi:10.1086/bblv227n2p175 pmid:25411375 fatcat:hkssqtokjvhollmrt34igmztbe

Pole-to-pole biogeography of surface and deep marine bacterial communities

J.-F. Ghiglione, P. E. Galand, T. Pommier, C. Pedros-Alio, E. W. Maas, K. Bakker, S. Bertilson, D. L. Kirchman, C. Lovejoy, P. L. Yager, A. E. Murray
2012 Proceedings of the National Academy of Sciences of the United States of America  
A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean.  ...  Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene  ...  We thank the members of field teams, shipboard crews, and logistics support personnel from all national polar programs involved in sample collection, without whom this study would not have  ... 
doi:10.1073/pnas.1208160109 pmid:23045668 pmcid:PMC3491513 fatcat:he6ufuiijzbcrb5mo4gvrixbsm

Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii

C L Moyer, F C Dobbs, D M Karl
1995 Applied and Environmental Microbiology  
The phylogenetic diversity of small-subunit rRNA genes associated with the domain Bacteria was examined (by using previously defined operational taxonomic units [C. L. Moyer, F.C. Dobbs, and D. M.  ...  of the small-subunit rRNA bacterial clone library from Pele's Vents.  ...  We thank the captain and crew of the R/V Kila, the DSRV Pisces V operations team, and the staff of the Hawaiian Undersea Research Laboratory.  ... 
pmid:7538279 pmcid:PMC167411 fatcat:mzra4fiogfbudkrzvnxzsyckfi

Contrasting Patterns of Community Assembly in the Stratified Water Column of Great Salt Lake, Utah

Jonathan E. Meuser, Bonnie K. Baxter, John R. Spear, John W. Peters, Matthew C. Posewitz, Eric S. Boyd
2013 Microbial Ecology  
Phylogenetic examinations of communities sampled along geochemical gradients provide a framework for inferring the relative importance of niche-based ecological interactions (competition, environmental  ...  Here, we examine the phylogenetic structure and composition of archaeal, bacterial, and eukaryal small subunit (SSU) rRNA genes sampled along a stratified water column (DWR3) in the south arm of GSL in  ...  We would also like to acknowledge the technical assistance of Devin Karns and Alex Trujillo as well as Shannon Ulrich and Dave Vuono for their careful review of a previous version of this manuscript.  ... 
doi:10.1007/s00248-013-0180-9 pmid:23354179 fatcat:3xy4i6py2rfofo26qdto7ooqh4

Fine-Scale Biogeography and the Inference of Ecological Interactions Among Neutrophilic Iron-Oxidizing Zetaproteobacteria as Determined by a Rule-Based Microbial Network

Katherine Duchinski, Craig L. Moyer, Kevin Hager, Heather Fullerton
2019 Frontiers in Microbiology  
taxonomic unit (OTU).  ...  DNA was then extracted and amplified for analysis of the SSU rRNA gene.  ...  We also thank the captain and crew of both the R/V Roger Revelle (for cruise RR1413) and R/V Thomas G. Thompson (for cruise TN293).  ... 
doi:10.3389/fmicb.2019.02389 pmid:31708884 pmcid:PMC6823593 fatcat:ucxkwzi6wjfoxktf3x3ia43i6i

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Yusuke Okazaki, Shohei Fujinaga, Michaela M. Salcher, Cristiana Callieri, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Hideyuki Tamaki, Shin-ichi Nakano
2021 Microbiome  
At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition  ...  Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological  ...  Koitabashi, Y Goda, T Denboh, Y Ito, M Sugiyama, and E Loher for their assistance in field sampling. 1 Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan.  ... 
doi:10.1186/s40168-020-00974-y pmid:33482922 fatcat:oljrc5gu45gdbanqwatkiheuci

Estimating Protistan Diversity Using High-Throughput Sequencing

Sarah K. Hu, Zhenfeng Liu, Alle A. Y. Lie, Peter D. Countway, Diane Y. Kim, Adriane C. Jones, Rebecca J. Gast, S. Craig Cary, Evelyn B. Sherr, Barry F. Sherr, David A. Caron
2015 Journal of Eukaryotic Microbiology  
A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations.  ...  Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution  ...  Sequence assembly and processing at JGI was performed by Ed Kirton, Jim Bristow, and Sussannah Tringe. William C. Nelson assisted with early bioinformatic analysis of the full-length sequence data.  ... 
doi:10.1111/jeu.12217 pmid:25851049 fatcat:7dl7bsz5greubcrlc676t6tbxu

25 years of serving the community with ribosomal RNA gene reference databases and tools

Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
2017 Journal of Biotechnology  
Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA  ...  A B S T R A C T SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea  ...  Your immediate critical evaluation is a great motivation for us to improve our databases and tools.  ... 
doi:10.1016/j.jbiotec.2017.06.1198 pmid:28648396 fatcat:u35qpimwazhhnip774tn433bha
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