Open Access‘FloraArray’ for screening of specific DNA probes representing the characteristics of a certain microbial community
Author(s) -
Yokoi Takahide,
Kaku Yoshiko,
Suzuki Hiroyuki,
Ohta Masayuki,
Ikuta Hajime,
Isaka Kazuichi,
Sumino Tatsuo,
Wagatsuma Masako
Publication year - 2007
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2007.00799.x
Subject(s) - anammox , dna microarray , library , genomic dna , biology , dna , computational biology , hybridization probe , activated sludge , microbiology and biotechnology , genetics , gene , chemistry , 16s ribosomal rna , gene expression , nitrogen , denitrification , sewage treatment , environmental science , denitrifying bacteria , organic chemistry , environmental engineering
To investigate uncharacterized microbial communities, a custom DNA microarray named ‘FloraArray’ was developed for screening specific probes that would represent the characteristics of a microbial community. The array was prepared by spotting 2000 plasmid DNAs from a genomic shotgun library of a sludge sample on a DNA microarray. By comparative hybridization of the array with two different samples of genomic DNA, one from the activated sludge and the other from a nonactivated sludge sample of an anaerobic ammonium oxidation (anammox) bacterial community, specific spots were visualized as a definite fluctuating profile in an MA (differential intensity ratio vs. spot intensity) plot. About 300 spots of the array accounted for the candidate probes to represent anammox reaction of the activated sludge. After sequence analysis of the probes and examination of the results of blastn searches against the reported anammox reference sequence, complete matches were found for 161 probes (58.3%) and >90% matches were found for 242 probes (87.1%). These results demonstrate that ‘FloraArray’ could be a useful tool for screening specific DNA molecules of unknown microbial communities.