skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »; « less
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618966
Alternate Identifier(s):
OSTI ID: 1379384
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344
Resource Type:
Published Article
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Carbohydrate active enzyme; Polysaccharide; Bioethanol; Gliding motility; Cellulose; Marine; Flavobacteriaceae; Bacteroidetes; GEBA; KMG I

Citation Formats

Panschin, Irina, Huang, Sixing, Meier-Kolthoff, Jan P., Tindall, Brian J., Rohde, Manfred, Verbarg, Susanne, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., and Hahnke, Richard L. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. United Kingdom: N. p., 2016. Web. doi:10.1186/s40793-016-0163-9.
Panschin, Irina, Huang, Sixing, Meier-Kolthoff, Jan P., Tindall, Brian J., Rohde, Manfred, Verbarg, Susanne, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., & Hahnke, Richard L. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. United Kingdom. doi:10.1186/s40793-016-0163-9.
Panschin, Irina, Huang, Sixing, Meier-Kolthoff, Jan P., Tindall, Brian J., Rohde, Manfred, Verbarg, Susanne, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., and Hahnke, Richard L. Fri . "Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005". United Kingdom. doi:10.1186/s40793-016-0163-9.
@article{osti_1618966,
title = {Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005},
author = {Panschin, Irina and Huang, Sixing and Meier-Kolthoff, Jan P. and Tindall, Brian J. and Rohde, Manfred and Verbarg, Susanne and Lapidus, Alla and Han, James and Trong, Stephan and Haynes, Matthew and Reddy, T. B. K. and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Mavromatis, Konstantinos and Markowitz, Victor and Woyke, Tanja and Göker, Markus and Klenk, Hans-Peter and Kyrpides, Nikos C. and Hahnke, Richard L.},
abstractNote = {},
doi = {10.1186/s40793-016-0163-9},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United Kingdom},
year = {2016},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s40793-016-0163-9

Citation Metrics:
Cited by: 10 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment
journal, May 2014

  • Hameed, A.; Shahina, M.; Lin, S. -Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 8
  • DOI: 10.1099/ijs.0.059881-0

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom
journal, December 2014

  • Xing, Peng; Hahnke, Richard L.; Unfried, Frank
  • The ISME Journal, Vol. 9, Issue 6
  • DOI: 10.1038/ismej.2014.225

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

The DNA Bank Network: The Start from a German Initiative
journal, March 2011

  • Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
  • Biopreservation and Biobanking, Vol. 9, Issue 1
  • DOI: 10.1089/bio.2010.0029

MEROPS : the database of proteolytic enzymes, their substrates and inhibitors
journal, October 2013

  • Rawlings, Neil D.; Waller, Matthew; Barrett, Alan J.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt953

Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment
journal, November 2005

  • Lau, S. C. K.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 6
  • DOI: 10.1099/ijs.0.63824-0

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
journal, May 2007

  • Grissa, I.; Vergnaud, G.; Pourcel, C.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm360

LPSN—list of prokaryotic names with standing in nomenclature
journal, November 2013


List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet
journal, April 1997

  • EuzéBy, J. P.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 47, Issue 2
  • DOI: 10.1099/00207713-47-2-590

Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis
journal, August 2009

  • McBride, M. J.; Xie, G.; Martens, E. C.
  • Applied and Environmental Microbiology, Vol. 75, Issue 21
  • DOI: 10.1128/AEM.01495-09

Complete genome sequence of Isosphaera pallida type strain (IS1BT)
journal, February 2011

  • Göker, Markus; Cleland, David; Saunders, Elizabeth
  • Standards in Genomic Sciences, Vol. 4, Issue 1
  • DOI: 10.4056/sigs.1533840

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola
journal, January 2013

  • Jeong, S. H.; Jin, H. M.; Jeon, C. O.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 8
  • DOI: 10.1099/ijs.0.048694-0

Approved Lists of Bacterial Names
journal, January 1980

  • Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
  • DOI: 10.1099/00207713-30-1-225

Solexa Ltd
journal, June 2004


Dilution cultivation of marine heterotrophic bacteria abundant after a spring phytoplankton bloom in the North Sea: Isolation of abundant bacteria linked to a diatom bloom
journal, May 2014

  • Hahnke, Richard L.; Bennke, Christin M.; Fuchs, Bernhard M.
  • Environmental Microbiology, Vol. 17, Issue 10
  • DOI: 10.1111/1462-2920.12479

Ecology of marine Bacteroidetes: a comparative genomics approach
journal, January 2013

  • Fernández-Gómez, Beatriz; Richter, Michael; Schüler, Margarete
  • The ISME Journal, Vol. 7, Issue 5
  • DOI: 10.1038/ismej.2012.169

Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius
journal, January 2005

  • Nedashkovskaya, O. I.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
  • DOI: 10.1099/ijs.0.63314-0

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

The Genomic Standards Consortium
journal, June 2011


Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses
journal, October 2010


Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014


Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age
journal, February 2014

  • Klenk, Hans-Peter; Meier-Kolthoff, Jan P.; Göker, Markus
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue 2
  • DOI: 10.1099/ijs.0.056994-0

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901 T Reveals a Broad Potential for Degradation of Algal Polysaccharides
journal, August 2013

  • Mann, Alexander J.; Hahnke, Richard L.; Huang, Sixing
  • Applied and Environmental Microbiology, Vol. 79, Issue 21
  • DOI: 10.1128/AEM.01937-13

Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil
journal, December 2010

  • Cho, S. -H.; Chae, S. -H.; Cho, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 11
  • DOI: 10.1099/ijs.0.027599-0

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media
journal, October 2013


High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes
journal, July 2015

  • Hahnke, Richard L.; Stackebrandt, Erko; Meier-Kolthoff, Jan P.
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0032-y

ARB: a software environment for sequence data
journal, February 2004


SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Gramella aestuariivivens sp. nov., isolated from a tidal flat
journal, April 2015

  • Park, Sooyeon; Won, Sung-Min; Jung, Yong-Taek
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 4
  • DOI: 10.1099/ijs.0.000093

Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment
journal, November 2001

  • Bruns, A.; Rohde, M.; Berthe-Corti, L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 51, Issue 6
  • DOI: 10.1099/00207713-51-6-1997

Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean
journal, January 2010

  • Gómez-Pereira, Paola R.; Fuchs, Bernhard M.; Alonso, Cecilia
  • The ISME Journal, Vol. 4, Issue 4
  • DOI: 10.1038/ismej.2009.142

Gliding Motility and Por Secretion System Genes Are Widespread among Members of the Phylum Bacteroidetes
journal, November 2012

  • McBride, Mark J.; Zhu, Yongtao
  • Journal of Bacteriology, Vol. 195, Issue 2
  • DOI: 10.1128/JB.01962-12

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010

  • Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.541628

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
journal, February 2013

  • Medema, Marnix H.; Takano, Eriko; Breitling, Rainer
  • Molecular Biology and Evolution, Vol. 30, Issue 5
  • DOI: 10.1093/molbev/mst025

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
journal, September 2008

  • Yarza, Pablo; Richter, Michael; Peplies, Jörg
  • Systematic and Applied Microbiology, Vol. 31, Issue 4
  • DOI: 10.1016/j.syapm.2008.07.001

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011

  • Pagani, I.; Liolios, K.; Jansson, J.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1100

A Comparative Study of the Lipid Composition of Halobacterium saccharovorum from Various Sources
journal, May 1990


Gramella flava sp. nov., a member of the family Flavobacteriaceae isolated from seawater
journal, September 2013

  • Liu, K.; Li, S.; Jiao, N.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 1
  • DOI: 10.1099/ijs.0.051987-0

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803
journal, February 2014

  • Kabisch, Antje; Otto, Andreas; König, Sten
  • The ISME Journal, Vol. 8, Issue 7
  • DOI: 10.1038/ismej.2014.4

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


A Rapid Method of Total Lipid Extraction and Purification
journal, August 1959

  • Bligh, E. G.; Dyer, W. J.
  • Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 8
  • DOI: 10.1139/o59-099

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009


En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


A Rapid Method of Total Lipid Extraction and Purification
journal, January 1959

  • Bligh, E. G.; Dyer, W. J.
  • Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 1
  • DOI: 10.1139/y59-099