Summary of Study ST000875

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000606. The data can be accessed directly via it's Project DOI: 10.21228/M82D92 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000875
Study TitleMetabolomic investigations on Nesterenkonia flava from different origins revealed significant intraspecies differences between marine and terrestrial actinomycetes
Study SummaryMarine is one of the most important resources of microorganisms, including bacteria, actinomycetes, and fungi. As marine and terrestrial environments differ a lot in many aspects it is not surprising that the species and characteristics of microorganisms living there are very different. Interestingly, many marine microorganisms can find their congeners of the same species from terrestrial resources. The aim of this work is to evaluate the intraspecies differences between marine and terrestrial actinomycetes on metabolic level and to uncover the mechanism responsible for the differences. To address this, we carried out comparative metabolomics study on Nesterenkonia flava strains isolated from marine and terrestrial environments. The results showed that marine strains were clearly distinguished from their terrestrial congeners on the principal components analysis (PCA) scores plot of intracellular metabolites. The markers responsible for the discrimination of marine and terrestrial strains were figured out using loading plot from partial least squares discrimination analysis (PLS-DA). Pathway analysis based on PLS-DA, univariate analysis, and correlation analysis of metabolites showed that the major differential metabolites between the terrestrial N. flava and the marine ones were involved in osmotic regulation, redox balancing, and energy metabolism. Together, these insights provide clues as to how the previous living environment of microbes affect their current metabolic performances under laboratory cultivation conditions.
Institute
Third Institute of Oceanography, State Oceanic Administration
Last NameXia
First NameJinmei
Address184 Daxue Road, Xiamen 361005, PR China
Emailxiajinmei@tio.org.cn
Phone86-13003995626
Submit Date2017-08-12
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2020-01-06
Release Version1
Jinmei Xia Jinmei Xia
https://dx.doi.org/10.21228/M82D92
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000606
Project DOI:doi: 10.21228/M82D92
Project Title:Metabolomic investigations on Nesterenkonia flava from different origins revealed significant intraspecies differences between marine and terrestrial actinomycetes
Project Summary:Marine is one of the most important resources of microorganisms, including bacteria, actinomycetes, and fungi. As marine and terrestrial environments differ a lot in many aspects it is not surprising that the species and characteristics of microorganisms living there are very different. Interestingly, many marine microorganisms can find their congeners of the same species from terrestrial resources. The aim of this work is to evaluate the intraspecies differences between marine and terrestrial actinomycetes on metabolic level and to uncover the mechanism responsible for the differences. To address this, we carried out comparative metabolomics study on Nesterenkonia flava strains isolated from marine and terrestrial environments. The results showed that marine strains were clearly distinguished from their terrestrial congeners on the principal components analysis (PCA) scores plot of intracellular metabolites. The markers responsible for the discrimination of marine and terrestrial strains were figured out using loading plot from partial least squares discrimination analysis (PLS-DA). Pathway analysis based on PLS-DA, univariate analysis, and correlation analysis of metabolites showed that the major differential metabolites between the terrestrial N. flava and the marine ones were involved in osmotic regulation, redox balancing, and energy metabolism. Together, these insights provide clues as to how the previous living environment of microbes affect their current metabolic performances under laboratory cultivation conditions.
Institute:Third Institute of Oceanography, State Oceanic Administration
Last Name:Xia
First Name:Jinmei
Address:184 Daxue Road, Xiamen 361005, PR China
Email:xiajinmei@tio.org.cn
Phone:86-13003995626

Subject:

Subject ID:SU001174
Subject Type:NMR based metabolomics of microbes
Subject Species:Nesterenkonia flava
Taxonomy ID:469799

Factors:

Subject type: NMR based metabolomics of microbes; Subject species: Nesterenkonia flava (Factor headings shown in green)

mb_sample_id local_sample_id Strain Strain source Medium
SA077589201A10663 Terrestrial A14
SA077590191A10663 Terrestrial A14
SA077591211A10663 Terrestrial A14
SA077592221A10663 Terrestrial A14
SA077593241A10663 Terrestrial A14
SA077594231A10663 Terrestrial A14
SA077595691A10663 Terrestrial A3
SA077596711A10663 Terrestrial A3
SA077597681A10663 Terrestrial A3
SA077598671A10663 Terrestrial A3
SA077599721A10663 Terrestrial A3
SA077600701A10663 Terrestrial A3
SA077601481A10663 Terrestrial A6
SA077602431A10663 Terrestrial A6
SA077603471A10663 Terrestrial A6
SA077604461A10663 Terrestrial A6
SA077605441A10663 Terrestrial A6
SA077606451A10663 Terrestrial A6
SA07760731K00606 Marine A14
SA07760821K00606 Marine A14
SA07760941K00606 Marine A14
SA07761011K00606 Marine A14
SA07761161K00606 Marine A14
SA07761251K00606 Marine A14
SA077613541K00606 Marine A3
SA077614531K00606 Marine A3
SA077615521K00606 Marine A3
SA077616511K00606 Marine A3
SA077617491K00606 Marine A3
SA077618501K00606 Marine A3
SA077619251K00606 Marine A6
SA077620271K00606 Marine A6
SA077621281K00606 Marine A6
SA077622261K00606 Marine A6
SA077623291K00606 Marine A6
SA077624301K00606 Marine A6
SA077625101K00607 Marine A14
SA077626111K00607 Marine A14
SA07762791K00607 Marine A14
SA07762871K00607 Marine A14
SA077629121K00607 Marine A14
SA07763081K00607 Marine A14
SA077631581K00607 Marine A3
SA077632561K00607 Marine A3
SA077633571K00607 Marine A3
SA077634551K00607 Marine A3
SA077635591K00607 Marine A3
SA077636601K00607 Marine A3
SA077637341K00607 Marine A6
SA077638311K00607 Marine A6
SA077639361K00607 Marine A6
SA077640321K00607 Marine A6
SA077641331K00607 Marine A6
SA077642351K00607 Marine A6
SA077643141K00610 Marine A14
SA077644131K00610 Marine A14
SA077645151K00610 Marine A14
SA077646161K00610 Marine A14
SA077647181K00610 Marine A14
SA077648171K00610 Marine A14
SA077649661K00610 Marine A3
SA077650651K00610 Marine A3
SA077651631K00610 Marine A3
SA077652611K00610 Marine A3
SA077653621K00610 Marine A3
SA077654641K00610 Marine A3
SA077655371K00610 Marine A6
SA077656381K00610 Marine A6
SA077657391K00610 Marine A6
SA077658401K00610 Marine A6
SA077659411K00610 Marine A6
SA077660421K00610 Marine A6
Showing results 1 to 72 of 72

Collection:

Collection ID:CO001168
Collection Summary:The broth cultures (50 mL) were harvested via centrifugation at 7000 g for 10 min under 4 °C. The pellet was quenched using 10 mL of 60% cold methanol (−80 °C) containing 0.85% (wt./vol.) of NaCl for 30 min. The quenched cell pellets were re-suspended in 10 mL of cold PBS and were washed for 3 times.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001188
Treatment Summary:For each cell pellet sample, 5 mL of the mixture of methanol/water (1:0.9, v/v) was added and ultrasonicated for 25 min to break cells bathing in ice. The mixture was added with 5 mL of cold chloroform, vortexed and subjected to 10 min of ultrasonic extraction under the bath of ice. The mixture was then centrifuged at 9500 g for 8 min. The upper layer phase containing methanol and water was taken out and evaporated in the fume cupboard to remove methanol. The remaining water solution was freezed under −80 °C, and then freeze-dried to afford dry samples, which were stored under −80 °C before analysis.

Sample Preparation:

Sampleprep ID:SP001181
Sampleprep Summary:The intracellular extract was re-suspended in 550 µL of phosphate buffer containing 1.5 M KH2PO4, 0.1% sodium 3-(trimethylsilyl) propionate-2,2,3,3-d4 (TSP), and 10% D2O. Subsequently, all the samples were vortexed and centrifuged at 12000 g for 15 min at 4°C to remove any insoluble components. The collected supernatants (500 μL) were transferred to 5 mm NMR tubes for analysis.

Analysis:

Analysis ID:AN001828
Analysis Type:NMR
Num Factors:12

NMR:

NMR ID:NM000141
Analysis ID:AN001828
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:850 MHz
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