Open Access Research article

Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein125*, Ludovic Cottret3, Janice Kielbassa12, Hubert Charles14, Christian Gautier12, Ana Tereza Ribeiro de Vasconcelos125, Vincent Lacroix12 and Marie-France Sagot12*

Author Affiliations

1 BAMBOO Team, INRIA Grenoble-Rhône-Alpes, Villeurbanne, France

2 Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, UMR5558, France

3 , UMR1089 Xénobiotiques INRA-ENVT

4 , UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INRA, INSA-Lyon, Villeurbanne, France

5 , Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil

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BMC Genomics 2012, 13:438  doi:10.1186/1471-2164-13-438

Published: 31 August 2012

Additional files

Additional file 1:

Additional results. Additional results exemplifying the issue of NOGD, controlling for the structuring ofMIV and connectivity of the partial EC number set for obligate intracellular and extracellular bacteria.

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Additional file 2:

The full list of the bacteria selected and their detailed classification. Additional file 2: Table S1: the full list of the bacteria selected and their detailed classification

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Additional file 3:

Number of Genes vs lifestyles. Additional file 3: Figure S1: Total number of genes and number of metabolic genes (small bars) according to lifestyles (A) and taxonomic classes (B).

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Additional file 4:

Compounds common to all dataset. Additional file 4: Table S2: compounds common to all dataset and their classification.

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Additional file 5:

Compounds and reactions common to groups of lifestyle. Additional file 5: Table S3: Size of the mean, union and intersections of the compound and the reaction sets among the different lifestyle groups of bacteria.

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Additional file 6:

The full list of the reactions analysed and the list of organisms that lack them. Additional file 6: Table S4: The full list of reactions represented by its MetaCyc ID, corresponding enzyme name and EC number. For each reaction, the number of organisms that possess it are presented as well as the list of the bacteria which lack it. The codes for the organisms are the ones from HAMAP [ [40]] and they can also be found in Figure 1 and in the Additional file 1. The reactions are sorted by the number of organisms that possess them.

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Additional file 7:

Partial EC numbers common to groups of lifestyle. Additional file 7: Table S5: size of the mean, union and intersections of the partial EC number sets among the different lifestyle groups.

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Additional file 8:

Metabolic core of the extracellular bacteria. Additional file 8: Figure S2: qualitative representation of the metabolic core of the extracellular symbionts.

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Additional file 9:

Distribution of reactions across metabolic processes. Additional file 9: Table S6: distribution of reactions across metabolic processes, as defined in BioCyc databases. Some reactions are classified in more than one process and this explains why it may happen that the two proportions add up to more than 100%. For clarity, we introduced a category for such reactions (Biosynthesis/Degradation). For the group CA, the values in-between parentheses correspond to the CA group without the two Mycoplasma species.

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Additional file 10:

Simulation of partial EC number sets of the MIV bacteria. Simulation of partial EC number sets of theMIV bacteria. Additional file 10: Figure S3: simulation of the size of the mean (A), union (B) and intersection (C) of the partial EC number sets of the MIV bacteria.

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Additional file 11:

Number of potential inputs. Additional file 11: Figure S4: the number of potential inputs of the metabolic networks according to Borenstein method [ [52]].

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Additional file 12:

Potential inputs common to groups of lifestyle. Additional file 2: Table S7: size of the mean, union and intersections of the potential input sets among the different lifestyle groups.

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