%0 Journal Article
%T Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database
%A Andrea Squartini
%J Microbial Informatics and Experimentation
%D 2011
%I BioMed Central
%R 10.1186/2042-5783-1-7
%X In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea. Over two and a half million records are filtered in their cross-association with each of 48 sets of keywords, defined to cover natural or artificial habitats, interactions with plant, animal or human hosts, and physical-chemical conditions. The results are processed showing: (a) how the different descriptors enrich or deplete the proportions at which the phyla occur in the total database; (b) in which order of abundance do the different keywords score for each phylum (preferred habitats or conditions), and to which extent are phyla clustered to few descriptors (specific) or spread across many (cosmopolitan); (c) which keywords individuate the communities ranking highest for diversity and evenness.A number of cues emerge from the results, contributing to sharpen the picture on the functional systematic diversity of prokaryotes. Suggestions are given for a future automated service dedicated to refining and updating such kind of analyses via public bioinformatic engines.The distribution of microbial taxa in relation to environmental factors is a theme of central interest in microbiology and has been addressed by different perspectives and means [1-9]. Several studies investigated community structure of bacterial assemblages assessing the proportions of the different taxonomical groups. These surveys span from highly selective or stressful environmental niches [10], to broader interfaces as the soil [11] or the ocean [12]. Other reports dealt with the wealth of biota composing the hosted microbiomes, as is the case of the human-associated microorganisms [13]. In microbial ecology studies, a particular interest is devoted to understanding which factors do primarily shape the structure of communities. In such sense patterns have emerged pointing towards the importance of
%U http://www.microbialinformaticsj.com/content/1/1/7