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The world bacterial biogeography and biodiversity through databases: a case study of NCBI Nucleotide Database and GBIF Database.

Selama O, James P, Nateche F, Wellington EM, Hacène H - Biomed Res Int (2013)

Bottom Line: These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database.Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented.This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria.

ABSTRACT
Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

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Related in: MedlinePlus

The relative abundance of the 24 common phyla in NCBI Nucleotide Database and GBIF Database.
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fig1: The relative abundance of the 24 common phyla in NCBI Nucleotide Database and GBIF Database.

Mentions: Records retrieved from both NCBI Nucleotide and GBIF databases summarized in Figure 1 and Table 3 show that Proteobacteria are the most abundant phylum in both databases with 64% and 49%, respectively, Firmicutes 13% and Actinobacteria (8%) were the second most abundant phyla for NCBI Nucleotide Database, and Bacteroidetes (11%) and then Cyanobacteria (9%) and Planctomycetes (7%) for GBIF Database. The remaining phyla represented less than 5% each. In the last position, we may find Chrysiogenetes and Dictyoglomi with less than 0,004% of records for both databases.


The world bacterial biogeography and biodiversity through databases: a case study of NCBI Nucleotide Database and GBIF Database.

Selama O, James P, Nateche F, Wellington EM, Hacène H - Biomed Res Int (2013)

The relative abundance of the 24 common phyla in NCBI Nucleotide Database and GBIF Database.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3818805&req=5

fig1: The relative abundance of the 24 common phyla in NCBI Nucleotide Database and GBIF Database.
Mentions: Records retrieved from both NCBI Nucleotide and GBIF databases summarized in Figure 1 and Table 3 show that Proteobacteria are the most abundant phylum in both databases with 64% and 49%, respectively, Firmicutes 13% and Actinobacteria (8%) were the second most abundant phyla for NCBI Nucleotide Database, and Bacteroidetes (11%) and then Cyanobacteria (9%) and Planctomycetes (7%) for GBIF Database. The remaining phyla represented less than 5% each. In the last position, we may find Chrysiogenetes and Dictyoglomi with less than 0,004% of records for both databases.

Bottom Line: These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database.Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented.This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria.

ABSTRACT
Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

Show MeSH
Related in: MedlinePlus