We thank Jean-Roch Mouret, Sylvie Dequin and Jean-Marie Sabalyrolles for contributing to the conception of the robotic-assisted fermentation system and Martine Pradal, Nicolas Bouvier and Pascale Brial for their technical support. Funding for this project was provided by the Minist&#232;re de l&#39;Education Nationale, de la Recherche et de la Technologie.

1. Fermentation and Sampling
<ol>
	<li>Preparation of media and fermenters 
	NOTE: All the fermentations are carried out in parallel, using the same strain and in the same chemically defined synthetic medium (SM, composition provided in Table 1), which includes a mixture of ammonium and amino acids as nitrogen sources15. For each fermentation, a single nitrogen compound is provided exclusively in a uniformly labeled 13C or 15N form (10...

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K., Moreirados Santos, M., Christensen, B., Nielsen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Network+identification+and+flux+quantification+in+the+central+metabolism+of+Saccharomyces+cerevisiae+under+different+conditions+of+glucose+repression.">Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression.</a> J Bacteriol. 183, 1441-1451 (2001).</li><li>Wiechert, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=13C+metabolic+flux+analysis.">13C metabolic flux analysis.</a> Metab Eng. 3, 195-206 (2001).</li><li>Fischer, E., Zamboni, N., Sauer, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+metabolic+flux+analysis+based+on+gas+chromatography-mass+spectrometry+derived+13C+constraints.">High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints.</a> Anal Biochem. 325, 308-316 (2004).</li><li>Rantanen, A., Rousu, J., Jouhten, P., Zamboni, N., Maaheimo, H., Ukkonen, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+analytic+and+systematic+framework+for+estimating+metabolic+flux+ratios+from+13C+tracer+experiments.">An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.</a> BMC Bioinformatics. 9, 266 (2008).</li><li>Zamboni, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=13C+metabolic+flux+analysis+in+complex+systems.">13C metabolic flux analysis in complex systems.</a> Curr Opin Biotechnol. 22, 103-108 (2011).</li><li>Kruger, N. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitrogen+metabolism+in+Saccharomyces+cerevisiae.">Nitrogen metabolism in Saccharomyces cerevisiae.</a> The molecular biology of the yeast Saccharomyces: Metabolism and gene expression. , 39-99 (1982).</li><li>Jones, E. W., Fink, G. R., Strathern, J. N., Jones, E. W., Broach, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+amino+acid+and+nucleotide+biosynthesis+in+yeast.">Regulation of amino acid and nucleotide biosynthesis in yeast.</a> The molecular biology of the yeast Saccharomyces: Metabolism and gene expression. , 182-299 (1982).</li><li>Hazelwood, L. A., Daran, J. -. M., van Maris, A. J. A., Pronk, J. T., Dickinson, J. 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O., Nielsen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-scale+reconstruction+of+the+Saccharomyces+cerevisiae+metabolic+network.">Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.</a> Genome Res. 13, 244-253 (2003).</li><li>Millard, P., Letisse, F., Sokol, S., Portais, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IsoCor:+correcting+MS+data+in+isotope+labeling+experiments.">IsoCor: correcting MS data in isotope labeling experiments.</a> Bioinformatics. 28, 1294-1296 (2012).</li></ol>

The authors have nothing to disclose.

Quantifying the partitioning of compounds through metabolic networks using isotopic tracer experiments is a promising approach for understanding the operation of microbial metabolism. This methodology, while successfully applied with one or two labeled substrates, cannot currently be implemented to study metabolism of various sources using multiple labeled elemental isotopes (i.e., more than two substrates). Indeed, the available analytical techniques enable the accurate determination of the labeling patterns of...

Understanding how microbial metabolism operates is a key issue for the design of efficient strategies to improve fermentation processes and modulate the production of fermentative compounds. Advances in genomics and functional genomics in these last two decades largely contributed to extending knowledge of the topology of metabolic networks in many microorganisms. Access to this information led to the development of approaches that aim for a comprehensive overview of cellular function1. These methodologies often rely on a model-based interpretation of measurable parameters. These experimental data include, on one hand, metabolite uptake and production rates and, on the other hand, quantitative intracellular information that is obtained from isotope tracer experiments. These data provide essential information for the deduction of the in vivo activity of different pathways in a defined metabolic network2,3,4. Currently, the available analytical techniques only enable the accurate detection of labeling patterns of molecules when using a single-element isotope and possibly when co-labeling with two isotopic elements. Moreover, under most growth conditions, the carbon source only consists of one or two-compounds. Consequently, approaches based on 13C-isotopic tracers from carbon substrates were widely and successfully applied to develop a complete understanding of carbon metabolic network operations5,6,7,8.
In contrast, in many natural and industrial environments, the available nitrogen resource that supports microbial growth is often composed of a wide range of molecules. For example, during wine or beer fermentation, nitrogen is provided as a mixture of 18 amino acids and ammonium at variable concentrations9. This array of N compounds that are accessible for anabolism makes these complex media conditions greatly different from those commonly used for physiological studies, as the latter are achieved using a unique source of nitrogen, typically ammonium.
Overall, internalized nitrogen compounds may be directly incorporated into proteins or catabolized. The network structure of nitrogen metabolism in many microorganisms, including the yeast Saccharomyces cerevisiae, is very complex in accordance with the diversity of substrates. Schematically, this system is based on the combination of the central core of nitrogen metabolism which catalyzes the interconversion of glutamine, glutamate, and &#945;-ketoglutarate10,11, with transaminases and deaminases. Through this network, amine groups from ammonium or other amino acids are gathered and &#945;-keto acids released. These intermediates are also synthetized through central carbon metabolism (CCM)12,13. This large number of branched reactions and intermediates, involved in both the catabolism of exogenous nitrogen sources and the anabolism of proteinogenic amino acids, fulfills the anabolic requirements of the cells. The activity through these different interconnected routes also results in the excretion of metabolites. In particular, &#945;-keto acids may be redirected through the Ehrlich pathway to produce higher alcohols and their acetate ester derivatives14, which are essential contributors to the sensory profiles of products. Subsequently, how nitrogen metabolism operates plays a key role in biomass production and the formation of volatile molecules (aroma).
The reactions, enzymes, and genes involved in nitrogen metabolism are extensively described in the literature. However, the issue of the distribution of multiple nitrogen sources throughout a metabolic network has not yet been addressed. There are two main reasons that explain this lack of information. First, in view of the important complexity of the nitrogen metabolism network, a large amount of quantitative data is required for a complete understanding of its operation that was unavailable until now. Second, many experimental constraints and limitations of analytical methods prevented the implementation of approaches that were previously used for the elucidation of CCM function.
To overcome these problems, we chose to develop a system-level approach that is based on the reconciliation of data from a series of isotopic tracer experiments. The workflow includes: 
- A set of fermentations carried out under the same environmental conditions, while a different selected nutrient source (substrate) is labeled each time. 
- A combination of analytical procedures (HPLC, GC-MS) for an accurate determination, at different stages of the fermentation, of the residual concentration of labeled substrate and the concentration and the isotopic enrichment of compounds that are derived from the catabolism of the labeled molecule, including derived biomass. 
- A calculation of the mass and isotopic balance for each consumed labeled molecule and a further integrated analysis of the dataset to obtain a global overview of the management of multiple nutrient sources by microorganisms through the determination of flux ratios.
To apply this methodology, attention must be paid to the reproducible behavior of the strain/microorganism between cultures. Furthermore, samples from different cultures must be taken during the same well-defined fermentation progress. In the experimental work reported in this manuscript, a robot-assisted system is used for online monitoring of fermentations to account for these constraints.
Furthermore, it is essential to choose a set of labeled substrates (compound, nature, and position of the labeling) that is appropriate to address the scientific problem of the study. Here, 15N-labeled ammonium, glutamine, and arginine were selected as the three major nitrogen sources found in grape juice. This allowed assessing the pattern of nitrogen redistribution from consumed compounds to the proteinogenic amino acids. We also aimed to investigate the fate of the carbon backbone of the consumed amino acids and their contribution to the production of volatile molecules. To meet this objective, uniformly 13C-labeled leucine, isoleucine, threonine, and valine were included in the study as amino acids that are derived from major intermediates of the Ehrlich pathway.
Overall, we quantitatively explored how yeast manages a complex nitrogen resource by redistributing exogenous nitrogen sources to fulfill its anabolic requirements throughout fermentation while additionally removing the excess of carbon precursors as volatile molecules. The experimental procedure reported in this paper can be applied to investigate other multiple nutrient sources used by any other microorganism. It appears to be an appropriate approach for the analysis of the impact of genetic background or environmental conditions on the metabolic behavior of microorganisms.

<table>
	<tbody>
		<tr>
			<td>D-Glucose</td>
			<td>PanReac</td>
			<td>141341.0416</td>
			<td></td>
		</tr>
		<tr>
			<td>D-Fructose</td>
			<td>PanReac</td>
			<td>142728.0416</td>
			<td></td>
		</tr>
		<tr>
			<td>DL-Malic acid</td>
			<td>Sigma Aldrich</td>
			<td>M0875</td>
			<td></td>
		</tr>
		<tr>
			<td>Citric acid monohydrate</td>
			<td>Sigma Aldrich</td>
			<td>C7129</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic</td>
			<td>Sigma Aldrich</td>
			<td>P5379</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium sulfate</td>
			<td>Sigma Aldrich</td>
			<td>P0772</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium sulfate heptahydrate</td>
			<td>Sigma Aldrich</td>
			<td>230391</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium chloride dihydrate</td>
			<td>Sigma Aldrich</td>
			<td>C7902</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Sigma Aldrich</td>
			<td>S9625</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium chloride</td>
			<td>Sigma Aldrich</td>
			<td>A4514</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydroxide</td>
			<td>Sigma Aldrich</td>
			<td>71690</td>
			<td></td>
		</tr>
		<tr>
			<td>Manganese sulfate monohydrate</td>
			<td>Sigma Aldrich</td>
			<td>M7634</td>
			<td></td>
		</tr>
		<tr>
			<td>Zinc sulfate heptahydrate</td>
			<td>Sigma Aldrich</td>
			<td>Z4750</td>
			<td></td>
		</tr>
		<tr>
			<td>Copper (II) sulfate pentahydrate</td>
			<td>Sigma Aldrich</td>
			<td>C7631</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium iodine</td>
			<td>Sigma Aldrich</td>
			<td>P4286</td>
			<td></td>
		</tr>
		<tr>
			<td>Cobalt (II) chloride hexahydrate</td>
			<td>Sigma Aldrich</td>
			<td>C3169</td>
			<td></td>
		</tr>
		<tr>
			<td>Boric acid</td>
			<td>Sigma Aldrich</td>
			<td>B7660</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium heptamolybdate</td>
			<td>Sigma Aldrich</td>
			<td>A7302</td>
			<td></td>
		</tr>
		<tr>
			<td>Myo-inositol</td>
			<td>Sigma Aldrich</td>
			<td>I5125</td>
			<td></td>
		</tr>
		<tr>
			<td>D-Pantothenic acid hemicalcium salt</td>
			<td>Sigma Aldrich</td>
			<td>21210</td>
			<td></td>
		</tr>
		<tr>
			<td>Thiamine, hydrochloride</td>
			<td>Sigma Aldrich</td>
			<td>T4625</td>
			<td></td>
		</tr>
		<tr>
			<td>Nicotinic acid</td>
			<td>Sigma Aldrich</td>
			<td>N4126</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyridoxine</td>
			<td>Sigma Aldrich</td>
			<td>P5669</td>
			<td></td>
		</tr>
		<tr>
			<td>Biotine</td>
			<td>Sigma Aldrich</td>
			<td>B4501</td>
			<td></td>
		</tr>
		<tr>
			<td>Ergost&#233;rol</td>
			<td>Sigma Aldrich</td>
			<td>E6510</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween 80</td>
			<td>Sigma Aldrich</td>
			<td>P1754</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>VWR Chemicals</td>
			<td>101074F</td>
			<td></td>
		</tr>
		<tr>
			<td>Iron (III) chloride hexahydrate</td>
			<td>Sigma Aldrich</td>
			<td>236489</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Aspartic acid</td>
			<td>Sigma Aldrich</td>
			<td>A9256</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Glutamic acid</td>
			<td>Sigma Aldrich</td>
			<td>G1251</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Alanine</td>
			<td>Sigma Aldrich</td>
			<td>A7627</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Arginine</td>
			<td>Sigma Aldrich</td>
			<td>A5006</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Cysteine</td>
			<td>Sigma Aldrich</td>
			<td>C7352</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>Sigma Aldrich</td>
			<td>G3126</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma Aldrich</td>
			<td>G7126</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Histidine</td>
			<td>Sigma Aldrich</td>
			<td>H8000</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Isoleucine</td>
			<td>Sigma Aldrich</td>
			<td>I2752</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Leucine</td>
			<td>Sigma Aldrich</td>
			<td>L8000</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Lysine</td>
			<td>Sigma Aldrich</td>
			<td>L5501</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Methionine</td>
			<td>Sigma Aldrich</td>
			<td>M9625</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Phenylalanine</td>
			<td>Sigma Aldrich</td>
			<td>P2126</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Proline</td>
			<td>Sigma Aldrich</td>
			<td>P0380</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Serine</td>
			<td>Sigma Aldrich</td>
			<td>S4500</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Threonine</td>
			<td>Sigma Aldrich</td>
			<td>T8625</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Tryptophane</td>
			<td>Sigma Aldrich</td>
			<td>T0254</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Tyrosine</td>
			<td>Sigma Aldrich</td>
			<td>T3754</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Valine</td>
			<td>Sigma Aldrich</td>
			<td>V0500</td>
			<td></td>
		</tr>
		<tr>
			<td>13C5-L-Valine</td>
			<td>Eurisotop</td>
			<td>CLM-2249-H-0.25</td>
			<td></td>
		</tr>
		<tr>
			<td>13C6-L-Leucine</td>
			<td>Eurisotop</td>
			<td>CLM-2262-H-0.25</td>
			<td></td>
		</tr>
		<tr>
			<td>15N-Ammonium chloride</td>
			<td>Eurisotop</td>
			<td>NLM-467-1</td>
			<td></td>
		</tr>
		<tr>
			<td>ALPHA-15N-L-Glutamine</td>
			<td>Eurisotop</td>
			<td>NLM-1016-1</td>
			<td></td>
		</tr>
		<tr>
			<td>U-15N4-L-Arginine</td>
			<td>Eurisotop</td>
			<td>NLM-396-PK</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl acetate</td>
			<td>Sigma Aldrich</td>
			<td>270989</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl propanoate</td>
			<td>Sigma Aldrich</td>
			<td>112305</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl 2-methylpropanoate</td>
			<td>Sigma Aldrich</td>
			<td>246085</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl butanoate</td>
			<td>Sigma Aldrich</td>
			<td>E15701</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl 2-methylbutanoate</td>
			<td>Sigma Aldrich</td>
			<td>306886</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl 3-methylbutanoate</td>
			<td>Sigma Aldrich</td>
			<td>8.08541.0250</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl hexanoate</td>
			<td>Sigma Aldrich</td>
			<td>148962</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl octanoate</td>
			<td>Sigma Aldrich</td>
			<td>W244910</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl decanoate</td>
			<td>Sigma Aldrich</td>
			<td>W243205</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl dodecanoate</td>
			<td>Sigma Aldrich</td>
			<td>W244112</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl lactate</td>
			<td>Sigma Aldrich</td>
			<td>W244015</td>
			<td></td>
		</tr>
		<tr>
			<td>Diethyl succinate</td>
			<td>Sigma Aldrich</td>
			<td>W237701</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylpropyl acetate</td>
			<td>Sigma Aldrich</td>
			<td>W217514</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylbutyl acetate</td>
			<td>Sigma Aldrich</td>
			<td>W364401</td>
			<td></td>
		</tr>
		<tr>
			<td>3-methyl butyl acetate</td>
			<td>Sigma Aldrich</td>
			<td>287725</td>
			<td></td>
		</tr>
		<tr>
			<td>2-phenylethyl acetate</td>
			<td>Sigma Aldrich</td>
			<td>290580</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylpropanol</td>
			<td>Sigma Aldrich</td>
			<td>294829</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylbutanol</td>
			<td>Sigma Aldrich</td>
			<td>133051</td>
			<td></td>
		</tr>
		<tr>
			<td>3-methylbutanol</td>
			<td>Sigma Aldrich</td>
			<td>309435</td>
			<td></td>
		</tr>
		<tr>
			<td>Hexanol</td>
			<td>Sigma Aldrich</td>
			<td>128570</td>
			<td></td>
		</tr>
		<tr>
			<td>2-phenylethanol</td>
			<td>Sigma Aldrich</td>
			<td>77861</td>
			<td></td>
		</tr>
		<tr>
			<td>Propanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>94425</td>
			<td></td>
		</tr>
		<tr>
			<td>Butanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>19215</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylpropanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>58360</td>
			<td></td>
		</tr>
		<tr>
			<td>2-methylbutanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>193070</td>
			<td></td>
		</tr>
		<tr>
			<td>3-methylbutanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>W310212</td>
			<td></td>
		</tr>
		<tr>
			<td>Hexanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>153745</td>
			<td></td>
		</tr>
		<tr>
			<td>Octanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>W279900</td>
			<td></td>
		</tr>
		<tr>
			<td>Decanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>W236403</td>
			<td></td>
		</tr>
		<tr>
			<td>Dodecanoic acid</td>
			<td>Sigma Aldrich</td>
			<td>L556</td>
			<td></td>
		</tr>
		<tr>
			<td>Fermentor 1L</td>
			<td>Legallais</td>
			<td>AT1357</td>
			<td>Fermenter handmade for fermentation</td>
		</tr>
		<tr>
			<td>Disposable vacuum filtration system</td>
			<td>Dominique Deutscher</td>
			<td>029311</td>
			<td></td>
		</tr>
		<tr>
			<td>Fermenters (250 ml)</td>
			<td>Legallais</td>
			<td>AT1352</td>
			<td>Fermenter handmade for fermentation</td>
		</tr>
		<tr>
			<td>Sterile tubes</td>
			<td>Sarstedt</td>
			<td>62.554.502</td>
			<td></td>
		</tr>
		<tr>
			<td>Fermentation locks</td>
			<td>Legallais</td>
			<td>AT1356</td>
			<td>Fermetation locks handmade for fermentation</td>
		</tr>
		<tr>
			<td>BactoYeast Extract</td>
			<td>Becton, Dickinson and Company</td>
			<td>212750</td>
			<td></td>
		</tr>
		<tr>
			<td>BactoPeptone</td>
			<td>Becton, Dickinson and Company</td>
			<td>211677</td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator shaker</td>
			<td>Infors HT</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Particle Counter</td>
			<td>Beckman Coulter</td>
			<td>6605697</td>
			<td>Multisizer 3 Coulter Counter</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Jouan</td>
			<td></td>
			<td>GR412</td>
		</tr>
		<tr>
			<td>Plate Butler Robotic system</td>
			<td>Lab Services BV</td>
			<td>PF0X-MA</td>
			<td>Automatic instrument</td>
		</tr>
		<tr>
			<td>Plate Butler Software</td>
			<td>Lab Services BV</td>
			<td></td>
			<td>Robot monitor software</td>
		</tr>
		<tr>
			<td>RobView</td>
			<td></td>
			<td></td>
			<td>In-house developed calculation software</td>
		</tr>
		<tr>
			<td>My SQL</td>
			<td></td>
			<td></td>
			<td>International source database</td>
		</tr>
		<tr>
			<td>Cimarec i Telesystem Multipoint Stirrers</td>
			<td>Thermo Fisher Scientific</td>
			<td>50088009</td>
			<td>String Drive 60</td>
		</tr>
		<tr>
			<td>BenchBlotter platform rocker</td>
			<td>Dutscher</td>
			<td>60903</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonia enzymatic kit</td>
			<td>R-Biopharm AG</td>
			<td>5390</td>
			<td></td>
		</tr>
		<tr>
			<td>Spectrophotometer cuvettes</td>
			<td>VWR</td>
			<td>634-0678</td>
			<td></td>
		</tr>
		<tr>
			<td>Spectrophotometer UviLine 9400</td>
			<td>Secomam</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Amino acids standards physiological - acidics and neutrals</td>
			<td>Sigma Aldrich</td>
			<td>A6407</td>
			<td></td>
		</tr>
		<tr>
			<td>Amino acids standards physiological - basics</td>
			<td>Sigma Aldrich</td>
			<td>A6282</td>
			<td></td>
		</tr>
		<tr>
			<td>Citrate lithium buffers - Ultra ninhydrin reagent</td>
			<td>Biochrom</td>
			<td>BC80-6000-06</td>
			<td></td>
		</tr>
		<tr>
			<td>Sulfosalycilic acid</td>
			<td>Sigma Aldrich</td>
			<td>S2130</td>
			<td></td>
		</tr>
		<tr>
			<td>Norleucine</td>
			<td>Sigma Aldrich</td>
			<td>N1398</td>
			<td></td>
		</tr>
		<tr>
			<td>Biochrom 30 AAA</td>
			<td>Biochrom</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>EZChrom Elite</td>
			<td>Biochrom</td>
			<td></td>
			<td>Instrument control and Data analysis software</td>
		</tr>
		<tr>
			<td>Ultropac 8 resin Lithium</td>
			<td>Biochrom</td>
			<td>BC80-6002-47</td>
			<td>Lithium High Resolution Physiological Column</td>
		</tr>
		<tr>
			<td>Filter Millex GV</td>
			<td>Merck Millipore</td>
			<td>SLGVX13NL</td>
			<td>Millex GV 13mm (pore size 0.22 &#181;m)</td>
		</tr>
		<tr>
			<td>Membrane filter PALL</td>
			<td>VWR</td>
			<td>514-4157</td>
			<td>Supor-450 47mm 0.45&#181;m</td>
		</tr>
		<tr>
			<td>Vacuum pump Millivac Mini</td>
			<td>Millipore</td>
			<td>XF5423050</td>
			<td></td>
		</tr>
		<tr>
			<td>Aluminium smooth weigh dish 70mm</td>
			<td>VWR</td>
			<td>611-1380</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision balance</td>
			<td>Mettler</td>
			<td></td>
			<td>Specifications AE163</td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxid dried</td>
			<td>Merck</td>
			<td>1029310161</td>
			<td>(max. 0.025% H2O) SeccoSolv</td>
		</tr>
		<tr>
			<td>Combustion oven</td>
			<td>Legallais</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Pierce BCA protein assay kit</td>
			<td>Interchim</td>
			<td>UP40840A</td>
			<td></td>
		</tr>
		<tr>
			<td>Formic acid</td>
			<td>Fluka</td>
			<td>94318</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrogen peroxide</td>
			<td>Sigma Aldrich</td>
			<td>H1009</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid Fuming 37% Emsure</td>
			<td>Merck</td>
			<td>1003171000</td>
			<td>Grade ACS,ISO,Reag. Ph Eur</td>
		</tr>
		<tr>
			<td>Lithium acetate buffer</td>
			<td>Biochrom</td>
			<td>80-2038-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Commercial solution of hydrolyzed amino acids</td>
			<td>Sigma Aldrich</td>
			<td>AAS18</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Methionine sulfone</td>
			<td>Sigma Aldrich</td>
			<td>M0876</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Cysteic acid monohydrate</td>
			<td>Sigma Aldrich</td>
			<td>30170</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyrex glass culture tubes</td>
			<td>Sigma Aldrich</td>
			<td>Z653586</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyridine</td>
			<td>Acros Organics</td>
			<td>131780500</td>
			<td>99% Extrapure</td>
		</tr>
		<tr>
			<td>Ethyl chloroformate</td>
			<td>Sigma Aldrich</td>
			<td>23131</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane</td>
			<td>Sigma Aldrich</td>
			<td>32222</td>
			<td></td>
		</tr>
		<tr>
			<td>Vials</td>
			<td>Sigma Aldrich</td>
			<td>854165</td>
			<td></td>
		</tr>
		<tr>
			<td>Microinserts for 1.5ml vials</td>
			<td>Sigma Aldrich</td>
			<td>SU860066</td>
			<td></td>
		</tr>
		<tr>
			<td>GC/MS</td>
			<td>Agilent Technologies</td>
			<td>5890 GC/5973 MS</td>
			<td></td>
		</tr>
		<tr>
			<td>Chemstation</td>
			<td>Agilent Technologies</td>
			<td></td>
			<td>Instrument control and data analysis software</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma Aldrich</td>
			<td>34860</td>
			<td>Chromasolv, for HPLC</td>
		</tr>
		<tr>
			<td>Acetonitrile</td>
			<td>Sigma Aldrich</td>
			<td>34998</td>
			<td>ChromasolvPlus, for HPLC</td>
		</tr>
		<tr>
			<td>N,N-Dimethylformamide dimethyl acetal</td>
			<td>Sigma Aldrich</td>
			<td>394963</td>
			<td></td>
		</tr>
		<tr>
			<td>BSTFA</td>
			<td>Sigma Aldrich</td>
			<td>33024</td>
			<td></td>
		</tr>
		<tr>
			<td>DB-17MS column</td>
			<td>Agilent Technologies</td>
			<td>122-4731</td>
			<td>30m*0.25mm*0.15&#181;m</td>
		</tr>
		<tr>
			<td>Sodium sulfate, anhydrous</td>
			<td>Sigma Aldrich</td>
			<td>238597</td>
			<td></td>
		</tr>
		<tr>
			<td>Technical nitrogen</td>
			<td>Air products</td>
			<td>14629</td>
			<td></td>
		</tr>
		<tr>
			<td>Zebron ZB-WAX column</td>
			<td>Phenomenex</td>
			<td>7HG-G007-11</td>
			<td>30m*0.25mm*0.25&#181;m</td>
		</tr>
		<tr>
			<td>Helium BIP</td>
			<td>Air products</td>
			<td>26699</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Pasteur pipettes</td>
			<td>VWR</td>
			<td>612-1702</td>
			<td></td>
		</tr>
	</tbody>
</table>

workflow based on the combination of isotopic tracer experiments to investigate microbial metabolism of multiple nutrient sources

Studies in the field of microbiology rely on the implementation of a wide range of methodologies. In particular, the development of appropriate methods substantially contributes to providing extensive knowledge of the metabolism of microorganisms growing in chemically defined media containing unique nitrogen and carbon sources. In contrast, the management through metabolism of multiple nutrient sources, despite their broad presence in natural or industrial environments, remains virtually unexplored. This situation is mainly due to the lack of suitable methodologies, which hinders investigations.
We report an experimental strategy to quantitatively and comprehensively explore how metabolism operates when a nutrient is provided as a mixture of different molecules, i.e., a complex resource. Here, we describe its application for assessing the partitioning of multiple nitrogen sources through the yeast metabolic network. The workflow combines information obtained during stable isotope tracer experiments using selected 13C- or 15N-labeled substrates. It first consists of parallel and reproducible fermentations in the same medium, which includes a mixture of N-containing molecules; however,a selected nitrogen source is labeled each time. A combination of analytical procedures (HPLC, GC-MS) is implemented to assess the labeling patterns of targeted compounds and to quantify the consumption and recovery of substrates in other metabolites. An integrated analysis of the complete dataset provides an overview of the fate of consumed substrates within cells. This approach requires an accurate protocol for the collection of samples&#8211;facilitated by a robot-assisted system for online monitoring of fermentations&#8211;and the achievement of numerous time-consuming analyses. Despite these constraints, it allowed understanding, for the first time, the partitioning of multiple nitrogen sources throughout the yeast metabolic network. We elucidated the redistribution of nitrogen from more abundant sources toward other N-compounds and determined the metabolic origins of volatile molecules and proteinogenic amino acids.

Figure 3 presents a schematic diagram of the workflow that was implemented to investigate the management by yeast of the multiple nitrogen sources that are found during wine fermentation. 
For different points of sampling, the biological parameters&#8211;growth characteristics, nitrogen consumption patterns, and the profile of proteinogenic amino acids&#8211;show a high reproducibility among fermentations (Figure 4). This co...

Watch this Scientific Journal Video about Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources at JoVE.com

Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources

This protocol describes an experimental procedure to quantitatively and comprehensively investigate the metabolism of multiple nutrient sources. This workflow, based on a combination of isotopic tracer experiments and an analytical procedure, allows the fate of consumed nutrients and the metabolic origin of molecules synthetized by microorganisms to be determined.

Studies in the field of microbiology rely on the implementation of a wide range of methodologies. In particular, the development of appropriate methods ...

The overall goal of this procedure is to quantitatively investigate the metabolism of multiple nutrient sources using labeled substrates. This workflow allows the fate of consumed nutrients and the metabolic origin of compounds synthesized by yeasts to be determined. This method can help to answer key questions in the microbial metabolism field such how all the metabolism operate depending on environmental conditions.The main advantage of this technique is that it allow the elucidation and quantification of the protein of nutrient distribution from multiple sources. This method was used to investigate the nitrogen metabolism of yeast, but it can also be applied to other metabolisms and microorganisms. The key to success with this experiment lies in the reproducibility of fermentations.Users must pay particular attention to collect the cells in the same defined physiological stage. Demonstrating the procedure will be Christian Picou from our technical staff, Pauline Seguinot, a PhD student from the laboratory, and Stephanie Rollero, a post-doctorate fellow. In an autoclave, pasteurize each synthetic medium prepared for each nitrogen source in a one-liter flask containing a magnetic stir bar.Dissolve the appropriate amount of labeled molecule to reach the desired final concentration in the medium. Sterilize the medium using a disposable vacuum filtration system. Using a sterile measuring cylinder, divide the medium between two pre-sterilized fermenters that contain a magnetic stir bar and are equipped with fermentation locks to avoid the entry of oxygen but allow the release of carbon dioxide.After growing a cerevisiae strain in YPD medium, collect a pre-culture aliquot under laminar flow and quantify the cell population using an electronic particle counter that is fitted with a 100-micrometer aperture. After centrifuging the pre-culture, suspend the pellet in an appropriate volume of sterile water to obtain a final concentration of 2.5 times 10 to the 9th cells per milliliter. Then, inoculate each fermenter with one milliliter of the cell suspension.Following this, prepare a fermentation platform by installing the fermenters in the support guides that are properly placed on the 21-position stirring plates and set the stirring rate at 270 RPM. To start the online monitoring of each fermentation, launch the robot control application, click the Start Assay button and select the fermentation volume to be carried out. To ensure that the displayed interface permits the indication of the number and the position of fermenters on the platform, right-click on the slot location and choose Disable to inactivate the monitoring of the empty positions.To initialize the calculation software, click on the Initializer button and validate with OK.Then, click on the Start button of the robot control application to start the weight acquisitions. Next, centrifuge two six-milliliter samples taken from the fermenters at 2, 000 times G for five minutes at four degrees Celsius. When finished, transfer each frozen supernatant into two tubes and store at minus 80 degrees Celsius.Wash each pellet twice with five milliliters of distilled water and store at minus 80 degrees Celsius for the measurement of isotopic enrichment. Add 200 microliters of a 25%sulfosalicylic acid solution that contains 2.5 millimolar norleucine as an internal standard to 800 microliters of sample to remove molecules with high molecular weights. After incubation and centrifugation, filter the mixture through a 0.22-micrometer pore-size nitrocellulose membrane and place the sample in an amino acid analysis system.In the program or software of the analysis system, click on the button Run to begin the liquid chromatography analyses with the analyzer equipped with a cation exchange column. Next, prepare an oxidized extract by suspending a previously prepared labeled cell pellet in 200 microliters of performic acid. After incubating for four hours at four degrees Celsius, stop the reaction by adding 33.6 milligrams of sodium sulfate.Add 800 microliters of six normal hydrochloric acid to the oxidized extract, and incubate the sample in a hermatically-sealed glass tube for 16 hours at 110 degrees Celsius in a dry-heat oven. After allowing the sample to cool to room temperature, add 200 microliters of 2.5 millimolar neuroleucine and remove the hydrogen chloride gas with a stream of nitrogen. Wash the dried extract twice with 800 microliters of distilled water, and then 800 microliters of ethanol.Then, add 800 microliters of 200-millimolar lithium acetate buffer to the extract. Determine the relative concentrations of amino acids within proteins in the sample using the chromatographic method previously described. Hydrolyze a labeled cell pellet by adding 1.2 milliliters of six-molar hydrochloric acid and incubating the sample for 16 hours at 105 degrees Celsius in a tightly-closed glass tube in a dry-heat oven.After allowing the sample to cool to room temperature, add 1.2 milliliters of distilled water. Following centrifugation to remove the cellular debris, distribute the supernatant into six 400-microliter fractions in open glass tubes. Dry the fractions in the dry-heat oven at 105 degrees Celsius for four to five hours until they reach the consistency of syrup.During the biomass hydrolysis, dry the fraction until the consistency of a syrup by frequently controlling the acid of operation. For ECF derivatization, dissolve the cooled dried hydrolysate in 200 microliters of 20-millimolar hydrochloric acid and 133 microliters of a one-to-four mixture of pyridine and ethanol. Add 50 microliters of ethyl chloroformate to derivatize the amino acids.After the carbon dioxide has been released, transfer the mixture to centrifuge tubes that contain 500 microliters of dichloromethane to extract the derivatized compounds. Vortex the samples for 10 seconds. After centrifuging for four minutes at 10, 000 times G, collect the lower organic phase of each sample with a Pasteur pipette and transfer to a GC autosampler vial that contains a conical glass insert so that each sample may be directly injected into the GCMS instrument.HPLC derivatization reagents are used for the ECF procedure. Change frequently the ECF reagents. For DMF-DMA derivatization, dissolve the dried hydrolysate in 50 microliters of methanol and 200 microliters of acetonitrile.Add 300 microliters of DMF-DMA and vortex the sample. Then, transfer the sample to a GC autosampler vial that contains a conical glass insert. For BSTFA derivatization, suspend the hydrolysate in 200 microliters of acetonitrile.Add 200 microliters of BSTFA to the sample and hermatically close the glass tube. After incubation for four hours at 135 degrees Celsius, transfer the cooled extract directly to a GC autosampler vial that contains a conical glass insert. Now, analyze the samples with a gas chromatograph equipped with an autosampler injector and coupled to a mass spectrometer.Click on Instrument in the menu of the computer software. Under the Sequence tab, click the Edit Sample Log Table to create a sample list, and click Run and Run Sequence to start the injections. After the analyses are complete, record a cluster of intensities for each amino acid that corresponds to its different mass isotopomers.Add 10 microliters of the appropriate deuterated internal standards to five milliliters of supernatant in a 15-milliliter glass tube. Add one milliliter of dichloromethane, tightly close the tube and shake the sample on a rocking platform for 20 minutes. After centrifugation, collect the lower organic phase in a 15-milliliter glass tube.After repeating the dichloromethane extraction, dry the organic extract over 500 milligrams of anhydrous sodium sulfate and collect the liquid phase with a Pasteur pipette. Concentrate the extract by a factor of four under nitrogen flux. Then, transfer the concentrated sample to a GC autosampler vial.For GCMS quantification, inject two microliters of sample with a split ratio of 10-to-one, and separate the extracted volatile molecules using the appropriate oven temperature profile. Using the spreadsheets in the text protocol, enter the raw data values that correspond to the concentration of extracellular amino acids, cell dry weight, protein content of cells, concentration of volatile molecules and isotopic enrichment of proteinogenic amino acids and volatile molecules. A schematic diagram of the workflow to investigate the management by yeast of the multiple nitrogen sources that are found during wine fermentation is shown here.For different points of sampling, the biological parameters show a high reproducibility among fermenations. An overview of the redistribution of nitrogen from the sources in grape juice to all the proteinogenic amino acids is shown here. Combined with the determination of the mass balances, the measurement of the isotopic enrichment of proteinogenic amino acids provided the first quantification of the contribution of nitrogen-originated arginine, glutamine, ammonium and other sources to the amine groups of each of these compounds.A comparison between the amount of consumed amino acid that is directly recovered into the biomass is depicted here. Partitioning of the consumed aliphatic amino acids, leucine and valine in the metabolic network in yeast is shown here. More than 96%of the consumed valine and leucine are recovered in their conversion products.Surprisingly, a substantial fraction of valine and leucine are catabolized despite a considerable imbalance between the availability of these compounds in the medium and their content in biomass. Once mastered, this technique can be done in five days. While attempting this procedure, it's important to remember to carefully select the labeling part of the substrate according to the scientific issues.To ensure a good biological reproducibility, perform the fermentation and chromatographic analysis in duplicate. After its development, this technique paved the way for researchers in microbiology field to explore how the metabolism and physiology of microorganism change depending on the environmental conditions. Don't forget that working with derivatization reagents and arginine solvent can be extremely hazardous, thus precautions such as wearing gloves and working under a fume hood should always be taken while performing this procedure.

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Research

JoVE Journal

Bioengineering

9.1K Views.  Université de Montpellier. The overall goal of this procedure is to quantitatively investigate the metabolism of multiple nutrient sources using labeled substrates. This workflow allows the fate of consumed nutrients and the metabolic origin of compounds synthesized by yeasts to be determined. This method can help to answer key questions in the microbial metabolism field such how all the metabolism operate depending on environmental conditions.The main advantage of this technique is that it allow the elucidation...