New monitoring approach for metabolic dynamics in microbial ecosystems using stable-isotope-labeling technologies |
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Authors: | Yasuhiro Date Yumiko Nakanishi Shinji Fukuda Tamotsu Kato Satoshi Tsuneda Hiroshi Ohno Jun Kikuchi |
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Affiliation: | 1 Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan;2 RIKEN Plant Science Center, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan;3 RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan;4 Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan;5 Graduate School of Bioagricultural Sciences, Nagoya University, 1, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan |
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Abstract: | We have developed a new approach for monitoring the metabolic dynamics in microbial ecosystems using a combination of DNA fingerprinting and metabolome analysis based on stable-isotope-labeling technologies. Stable-isotope probing of DNA (DNA-SIP) has been used previously for the evaluation of cross-feeding in microbial communities. For the development and validation of our monitoring approach, fecal microbiota were analyzed with stable-isotope-labeled glucose used as the sole carbon source. In order to link the metabolic information and the microbial variability, we performed metabolic–microbial correlation analysis based on nuclear magnetic resonance (NMR) profiles and denaturing gradient gel electrophoresis (DGGE) fingerprints, which successfully identified the glucose-utilizing bacteria and their related extracellular metabolites. Moreover, our approach revealed information regarding the carbon flux, in that the “first” wave of extracellular metabolites secreted by the glucose-utilizing bacteria were incorporated into the “secondary” group of substrate-utilizing bacteria, and that this “secondary” group further produced their own secondary metabolized substrates. Thus, this approach is a powerful tool for monitoring the metabolic dynamics in microbial ecosystems and allows for the tracking of the carbon flux within a microbial community. |
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Keywords: | Nuclear magnetic resonance (NMR) Stable-isotope probing (SIP) Metabolic dynamics Carbon flux Denaturing gradient gel electrophoresis (DGGE) |
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