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. 2019 Jan 1:2019:baz049.
doi: 10.1093/database/baz049.

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Malo Le Boulch  1 , Patrice Déhais  2 , Sylvie Combes  1 , Géraldine Pascal  1
Affiliations

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Malo Le Boulch et al. Database (Oxford). .

Abstract

Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally, MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface.

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Figures

Figure 1
Figure 1
MACADAM building workflow.
Figure 2
Figure 2
At the top, formulas for the computation of the PS and PFS. Below, examples of two types of computations of the PS and PFS based on an example of a hypothetical metabolic pathway. By comparing the PS and PFS in A and B, pathway A shows greater evidence of its veracity.
Figure 3
Figure 3
Comparison of PS of all metabolic pathways of PGDBs present in both MetaCyc PGDBs and MicroCyc PGDBs. A: among Bacteria; B: among Archaea.
Figure 4
Figure 4
MACADAM database schema. Yellow arrows indicate the entry points of the database.
Figure 5
Figure 5
Screenshot of MACADAM Explore website showing the query of all functional information containing the word ‘urea’ in the species ‘Staphylococcus aureus’ and ‘Kitasatospora aureofaciens’.
Figure 6
Figure 6
Examples of output files corresponding to requests on MACADAM. (A) The user has searched for all metabolic pathways in S. aureus and K. aureofaciens, using the term ‘urea’ in the function field text. (B) The user has searched for all metabolic pathways in Lactobacillus cerevisiae using the term ‘urea’ in the function field text. Since there is no data on this organism in MACADAM, the information was searched for higher up in the taxonomy hierarchy, i.e. Lactobacillus. (1)List of organisms in MACADAM with the targeted metabolic pathway.
Figure 7
Figure 7
Phyla distribution in the MACADAM database according to their database of origin. (A) MetaCyc and MicroCyc for bacterial organisms, (B) MetaCyc and MicroCyc for archaea organisms, (C) FAPROTAX for bacterial organisms, (D) FAPROTAX for archaea organisms, (E) IJSEM phenotypic database for bacterial organisms and (F) IJSEM phenotypic database for archaea organisms.
Figure 8
Figure 8
MACADAM functional diversity for phyla with >10 PGDBs in MACADA (A) among bacterial phyla, (B) among archaea phyla, (C) the 10 main hierarchical groups of pathways in all bacterial organisms and (D) the 10 main hierarchical groups of pathways in all archaea organisms.
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References

    1. Bergey D.H., Buchanan R.E., Gibbons N.E. et al. (1974) Bergey’s Manual of Determinative Bacteriology. Williams & Wilkins Co, Baltimore.
    1. Garrity G., Boone D.R. and Castenholz R.W. (eds) (2001) Bergey’s Manual of Systematic Bacteriology: The Archaea and the Deeply Branching and Phototrophic Bacteria, Vol. 1, 2nd edn. Springer-Verlag, New York.
    1. Garrity G. (ed) (2005) Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, Vol. 2, 2nd edn. Springer, USA.
    1. Vos P., Garrity G., Jones D. et al. (eds) (2009) Bergey’s Manual of Systematic Bacteriology: The Firmicutes, Vol. 3, 2nd edn. Springer-Verlag, New York.
    1. Krieg N.R., Ludwig W., Whitman W. et al. (eds) (2010) Bergey’s Manual of Systematic Bacteriology: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, Vol. 4, 2nd edn. Springer-Verlag, New York.

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