Statistical Indices for Simultaneous Large-Scale Metabolite Detections for a Single NMR Spectrum

Chikayama, Eisuke; Sekiyama, Yasuyo; Okamoto, Mami; Nakanishi, Yumiko; Tsuboi, Yuuri; Akiyama, Kenji; Saito, Kazuki; Shinozaki, Kazuo; Kikuchi, Jun

doi:10.1021/ac9022023

Cited by 128 publications

(130 citation statements)

References 55 publications

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“…The acquired spectra were manually phased and baseline-corrected. NMR spectra were processed using NMRPipe software [34] and assigned using the SpinAssign program on the PRIMe website [35][36][37].…”

Section: Solution-state Nmr Spectroscopymentioning

confidence: 99%

Solid-, Solution-, and Gas-state NMR Monitoring of 13C-Cellulose Degradation in an Anaerobic Microbial Ecosystem

et al. 2013

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Anaerobic digestion of biomacromolecules in various microbial ecosystems is influenced by the variations in types, qualities, and quantities of chemical components. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for characterizing the degradation of solids to gases in anaerobic digestion processes. Here we describe a characterization strategy using NMR spectroscopy for targeting the input solid insoluble biomass, catabolized soluble metabolites, and produced gases. C-labeled cellulose produced by Gluconacetobacter xylinus was added as a substrate to stirred tank reactors and gradually degraded for 120 h. The time-course variations in structural heterogeneity of cellulose catabolism were determined using solid-state NMR, and soluble metabolites produced by cellulose degradation were monitored using solution-state NMR. In particular, cooperative changes between the solid NMR signal and phase NMR measurements demonstrated that cellulose was anaerobically degraded, fermented, and converted to methane gas from organic acids such as acetic acid and butyric acid.

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Section: Solution-state Nmr Spectroscopymentioning

confidence: 99%

Solid-, Solution-, and Gas-state NMR Monitoring of 13C-Cellulose Degradation in an Anaerobic Microbial Ecosystem

et al. 2013

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“…The HSQC TOCSY spectra were acquired as 1024 (F2) and 256 (F1) data points with 180 scans and an interscan delay of 1 s with 16 dummy scans. The NMR spectra were processed using Bruker TopSpin software (Bruker BioSpin GmbH) and assigned using the SpinAssign program at the PRIMe website (http://prime.psc.riken.jp/) (Akiyama et al 2008;Chikayama et al 2010;Chikayama et al 2008) and the Biological Magnetic Resonance Bank (http://www.bmrb.wisc.edu/metabolomics/query_metab.php) (Ulrich et al 2008). …”

Section: Nmr Measurementsmentioning

confidence: 99%

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

Asakura

Sakata

Yoshida

et al. 2014

Preprint

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An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan's coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fishmicrobial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested. PrePrints ABSTRACT An NMR based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan's coastal waters using next generation sequencing, followed by evaluation of the effects of feed type on co metabolic modulations in fish microbial symbiotic ecosystems in laboratory scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non invasive inspection technique in aquaculture is suggested.

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“…23,24 Peak assignments were made using the SpinAssign program on the PRIMe website (http://prime.psc.riken.jp/). [25][26][27] To evaluate the water-insoluble seaweed components, lyophilized samples were powdered and processed by various procedures to identify the best extraction method (Supplementary Table 2), and the optimal-modified process was used for all further analyses. In the optimal process, the lyophilized samples were roughly crushed in a food blender and then powdered using an Automill machine.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

“…The characterization of the water-soluble components via an NMR-based metabolomics approach has been used extensively to study metabolites in a wide range of biological systems in various environments, [6][7][8][9][10][11][12][13] and is capable of creating assignments using our database (that is, SpinAssign program at the PRIMe website). [25][26][27] The water-insoluble …”

Section: Chemical Profiling Of Complex Seaweed Polymers Y Date Et Almentioning

confidence: 99%

Chemical profiling of complex biochemical mixtures from various seaweeds

Date

Sakata

Kikuchi

2012

Polym J

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Development of an approach to describing and comparing complex biochemical mixtures presented by natural biomacromolecular sources is a promising new field in polymer science. The generation of a comprehensive strategy for evaluating and characterizing natural biomass mixtures presents a significant challenge. Here, we describe a chemical profiling methodology for seaweed biomass based on the comprehensive characterization of water-soluble, water-insoluble and solid-state components. An extraction method was developed for the nuclear magnetic resonance measurement of the water-insoluble seaweed components by modifying and optimizing physical pretreatments and extraction processes. Evaluating the compositional variations in various seaweeds from biomass profiles by principal component analysis score plots showed that the species clustered according to their taxonomic group differences. In addition, this profiling strategy revealed that it was possible to annotate the primary components that are characteristic of each taxonomic group, such as mannitol and laminaran in brown algae, D-galactose and agar in red algae, and xylopyranose and glucopyranose in green algae. Therefore, this profiling strategy was capable of discerning and evaluating individual characteristics among these seaweeds.

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Statistical Indices for Simultaneous Large-Scale Metabolite Detections for a Single NMR Spectrum

Cited by 128 publications

References 55 publications

Solid-, Solution-, and Gas-state NMR Monitoring of 13C-Cellulose Degradation in an Anaerobic Microbial Ecosystem

Solid-, Solution-, and Gas-state NMR Monitoring of 13C-Cellulose Degradation in an Anaerobic Microbial Ecosystem

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

Chemical profiling of complex biochemical mixtures from various seaweeds

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