How to Distinguish Organic Coffee with NMR-Based Metabolmics

Man-made chemical treatments like chemical pesticides, fertilizers, and herbicides are not used to grow organic coffee. The soil is enriched with the utilization of manure, compost, and crop rotation instead.

The environment that food is grown in can play a key part in its subsequent metabolic composition, and researchers have been studying how organic coffee and other organic foods can be identified on the basis of these properties.

Research that was carried out previously has examined how organic coffee is distinct from conventionally grown beans. A number of studies have looked at the microbiologic properties of the soil related to the activity of microbiota. These include boron, carbon, alkaline phosphatase content and calcium metabolic quotient acid.

Some studies have examined the mineral content of the coffee itself. One study demonstrated that FT-MIR-PAS could detect chemical differences successfully and enable the distinction between non-organic and organic coffee.

Metabolomics studies have also been performed using combined analytic methods, which have demonstrated the ability to distinguish organic produce, among other foods, such as potatoes, tomatoes, and oranges.

Recently, researchers looked at whether, by supplying the opportunity for untargeted metabolomics, NMR could enable them to distinguish between organic and conventionally grown coffee from different geographic origins.

To test whether these were enough to enable the distinction between the two farming methods, they characterized the major soluble metabolite content of the coffees.

NMR, which has been shown previously as a way to detect the authenticity of coffee and its geographic origins, enables multiple chemical compounds to be monitored and quantitated within the same experiment. The researchers used this to explore the various soluble metabolites present in roasted coffee.

A spectrum of metabolites

The team found that 68 samples of roasted and ground C.arabica coffee. Of these, 42 were conventionally farmed and 26 were organic. Before centrifugation and analysis, 100 milligrams of each sample were dissolved in buffered deuterated water solution.

The team discovered that the presence of major soluble metabolites dominated the NMR spectra from these samples. In the aliphatic region, there were organic acids like citrate and acetate, plus fatty acids, sucrose, and other small compounds. In the aromatic region, this included trigonelline, N-methyl-pyridine, chlorogenic acids, and caffeine.

The spectra from conventionally grown and organic coffee looked to be very similar, so for further analysis, the researchers used chemometrics. For this purpose, PCA (Principal Component Analysis) was ineffective and could not find adequate discrimination between the sample types.

Next, the researchers used PLS-DA (Partial Least Square-Discrimination Analysis) to increase the separation between the samples. The plot that was used enabled them to separate samples of the different varieties of coffee quite well and the model had good predictive capability.

OPLS-DA (Orthogonal Projection to Latent Structures-Discriminant Analysis) was needed to achieve even better discrimination. It is a method that removes noise and supplies a very effective separation between the classes. This technique also enabled the team to study which of the metabolites in the samples were responsible for the distinction between them.

The researchers identified the metabolites, which had the highest discriminatory power between the two classes of coffee. In order to remove a large proportion of uncorrelated variables from the data, they applied two orthogonal signal correction filters.

Analysis of the resulting plot exhibited that, for organic coffee, β-(1-3)-D-galactopyranose, fatty acids, quinic acid and quinides, were the major distinguishing metabolites, while conventionally grown coffee was characterized by the presence of chlorogenic acid and trigonelline.

These compounds have a crucial effect on the flavor of coffee. Water-soluble polysaccharides, such as those in organic coffee, help form the “body” of coffee and are generated during the roasting process. Meanwhile, one of the most bitter-tasting compounds in coffee is quinic acid.

Body and bitterness have been shown to be associated with the quinide, lipid, and quinic acid content. Trigonelline is associated with a sour taste and was crucial in conventional roasted coffee. The researchers say their findings show the efficacy of NMR as a technique of nontargeted metabolomics.

It gave detailed information regarding the metabolite content of the samples, which contained all of the information needed to distinguish between conventional and organic samples, as shown by the research. This was in spite of the roasting conditions of the samples being unknown and that they came from numerous geographic regions.

Next generation NMR

The researchers used a Bruker Avance NMR spectrometer to perform this study. The Avance Neo is the latest generation of Avance technology from Bruker, and it builds on the cutting-edge performance of previous editions.

The Avance Neo incorporates ‘transceiver’ principles, meaning each channel effectively works as an independent spectrometer as each NMR channel acts as both transmitter and receiver. The Avance Neo is compatible with user control via the cloud and also comes equipped with Bruker’s industry-standard TopSpin software.


Consonni R, Polla D & Cagliani LR. Organic and conventional coffee differentiation by NMR spectroscopy. Food Control 2018; 94: 284-288. doi: 10.1016/j.foodcont.2018.07.013.

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Last updated: Dec 1, 2020 at 7:53 AM


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