Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Abstract
Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Calgary, AB (Canada)
- Univ. of Nevada, Las Vegas, NV (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Geological Survey of Canada, Calgary, AB (Canada)
- McMaster Univ., Hamilton, ON (Canada)
- Miami Univ., Oxford, OH (United States)
- Univ. of Alaska, Anchorage, AK (United States)
- Sun Yat-Sen Univ., Guangzhou, (China)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1467799
- Alternate Identifier(s):
- OSTI ID: 1379050
- Report Number(s):
- LLNL-JRNL-737993
Journal ID: ISSN 2041-1723; 891150
- Grant/Contract Number:
- AC52-07NA27344; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: na; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Biodiversity; Metagenomics
Citation Formats
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States: N. p., 2016.
Web. doi:10.1038/ncomms10476.
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., & Ivanova, Natalia N. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States. https://doi.org/10.1038/ncomms10476
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Wed .
"Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs". United States. https://doi.org/10.1038/ncomms10476. https://www.osti.gov/servlets/purl/1467799.
@article{osti_1467799,
title = {Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs},
author = {Eloe-Fadrosh, Emiley A. and Paez-Espino, David and Jarett, Jessica and Dunfield, Peter F. and Hedlund, Brian P. and Dekas, Anne E. and Grasby, Stephen E. and Brady, Allyson L. and Dong, Hailiang and Briggs, Brandon R. and Li, Wen-Jun and Goudeau, Danielle and Malmstrom, Rex and Pati, Amrita and Pett-Ridge, Jennifer and Rubin, Edward M. and Woyke, Tanja and Kyrpides, Nikos C. and Ivanova, Natalia N.},
abstractNote = {Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.},
doi = {10.1038/ncomms10476},
journal = {Nature Communications},
number = na,
volume = 7,
place = {United States},
year = {Wed Jan 27 00:00:00 EST 2016},
month = {Wed Jan 27 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus
journal, July 2011
- Holmes, Dawn E.; Risso, Carla; Smith, Jessica A.
- The ISME Journal, Vol. 6, Issue 1
mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evaluation of Oligonucleotide Probes for Fluorescence In Situ Hybridization
journal, December 2010
- Yilmaz, L. Safak; Parnerkar, Shreyas; Noguera, Daniel R.
- Applied and Environmental Microbiology, Vol. 77, Issue 3
IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
Ecology and exploration of the rare biosphere
journal, March 2015
- Lynch, Michael D. J.; Neufeld, Josh D.
- Nature Reviews Microbiology, Vol. 13, Issue 4
The linkage between reverse gyrase and hyperthermophiles: A review of their invariable association
journal, June 2009
- Heine, Michelle; Chandra, Sathees B. C.
- The Journal of Microbiology, Vol. 47, Issue 3
Dendroscope: An interactive viewer for large phylogenetic trees
journal, November 2007
- Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian
- BMC Bioinformatics, Vol. 8, Issue 1
Extreme genome reduction in symbiotic bacteria
journal, November 2011
- McCutcheon, John P.; Moran, Nancy A.
- Nature Reviews Microbiology, Vol. 10, Issue 1
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
journal, August 2014
- Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz A.
- Bioinformatics, Vol. 30, Issue 17
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
journal, September 2012
- Wrighton, K. C.; Thomas, B. C.; Sharon, I.
- Science, Vol. 337, Issue 6102
Community-wide analysis of microbial genome sequence signatures
journal, January 2009
- Dick, Gregory J.; Andersson, Anders F.; Baker, Brett J.
- Genome Biology, Vol. 10, Issue 8
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
journal, January 2015
- Sekiguchi, Yuji; Ohashi, Akiko; Parks, Donovan H.
- PeerJ, Vol. 3
A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing
journal, January 2013
- Hou, Weiguo; Wang, Shang; Dong, Hailiang
- PLoS ONE, Vol. 8, Issue 1
Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin: N2O production by Thermus thermophilus and T. oshimai
journal, September 2011
- Hedlund, B. P.; Mcdonald, A. I.; Lam, J.
- Geobiology, Vol. 9, Issue 6
Microbial species delineation using whole genome sequences
journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
ProtTest: selection of best-fit models of protein evolution
journal, January 2005
- Abascal, F.; Zardoya, R.; Posada, D.
- Bioinformatics, Vol. 21, Issue 9
Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria
journal, August 2009
- Iino, T.; Mori, K.; Uchino, Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 6
ProDeGe: a computational protocol for fully automated decontamination of genomes
journal, June 2015
- Tennessen, Kristin; Andersen, Evan; Clingenpeel, Scott
- The ISME Journal, Vol. 10, Issue 1
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments
journal, January 2014
- Sharp, Christine E.; Brady, Allyson L.; Sharp, Glen H.
- The ISME Journal, Vol. 8, Issue 6
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015
- Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
- Current Biology, Vol. 25, Issue 6
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012
- Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver
- Bioinformatics, Vol. 28, Issue 14
ARB: a software environment for sequence data
journal, February 2004
- Ludwig, W.
- Nucleic Acids Research, Vol. 32, Issue 4
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007
- Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
- BMC Bioinformatics, Vol. 8, Issue 1
Searching for new branches on the tree of life
journal, November 2014
- Woyke, T.; Rubin, E. M.
- Science, Vol. 346, Issue 6210
Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling
journal, February 2013
- Murugapiran, Senthil K.; Huntemann, Marcel; Wei, Chia-Lin
- Standards in Genomic Sciences, Vol. 7, Issue 3
Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015
- Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
- Nature, Vol. 523, Issue 7559
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
journal, February 2012
- Iverson, V.; Morris, R. M.; Frazar, C. D.
- Science, Vol. 335, Issue 6068
Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry
journal, January 2013
- Inskeep, William P.; Jay, Zackary J.; Herrgard, Markus J.
- Frontiers in Microbiology, Vol. 4
Implications of streamlining theory for microbial ecology
journal, April 2014
- Giovannoni, Stephen J.; Cameron Thrash, J.; Temperton, Ben
- The ISME Journal, Vol. 8, Issue 8
HMMER web server: interactive sequence similarity searching
journal, May 2011
- Finn, R. D.; Clements, J.; Eddy, S. R.
- Nucleic Acids Research, Vol. 39, Issue suppl
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
MrBayes 3: Bayesian phylogenetic inference under mixed models
journal, August 2003
- Ronquist, Fredrik; Huelsenbeck, John P.
- Bioinformatics, Vol. 19, Issue 12, p. 1572-1574
Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013
- Nawrocki, E. P.; Eddy, S. R.
- Bioinformatics, Vol. 29, Issue 22
The basic building blocks and evolution of CRISPR–Cas systems
journal, November 2013
- Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.
- Biochemical Society Transactions, Vol. 41, Issue 6
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
journal, August 2013
- Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.
- Nature Communications, Vol. 4, Issue 1
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
BLAT---The BLAST-Like Alignment Tool
journal, March 2002
- Kent, W. J.
- Genome Research, Vol. 12, Issue 4
Curli biogenesis: Order out of disorder
journal, August 2014
- Evans, Margery L.; Chapman, Matthew R.
- Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1843, Issue 8
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
journal, October 2013
- Nurk, Sergey; Bankevich, Anton; Antipov, Dmitry
- Journal of Computational Biology, Vol. 20, Issue 10
Structure of the nonameric bacterial amyloid secretion channel
journal, December 2014
- Cao, Baohua; Zhao, Yan; Kou, Yongjun
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 50
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
journal, January 2005
- Haft, Daniel H.; Selengut, Jeremy; Mongodin, Emmanuel F.
- PLoS Computational Biology, Vol. 1, Issue 6
The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution
journal, January 2008
- Hernandez-Montes, Georgina; Diaz-Mejia, J. Javier; Perez-Rueda, Ernesto
- Genome Biology, Vol. 9, Issue 6
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
journal, August 2014
- Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar
- Nature Reviews Microbiology, Vol. 12, Issue 9
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
journal, July 2013
- Lange, Sita J.; Alkhnbashi, Omer S.; Rose, Dominic
- Nucleic Acids Research, Vol. 41, Issue 17
Mapping the Tree of Life: Progress and Prospects
journal, November 2009
- Pace, N. R.
- Microbiology and Molecular Biology Reviews, Vol. 73, Issue 4
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006
- Stamatakis, Alexandros
- Bioinformatics, Vol. 22, Issue 21
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
journal, October 2013
- Kantor, Rose S.; Wrighton, Kelly C.; Handley, Kim M.
- mBio, Vol. 4, Issue 5
Rfam 11.0: 10 years of RNA families
journal, November 2012
- Burge, Sarah W.; Daub, Jennifer; Eberhardt, Ruth
- Nucleic Acids Research, Vol. 41, Issue D1
Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities
journal, December 2012
- Cole, Jessica K.; Peacock, Joseph P.; Dodsworth, Jeremy A.
- The ISME Journal, Vol. 7, Issue 4
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Evolution and classification of the CRISPR–Cas systems
journal, May 2011
- Makarova, Kira S.; Haft, Daniel H.; Barrangou, Rodolphe
- Nature Reviews Microbiology, Vol. 9, Issue 6, p. 467-477
Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin
journal, February 2009
- Costa, Kyle C.; Navarro, Jason B.; Shock, Everett L.
- Extremophiles, Vol. 13, Issue 3
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
journal, June 2009
- Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T.
- Bioinformatics, Vol. 25, Issue 15
Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus
journal, September 2014
- Aklujkar, M.; Risso, C.; Smith, J.
- Microbiology, Vol. 160, Issue Pt_12
Genome Streamlining in a Cosmopolitan Oceanic Bacterium
journal, August 2005
- Giovannoni, S. J.
- Science, Vol. 309, Issue 5738
Unravelling the structural and mechanistic basis of CRISPR–Cas systems
journal, June 2014
- van der Oost, John; Westra, Edze R.; Jackson, Ryan N.
- Nature Reviews Microbiology, Vol. 12, Issue 7
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.
journal, March 1994
- Barns, S. M.; Fundyga, R. E.; Jeffries, M. W.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 5
Genome sequencing in microfabricated high-density picolitre reactors
journal, July 2005
- Margulies, Marcel; Egholm, Michael; Altman, William E.
- Nature, Vol. 437, Issue 7057, p. 376-380
Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015
- Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
- Nature, Vol. 521, Issue 7551
Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction
journal, October 2006
- Weber, Karrie A.; Achenbach, Laurie A.; Coates, John D.
- Nature Reviews Microbiology, Vol. 4, Issue 10, p. 752-764
Amyloid Formation by Human Carboxypeptidase D Transthyretin-like Domain under Physiological Conditions
journal, October 2014
- Garcia-Pardo, Javier; Graña-Montes, Ricardo; Fernandez-Mendez, Marc
- Journal of Biological Chemistry, Vol. 289, Issue 49
Expanding the catalog of cas genes with metagenomes
journal, December 2013
- Zhang, Quan; Doak, Thomas G.; Ye, Yuzhen
- Nucleic Acids Research, Vol. 42, Issue 4
Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria: Candidatus Chloracidobacterium thermophilum genome
journal, September 2011
- Garcia Costas, Amaya M.; Liu, Zhenfeng; Tomsho, Lynn P.
- Environmental Microbiology, Vol. 14, Issue 1
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
journal, March 2013
- Skennerton, Connor T.; Imelfort, Michael; Tyson, Gene W.
- Nucleic Acids Research, Vol. 41, Issue 10
The Phylogeny and Signature Sequences Characteristics of Fibrobacteres , Chlorobi , and Bacteroidetes
journal, January 2004
- Gupta, Radhey S.
- Critical Reviews in Microbiology, Vol. 30, Issue 2
Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria , and a proposal of a novel bacterial phylum I gnavibacteriae
journal, January 2013
- Podosokorskaya, Olga A.; Kadnikov, Vitaly V.; Gavrilov, Sergey N.
- Environmental Microbiology, Vol. 15, Issue 6
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
journal, December 2011
- Dupont, Chris L.; Rusch, Douglas B.; Yooseph, Shibu
- The ISME Journal, Vol. 6, Issue 6
Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics
journal, August 2012
- Yilmaz, L. Safak; Loy, Alexander; Wright, Erik S.
- PLoS ONE, Vol. 7, Issue 8
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
journal, January 1998
- Hugenholtz, Philip; Pitulle, Christian; Hershberger, Karen L.
- Journal of Bacteriology, Vol. 180, Issue 2
PhyloSift: Phylogenetic analysis of genomes and metagenomes
dataset, January 2013
- Bik, Holly; Matsen, Erick; Lowe, Eric
- Figshare
Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015
- Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
- Nature, Vol. 521, Issue 7551
Microbiology in transition.
journal, March 1994
- Woese, C. R.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 5
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
journal, October 2013
- Nurk, Sergey; Bankevich, Anton; Antipov, Dmitry
- Journal of Computational Biology, Vol. 20, Issue 10
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
journal, June 2009
- Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T.
- Bioinformatics, Vol. 25, Issue 15
Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013
- Nawrocki, E. P.; Eddy, S. R.
- Bioinformatics, Vol. 29, Issue 22
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
journal, August 2014
- Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz A.
- Bioinformatics, Vol. 30, Issue 17
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
HMMER web server: interactive sequence similarity searching
journal, May 2011
- Finn, R. D.; Clements, J.; Eddy, S. R.
- Nucleic Acids Research, Vol. 39, Issue suppl
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
journal, March 2013
- Skennerton, Connor T.; Imelfort, Michael; Tyson, Gene W.
- Nucleic Acids Research, Vol. 41, Issue 10
Microbial species delineation using whole genome sequences
journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus
journal, September 2014
- Aklujkar, M.; Risso, C.; Smith, J.
- Microbiology, Vol. 160, Issue Pt_12
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
journal, September 2012
- Wrighton, K. C.; Thomas, B. C.; Sharon, I.
- Science, Vol. 337, Issue 6102
Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria
journal, June 2002
- Pernthaler, A.; Pernthaler, J.; Amann, R.
- Applied and Environmental Microbiology, Vol. 68, Issue 6
Dendroscope: An interactive viewer for large phylogenetic trees
journal, November 2007
- Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian
- BMC Bioinformatics, Vol. 8, Issue 1
Community-wide analysis of microbial genome sequence signatures
journal, January 2009
- Dick, Gregory J.; Andersson, Anders F.; Baker, Brett J.
- Genome Biology, Vol. 10, Issue 8
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
journal, January 2005
- Haft, Daniel H.; Selengut, Jeremy; Mongodin, Emmanuel F.
- PLoS Computational Biology, Vol. 1, Issue 6
The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem
journal, January 2013
- Inskeep, William
- Frontiers in Microbiology, Vol. 4
Works referencing / citing this record:
Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams
journal, August 2018
- Hotaling, Scott; Quackenbush, Corey R.; Bennett-Ponsford, Julian
- Microbial Ecology, Vol. 77, Issue 3
Measurement of bacterial replication rates in microbial communities
journal, November 2016
- Brown, Christopher T.; Olm, Matthew R.; Thomas, Brian C.
- Nature Biotechnology, Vol. 34, Issue 12
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
journal, June 2017
- Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.
- Nature Biotechnology, Vol. 35, Issue 7
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
journal, March 2018
- Seshadri, Rekha; Leahy, Sinead C.; Attwood, Graeme T.
- Nature Biotechnology, Vol. 36, Issue 4
The trajectory of microbial single-cell sequencing
journal, October 2017
- Woyke, Tanja; Doud, Devin F. R.; Schulz, Frederik
- Nature Methods, Vol. 14, Issue 11
Novel prosthecate bacteria from the candidate phylum Acetothermia
journal, June 2018
- Hao, Liping; McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen
- The ISME Journal, Vol. 12, Issue 9
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
journal, November 2019
- Doud, Devin F. R.; Bowers, Robert M.; Schulz, Frederik
- The ISME Journal, Vol. 14, Issue 3
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
journal, January 2019
- Matheus Carnevali, Paula B.; Schulz, Frederik; Castelle, Cindy J.
- Nature Communications, Vol. 10, Issue 1
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
journal, July 2019
- Roux, Simon; Krupovic, Mart; Daly, Rebecca A.
- Nature Microbiology
HydDB: A web tool for hydrogenase classification and analysis
journal, September 2016
- Søndergaard, Dan; Pedersen, Christian N. S.; Greening, Chris
- Scientific Reports, Vol. 6, Issue 1
Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens
journal, February 2019
- Berghuis, Bojk A.; Yu, Feiqiao Brian; Schulz, Frederik
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 11
Living on the edge: biofilms developing in oscillating environmental conditions
journal, October 2018
- Dobretsov, Sergey; Abed, Raeid M. M.; Muthukrishnan, Thirumahal
- Biofouling, Vol. 34, Issue 9
Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA Cys and elongation factor SelB
journal, November 2017
- Vargas-Rodriguez, Oscar; Englert, Markus; Merkuryev, Anna
- RNA Biology, Vol. 15, Issue 4-5
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor
journal, September 2019
- Catchpole, Ryan J.; Forterre, Patrick
- Molecular Biology and Evolution, Vol. 36, Issue 12
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
journal, October 2016
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 45, Issue D1
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
journal, May 2018
- Raden, Martin; Ali, Syed M.; Alkhnbashi, Omer S.
- Nucleic Acids Research, Vol. 46, Issue W1
Abundance and taxonomic affiliation of molybdenum transport and utilization genes in Tengchong hot springs, China
journal, May 2018
- Srivastava, Shreya; Briggs, Brandon R.; Dong, Hailiang
- Environmental Microbiology, Vol. 20, Issue 7
Characterization of microbial community profiles associated with quality of Chinese strong‐aromatic liquor through metagenomics
journal, June 2019
- Guo, M. Y.; Hou, C. J.; Bian, M. H.
- Journal of Applied Microbiology, Vol. 127, Issue 3
Evaluation of prokaryotic diversity of five hot springs in Eritrea
journal, September 2017
- Ghilamicael, Amanuel M.; Budambula, Nancy L. M.; Anami, Sylvester E.
- BMC Microbiology, Vol. 17, Issue 1
Functional and taxonomic classification of a greenhouse water drain metagenome
journal, October 2018
- López-Leal, Gamaliel; Cornejo-Granados, Fernanda; Hurtado-Ramírez, Juan Manuel
- Standards in Genomic Sciences, Vol. 13, Issue 1
Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs
journal, January 2019
- Ward, Lewis M.; Idei, Airi; Nakagawa, Mayuko
- Microbes and Environments, Vol. 34, Issue 3
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
journal, January 2017
- Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul
- Frontiers in Microbiology, Vol. 7
Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes
journal, August 2018
- Momper, Lily; Aronson, Heidi S.; Amend, Jan P.
- Frontiers in Microbiology, Vol. 9
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
journal, July 2019
- Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O.
- Frontiers in Microbiology, Vol. 10
Living on the edge: biofilms developing in oscillating environmental conditions
text, January 2019
- Dobretsov, Sergey; Abed, Raeid M. M.; Muthukrishnan, Thirumahal
- Taylor & Francis
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
text, January 2018
- Raden, Martin; Ali, Syed M.; Alkhnbashi, Omer S.
- Apollo - University of Cambridge Repository
Exemplar Abstract for Kryptonium thompsonii corrig. Eloe-Fadrosh et al. 2016 and Kryptonium thompsoni (sic) Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Exemplar Abstract for Kryptobacter tengchongensis Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Exemplar Abstract for Thermokryptus mobilis Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Exemplar Abstract for Chrysopegis kryptomonas (sic) Eloe-Fadrosh et al. 2016 and Chryseopegocella kryptomonas corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Kryptonia Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Incertae sedis 386 Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Kryptonium Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Kryptobacter Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Kryptobacter tengchongensis Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Thermokryptus Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Thermokryptus mobilis Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Nomenclature Abstract for Chrysopegis (sic) Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Chrysopegis kryptomonas (sic) Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Nomenclature Abstract for Chryseopegocella corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Chryseopegocella kryptomonas corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Nomenclature Abstract for Kryptonium thompsonii corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Taxonomic Abstract for the class Incertae sedis 384 Eloe-Fadrosh et al. 2016
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Taxonomic Abstract for the species.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Taxonomic Abstract for the species.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Taxonomic Abstract for the species.
dataset, January 2019
- Parker, Charles Thomas; Garrity, George M.
Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing
journal, March 2017
- Padilla-Del Valle, Ricky; Morales-Vale, Luis R.; Ríos-Velázquez, Carlos
- Genomics Data, Vol. 11
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
journal, June 2017
- Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.
- Nature Biotechnology, Vol. 35, Issue 7
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, July 2018
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 36, Issue 7
Novel prosthecate bacteria from the candidate phylum Acetothermia
journal, June 2018
- Hao, Liping; McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen
- The ISME Journal, Vol. 12, Issue 9
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
journal, November 2019
- Doud, Devin F. R.; Bowers, Robert M.; Schulz, Frederik
- The ISME Journal, Vol. 14, Issue 3
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
journal, July 2019
- Roux, Simon; Krupovic, Mart; Daly, Rebecca A.
- Nature Microbiology
Analyzing large scale genomic data on the cloud with Sparkhit
journal, December 2017
- Huang, Liren; Krüger, Jan; Sczyrba, Alexander
- Bioinformatics, Vol. 34, Issue 9
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor
journal, September 2019
- Catchpole, Ryan J.; Forterre, Patrick
- Molecular Biology and Evolution, Vol. 36, Issue 12
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
journal, October 2016
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 45, Issue D1
The MAR databases: development and implementation of databases specific for marine metagenomics
journal, November 2017
- Klemetsen, Terje; Raknes, Inge A.; Fu, Juan
- Nucleic Acids Research, Vol. 46, Issue D1
Novel prosthecate bacteria from the candidate phylum Acetothermia revealed by culture-independent genomics and advanced microscopy
journal, October 2017
- Hao, Li-Ping; Mcllroy, Simon Jon; Kirkegaard, Rasmus Hansen
- The ISME Journal
Bioremediation at a global scale: from the test tube to planet Earth
journal, August 2016
- de Lorenzo, Víctor; Marlière, Philippe; Solé, Ricard
- Microbial Biotechnology, Vol. 9, Issue 5
Functional and taxonomic classification of a greenhouse water drain metagenome
journal, October 2018
- López-Leal, Gamaliel; Cornejo-Granados, Fernanda; Hurtado-Ramírez, Juan Manuel
- Standards in Genomic Sciences, Vol. 13, Issue 1
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
text, January 2018
- Raden, Martin; Ali, Syed M.; Alkhnbashi, Omer S.
- Apollo - University of Cambridge Repository
Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria
journal, April 2016
- Hamilton, Trinity L.; Bovee, Roderick J.; Sattin, Sarah R.
- Frontiers in Microbiology, Vol. 7
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
journal, January 2017
- Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul
- Frontiers in Microbiology, Vol. 7
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
journal, July 2019
- Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O.
- Frontiers in Microbiology, Vol. 10
Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov
journal, June 2022
- Bello, Sarah; Howard-Azzeh, Mohammad; Schellhorn, Herb E.
- Microorganisms, Vol. 10, Issue 7