Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes

Soo Je Park; Dong Hwan Kim; Man Young Jung; So Jeong Kim; Hongik Kim; Yang Hoon Kim; Jong Chan Chae; Sung Keun Rhee

doi:10.1007/s12275-012-2115-4

Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes

Soo Je Park
, Dong Hwan Kim
, Man Young Jung
, So Jeong Kim
, Hongik Kim
, Yang Hoon Kim
, Jong Chan Chae
, Sung Keun Rhee^*

^*Corresponding author for this work

Bioresource and Biomolecule Engineering

Chungbuk National University
Korea Institute of Oriental Medicine

Research output: Contribution to journal › Journal article › peer-review

3 Scopus citations

Abstract

Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 10⁶ bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20-100 ng) were observed (r²=0. 98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

Original language	English
Pages (from-to)	684-688
Number of pages	5
Journal	Journal of Microbiology
Volume	50
Issue number	4
DOIs	https://doi.org/10.1007/s12275-012-2115-4
State	Published - 2012.08

Keywords

community analysis
fosmid clone
gut
microarray

Quacquarelli Symonds(QS) Subject Topics

Biological Sciences

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10.1007/s12275-012-2115-4

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title = "Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes",

abstract = "Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20-100 ng) were observed (r2=0. 98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.",

keywords = "community analysis, fosmid clone, gut, microarray",

author = "Park, \{Soo Je\} and Kim, \{Dong Hwan\} and Jung, \{Man Young\} and Kim, \{So Jeong\} and Hongik Kim and Kim, \{Yang Hoon\} and Chae, \{Jong Chan\} and Rhee, \{Sung Keun\}",

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AU - Park, Soo Je

AU - Kim, Dong Hwan

AU - Jung, Man Young

AU - Kim, So Jeong

AU - Kim, Hongik

AU - Kim, Yang Hoon

AU - Chae, Jong Chan

AU - Rhee, Sung Keun

PY - 2012/8

Y1 - 2012/8

N2 - Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20-100 ng) were observed (r2=0. 98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

AB - Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20-100 ng) were observed (r2=0. 98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

KW - community analysis

KW - fosmid clone

KW - gut

KW - microarray

UR - https://www.scopus.com/pages/publications/84865771135

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DO - 10.1007/s12275-012-2115-4

M3 - Journal article

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SN - 1225-8873

VL - 50

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JO - Journal of Microbiology

JF - Journal of Microbiology

IS - 4

ER -

Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes

Abstract

Keywords

Quacquarelli Symonds(QS) Subject Topics

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