Metabolic-network-driven analysis of bacterial ecological strategies

doi:10.1186/gb-2009-10-6-r61

Genome Biology

Volume 10
Issue 6

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Freilich S
Kreimer A
Borenstein E
Yosef N
Sharan R
Gophna U
Ruppin E

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Kreimer A
Borenstein E
Yosef N
Sharan R
Gophna U
Ruppin E
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Metabolic-network-driven analysis of bacterial ecological strategies

Shiri Freilich¹^,2^* , Anat Kreimer³^* , Elhanan Borenstein⁴^,5 , Nir Yosef¹ , Roded Sharan¹ , Uri Gophna⁶ and Eytan Ruppin¹^,2

¹The Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

²School of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

³School of Mathematical Science, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

⁴Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA

⁵Santa Fe Institute, Santa Fe, NM 87501, USA

⁶Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R61doi:10.1186/gb-2009-10-6-r61


Published:	5 June 2009

Subject areas: Ecology, Evolution, Microbiology and parasitology

Additional files

Additional data file 1:

Genomic and ecological attributes for the 113 species in the analysis.

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Additional data file 2:

NCBI annotations and description of environmental samples for species that can be identified in an environmental sample.

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Additional data file 3:

Supplementary notes and figures, detailed description of all tables in the Additional data files and a table. Table S5: Correlation (P value) versus duplication time in random environments. Figure S1: Distribution of the correlations between doubling time and ESI and maximal-CHS in random samples of species selected in a way that allows equal number of representatives for each ecological habitat. Figure S2: Distribution of the correlations between doubling time and ESI and maximal-CHS in random samples of species selected in a way that allows a single representative for each taxonomic group. Figure S3: The distribution of Pearson correlation coefficients of the ESI values with randomized maximal CHS values. Figure S4: General distribution of species/environment in 3 different sets of environments (original and random). Figure S5: Mean maximal CHS levels of bacteria of a given life style. Figure S6: The distribution of log doubling time of the 113 species studied. Figure S7: The mean and standard deviation of the recoever operating characteristics (ROC) curve obtained in 50 cross validation experiments.

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Additional data file 4:

Original and manually curated values of environmental complexity.

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Additional data file 5:

Biomass target metabolites.

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Additional data file 6:

Genomic and ecological attributes for the 528 species in the metabolic analysis.

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