title: Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging.
abstract: Most molecular fingerprinting techniques, including denaturing gradient gel electrophoresis (DGGE) [1], comparative genomic hybridization (CGH) [2], real-time polymerase chain reaction (RT-PCR) [3], destroy community structure and/or cellular integrity, therefore lost the info. of the spatial locus and the in situ genomic copy number of the cells. An alternative technique, fluorescence in situ hybridization (FISH) doesn't require sample disintegration but needs to develop specific markers and doesn't provide info. related to genomic copy number. Here, a microbial analysis tool, Spatial Analytical Microbial Imaging (SAMI), is described. An application was performed with a mixture of Synechocystis sp. PCC 6803 and E. coli K-12 MG1655. The intrinsic property of their genome, reflected by the average fluorescence intensity (AFI), distinguished them in 3D. And their growth rates were inferred by comparing the total genomic fluorescence binding area (GFA) with that of the pure culture standards. A 93% of accuracy in differentiating the species was achieved. •SAMI does not require sample disintegration and preserves the community spatial structure.•It measures the 3D locus of cells within the mixture and may differentiate them according to the property of their genome.•It allows assessment of the growth rate of the cells within the mixture by comparing their genomic copy number with that of the pure culture standards.
authors.affiliation: Department of Civil, Environmental & Sustainable Engineering, Arizona State University, Arizona State University, PO Box 5306, Tempe, AZ 85287, USA ; Biodesign Institute at Arizona State University, 1001 S. McAllister Ave., PO Box 875001, Tempe, AZ 85287-5710, USA ; Department of Sciences, Wentworth Institute of Technology, 550 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Sciences, Wentworth Institute of Technology, 550 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Paloma
authors.initials: P
authors.lastname: Valverde
authors.affiliation: Biodesign Institute at Arizona State University, 1001 S. McAllister Ave., PO Box 875001, Tempe, AZ 85287-5710, USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Daniel
authors.affiliation: Department of Civil, Environmental & Sustainable Engineering, Arizona State University, Arizona State University, PO Box 5306, Tempe, AZ 85287, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Fox
keywords: 3D imaging analysis; 3D locus; Co-culture; Genomic copy number; Inferential comparative genomic copy number; Microbial community analysis; Spatial Analytical Microbial Imaging; Spatiotemporal microbial community