High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James; Trong, Stephan; Haynes, Matthew; Reddy, T. B.  K.; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N.; Pukall, Rüdiger; Markowitz, Victor M.; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C.; Ohkuma, Moriya

doi:10.1186/s40793-015-0045-6

Title: High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

Journal Article · Sun Aug 02 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0045-6· OSTI ID:1256930

Sakamoto, Mitsuo ^[1]; Lapidus, Alla L. ^[2]; Han, James ^[3]; Trong, Stephan ^[3]; Haynes, Matthew ^[3]; Reddy, T. B. K. ^[3]; Mikhailova, Natalia ^[3]; Huntemann, Marcel ^[3]; Pati, Amrita ^[3]; Ivanova, Natalia N. ^[3]; Pukall, Rüdiger ^[4]; Markowitz, Victor M. ^[5]; Woyke, Tanja ^[3]; Klenk, Hans-Peter ^[4]; Kyrpides, Nikos C. ^[6]; Ohkuma, Moriya ^[1]

RIKEN BioResource Center, Ibaraki (Japan)
St. Petersburg State Univ. (Russia); St. Petersburg Academic Univ. (Russia)
DOE Joint Genome Institute, Walnut Creek, CA (United States)
Leibniz-Inst. DSMZ, Braunschweig (Germany)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2T is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. We report that the 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344

OSTI ID:: 1256930

Journal Information:: Standards in Genomic Sciences, Vol. 10, Issue 1; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 3 works

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References (36)

Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names Yarza, Pablo; Spröer, Cathrin; Swiderski, Jolantha Systematic and Applied Microbiology, Vol. 36, Issue 1 https://doi.org/10.1016/j.syapm.2012.12.006	journal	February 2013
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
The DNA Bank Network: The Start from a German Initiative Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger Biopreservation and Biobanking, Vol. 9, Issue 1 https://doi.org/10.1089/bio.2010.0029	journal	March 2011
Studies on the Cecal Microflora of Commercial Broiler Chickens Salanitro, J. P.; Blake, I. G.; Muirhead, P. A. Applied Microbiology, Vol. 28, Issue 3 https://doi.org/10.1128/am.28.3.439-447.1974	journal	September 1974
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0048837	journal	December 2012
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A. Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5068949	journal	December 2013
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects Göker, Markus; Klenk, Hans-Peter Standards in Genomic Sciences, Vol. 8, Issue 2 https://doi.org/10.4056/sigs.3446951	journal	May 2013
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Notification that new names and new combinations have appeared in volume 62, part 3, of the IJSEM Euzeby, J. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 6 https://doi.org/10.1099/ijs.0.043935-0	journal	June 2012
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A. PLoS Biology, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pbio.1001920	journal	August 2014
Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition Li, Ellen; Hamm, Christina M.; Gulati, Ajay S. PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0026284	journal	June 2012
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Isolation, Culture Characteristics, and Identification of Anaerobic Bacteria from the Chicken Cecum Salanitro, J. P.; Fairchilds, I. G.; Zgornicki, Y. D. Applied Microbiology, Vol. 27, Issue 4 https://doi.org/10.1128/am.27.4.678-687.1974	journal	April 1974
Genome sequence-based species delimitation with confidence intervals and improved distance functions Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-60	journal	January 2013
PICRUSt2 for prediction of metagenome functions Douglas, Gavin M.; Maffei, Vincent J.; Zaneveld, Jesse R. Nature Biotechnology, Vol. 38, Issue 6 https://doi.org/10.1038/s41587-020-0548-6	journal	June 2020
Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum Lan, P. T. N.; Sakamoto, M.; Sakata, S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 12 https://doi.org/10.1099/ijs.0.64517-0	journal	December 2006
Isolation, Culture Characteristics, and Identification of Anaerobic Bacteria from the Chicken Cecum Salanitro, J. P.; Fairchilds, I. G.; Zgornicki, Y. D. Applied Microbiology, Vol. 27, Issue 4, 678-687 https://doi.org/10.1128/AEM.27.4.678-687.1974	journal	April 1974
Studies on the Cecal Microflora of Commercial Broiler Chickens Salanitro, J. P.; Blake, I. G.; Muirhead, P. A. Applied Microbiology, Vol. 28, Issue 3, 439-447 https://doi.org/10.1128/AEM.28.3.439-447.1974	journal	September 1974
Starch Utilization by Bacteroides ovatus Isolated from the Human Large Intestine Degnan, Beverley A.; Macfarlane, Sandra; Quigley, M. E. Current Microbiology, Vol. 34, Issue 5 https://doi.org/10.1007/s002849900184	journal	May 1997
Anaerobes as Normal Flora Hentges, David J. Anaerobic Infections in Humans https://doi.org/10.1016/B978-0-12-256745-2.50007-6	book	January 1989
Role of the Intestinal Microflora in Host Defense against Infection Hentges, David J. Human Intestinal Microflora in Health and Disease https://doi.org/10.1016/B978-0-12-341280-5.50020-3	book	January 1983
Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation: Context-Guided Identification of Novel Cellulases Piao, Hailan; Froula, Jeff; Du, Changbin Biotechnology and Bioengineering, Vol. 111, Issue 8 https://doi.org/10.1002/bit.25250	journal	May 2014
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Pagani, I.; Liolios, K.; Jansson, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1100	journal	December 2011
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Gnerre, S.; MacCallum, I.; Przybylski, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 4 https://doi.org/10.1073/pnas.1017351108	journal	December 2010
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.632	journal	July 2009
Improving Microbial Genome Annotations in an Integrated Database Context Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0054859	journal	February 2013
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
The Genomic Standards Consortium Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy PLoS Biology, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pbio.1001088	journal	June 2011
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000

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Title: High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

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