MICROBIAL DATABASES

A follow up for microbial databases

When you use the databases please remember that the only way for us to provide continuous support is to show granting agencies that this work is used. Please quote the reference articles in your work.

As novel sequencing techniques develops it becomes essential to construct databases with a large number of genomes. A collaboration with the Beijing Genome Institute located in Shenzhen, China, will provide novel information. It mirrored the GenoChore suite, before creating a novel suite on a completely novel data schema, until 2016. Unfortunately, because of changes at the head of the Chinese National DataBank at the BGI, this service was discontinued, and the address http://microme.genomics.org.cn/ is no longer valid.

When you use the databases please remember that the only way for us to provide continuous support is to show granting agencies that this work is used. Please quote the reference articles in your work.

The initial data model and algorithm is published in:

G Fang, C Ho, YW Qiu, V Cubas, Z Yu, C Cabau, F Cheung, I Moszer, A Danchin
Specialized microbial databases for inductive exploration of microbial genome sequences
BMC Genomics (2005) 6: 14

This effort had to be discontinued at the end of 2010 and it was replaced by a totally novel approach at the Beijing Genome Institute in Shenzhen until 2016. We hope that a further program will develop.

• Collaboration with the Genoscope: The Bacillus subtilis sequencing program
  

Several updates followed after the complete resequencing of the original strain, deposited at the German Collection of Microorganisms and Cell Cultures DSMZ under accession number DSM 23778

For resequencing please quote:

V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, TZ Wang, I Moszer, C Médigue, A Danchin
From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later
Microbiology (2009) 155: 1758-1775   

Several updates of the Bacillus subtilis program followed

For an update with the methionine salvage pathway please quote:

	E Belda, A Sekowska, F Le Fèvre, A Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A Danchin An updated metabolic view of the Bacillus subtilis 168 genome Microbiology (2013) 159: 757-770. doi: 10.1099/mic.0.064691-0
	A Sekowska, H Ashida, A Danchin Revisiting the methionine salvage pathway and its paralogues Microb Biotechnol. (2019) 12: 77-97 doi: 10.1111/1751-7915.13324

For an update after 20 years please quote:

R Borriss, A Danchin, CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement Microb Biotechnol. (2018) 11: 3-17 doi: 10.1111/1751-7915.12461

Collaboration with the University of Florida and Yale University

Escherichia coli K12 (MG1655)
Colibri

Please quote:
C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654

C. Médigue, T. Rouxel, P. Vigier, A. Hénaut & A. Danchin
Evidence for horizontal gene transfer in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856

• Collaboration with the Unit of Genomics of Pathogenic Microorganisms

  Photorhabdus luminescens TT01
  PhotoScope

Please quote:
E. Duchaud, C. Rusniok, L. Frangeul, C. Buchrieser, A. Givaudan, S. Taourit, S. Bocs, C. Boursaux-Eude, M. Chandler, J-F. Charles, E. Dassa, R. Derose, S. Derzelle, G. Freyssinet, S. Gaudriault, C. Médigue, A. Lanois, K. Powell, P. Siguier , R. Vincent, V. Wingate, M. Zouine, P. Glaser, N. Boemare, A. Danchin & F. Kunst
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.
Nature Biotechnol (2003) 21: 1307-1313

• Collaboration with the HKU Computer Centre and the BIOSUPPORT programme
  and the Shanghai Genome Centre (China)

		Leptospira interrogans LAI
		S.X. Ren, G. Fu, X.G. Jiang, R. Zeng, Y.G. Miao, H. Xu, Y.X. Zhang, H. Xiong, G. Lu, L.F. Lu, H.Q. Jiang, J. Jia, Y.F. Tu, J.X. Jiang, W.Y. Gu, Y.Q. Zhang, Z. Cai, H.H. Sheng, H.F. Yin, Y. Zhang, G.F. Zhu, M. Wan, H.L. Huang, Z. Qian, S.Y. Wang, W. Ma, Z.J. Yao, Y. Shen, B.Q. Qiang, Q.C. Xia, X.K. Guo, A. Danchin, I. Saint Girons, R.L. Somerville, Y.M. Wen, M.H. Shi, Z. Chen, J.G. Xu & G.P. Zhao Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing Nature (2003) 422: 888-893

		Staphylococcus epidermidis ATCC 12228
		Y.Q. Zhang, S.X. Ren, H.L. Li, Y.X. Wang, G. Fu, J. Yang, Z.Q. Qin, Y.G. Miao, W.Y. Wang, R.S. Chen, Y. Shen, Z. Chen, Z.H. Yuan, G.P. Zhao, D. Qu, A. Danchin & Y.M. Wen Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol Microbiol (2003) 49:1577-1593

and the Beijing Genome Centre (China)

		Thermoanaerobacter tencongensis

and Fondaçao de Amparo a Pesquisa do Estado da Sao Paolo (Brasil)

		Xylella fastidiosa

and also, at the HKU Computer Centre

		Clostridium acetobutylicum

 

		Bacillus anthracis

 

		Bacillus cereus

 

		Campylobacter jejuni

 

		Haemophilus influenzae

 

		Neisseria meningitidis

 

		Pseudomonas aeruginosa

 

		Pseudomonas putida

 

		Vibrio cholerae

 

		Vibrio vulnificus

Collaboration with the Genoscope

		Pseudoalteromonas haloplanktis TAC125

Please quote:
C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino, J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, G von Heijne, A Danchin
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Genome Res (2005) 15: 1325-1335 

and a small eukaryote, the Microsporidion Encephalitozoon cuniculi

		Encephalitozoon cuniculi