Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging
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...
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ftdoajarticles:oai:doaj.org/article:143f77da0169470a8f6939965c7b32ad 2023-05-15T18:11:40+02:00 Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging Pei Zhang Paloma Valverde Douglas Daniel Peter Fox 2015-01-01T00:00:00Z https://doi.org/10.1016/j.mex.2015.06.004 https://doaj.org/article/143f77da0169470a8f6939965c7b32ad EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S2215016115000394 https://doaj.org/toc/2215-0161 2215-0161 doi:10.1016/j.mex.2015.06.004 https://doaj.org/article/143f77da0169470a8f6939965c7b32ad MethodsX, Vol 2, Iss C, Pp 331-339 (2015) Spatial Analytical Microbial Imaging Science Q article 2015 ftdoajarticles https://doi.org/10.1016/j.mex.2015.06.004 2022-12-31T12:24:24Z 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. Article in Journal/Newspaper sami sami Directory of Open Access Journals: DOAJ Articles MethodsX 2 331 339 |
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ftdoajarticles |
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Spatial Analytical Microbial Imaging Science Q |
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Spatial Analytical Microbial Imaging Science Q Pei Zhang Paloma Valverde Douglas Daniel Peter Fox Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
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Spatial Analytical Microbial Imaging Science Q |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Pei Zhang Paloma Valverde Douglas Daniel Peter Fox |
author_facet |
Pei Zhang Paloma Valverde Douglas Daniel Peter Fox |
author_sort |
Pei Zhang |
title |
Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
title_short |
Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
title_full |
Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
title_fullStr |
Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
title_full_unstemmed |
Study of a two species microbial community by an inferential comparative genomic analysis tool: Spatial Analytical Microbial Imaging |
title_sort |
study of a two species microbial community by an inferential comparative genomic analysis tool: spatial analytical microbial imaging |
publisher |
Elsevier |
publishDate |
2015 |
url |
https://doi.org/10.1016/j.mex.2015.06.004 https://doaj.org/article/143f77da0169470a8f6939965c7b32ad |
genre |
sami sami |
genre_facet |
sami sami |
op_source |
MethodsX, Vol 2, Iss C, Pp 331-339 (2015) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S2215016115000394 https://doaj.org/toc/2215-0161 2215-0161 doi:10.1016/j.mex.2015.06.004 https://doaj.org/article/143f77da0169470a8f6939965c7b32ad |
op_doi |
https://doi.org/10.1016/j.mex.2015.06.004 |
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MethodsX |
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331 |
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339 |
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1766184305144365056 |