Food Metabolome Review

Narrative Review
The food metabolome: a window over dietary exposure1–3

Augustin Scalbert, Lorraine Brennan, Claudine Manach, Cristina Andres-Lacueva, Lars O Dragsted, John Draper,
Stephen M Rappaport, Justin JJ van der Hooft, and David S Wishart
ABSTRACT Although classical hypothesis-driven approaches have been

The food metabolome is defined as the part of the human metabo- very successful in discovering essential nutrients, they are ill
lome directly derived from the digestion and biotransformation of adapted to aid our understanding of the role of highly diverse
foods and their constituents. With .25,000 compounds known in nonessential compounds in foods. Data-driven approaches and
various foods, the food metabolome is extremely complex, with a “omics” technologies offer opportunities to explore the complex
composition varying widely according to the diet. By its very nature interactions between diet and the human organism. In particular,
it represents a considerable and still largely unexploited source of the measurement of hundreds or thousands of metabolites in
novel dietary biomarkers that could be used to measure dietary ex- metabolomic experiments now allows the characterization of in-
posures with a high level of detail and precision. Most dietary bio- dividual phenotypes with a level of precision never before achieved
markers currently have been identified on the basis of our knowledge (2). Individuals or populations exposed to different environments,
of food compositions by using hypothesis-driven approaches. However, lifestyles, or diets can be distinguished and characteristic metabolic
the rapid development of metabolomics resulting from the develop- differences identified (3).
ment of highly sensitive modern analytic instruments, the availabil- A growing number of metabolomic studies have been pub-
ity of metabolite databases, and progress in (bio)informatics has lished over the past 5 y in the field of nutrition (3–6). Metab-
made agnostic approaches more attractive as shown by the recent olomics was used to show the alteration of metabolic profiles on
identification of novel biomarkers of intakes for fruit, vegetables, the consumption of specific nutrients, foods, or diets in small-
beverages, meats, or complex diets. Moreover, examples also show scale intervention studies. Two different fractions of the human
how the scrutiny of the food metabolome can lead to the discovery metabolome are influenced by the diet: the endogenous metab-
of bioactive molecules and dietary factors associated with diseases.
olome and the food metabolome (Figure 1). The endogenous
However, researchers still face hurdles, which slow progress and need
metabolome includes all metabolites from the host. Its variations
to be resolved to bring this emerging field of research to maturity.
show novel metabolic effects of the diet that may affect human
These limits were discussed during the First International Workshop
health. The “food metabolome” has been defined as the sum of
on the Food Metabolome held in Glasgow. Key recommendations
made during the workshop included more coordination of efforts;
1
development of new databases, software tools, and chemical libraries From the International Agency for Research on Cancer, Lyon, France
for the food metabolome; and shared repositories of metabolomic data. (AS); University College Dublin, Dublin, Ireland (LB); the Institut National
de la Recherche Agronomique, Clermont-Ferrand, France (CM); Clermont
Once achieved, major progress can be expected toward a better un-
University, Clermont-Ferrand, France (CM); the University of Barcelona,
derstanding of the complex interactions between diet and human Barcelona, Spain (CA-L); the University of Copenhagen, Frederiksberg,
health. Am J Clin Nutr 2014;99:1286–308. Denmark (LOD); Aberystwyth University, Aberystwyth, United Kingdom
(JD); the University of California, Berkeley, CA (SMR); the University of
INTRODUCTION Glasgow, Glasgow, United Kingdom (JJJvdH); and the University of Alberta,
The 2 major achievements of nutrition research in the 20th Edmonton, Canada (DSW).
2
Supported by the European Union (NutriTech FP7-KBBE-2011-5 grant
century were the discovery of essential nutrients and the eluci-
289511, EUROCAN FP7-KBBE-2010.2.4.1-2 grant 260791); the Danish
dation of their role in key physiologic functions. Recommen- Ministry of Science, Technology, and Innovation (for the UNIK Food, Fit-
dations were defined to provide adequate intakes of these ness and Pharma Project); the French National Agency for Research (Phe-
nutrients that led to reduction in risks of deficiency diseases, at noMeNEp ANR-10-ALIA-007); the Medical Research Council (MR/
least in high-income Western societies. The past 2 decades have J010308/1); and the Spanish Ministerio de Economia y Competitividad
seen a shift in nutrition research away from the prevention of (MINECO; project AGL2009-13906-C02-01) and by a Senior Visiting Sci-
deficiency diseases toward the prevention of chronic diseases and entist Award (to SMR) granted by the International Agency for Research on
the elucidation of the role of nonessential food constituents on Cancer.
3
Address correspondence to A Scalbert, International Agency for Re-
such diseases (1). This constitutes a considerable challenge for
search on Cancer (IARC), Nutrition and Metabolism Section, Biomarkers
nutrition research in the 21st century, in particular because of the Group, 150 Cours Albert Thomas, F-69372 Lyon Cedex 08, France. E-mail:
extreme variety of these bioactive constituents and the large [email protected].
diversity of biochemical targets and signaling and metabolic Received September 19, 2013. Accepted for publication March 24, 2014.
pathways they may interact with. First published online April 23, 2014; doi: 10.3945/ajcn.113.076133.
1286 Am J Clin Nutr 2014;99:1286–308. Printed in USA. Ó 2014 American Society for Nutrition
Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

by Universidade de São Paulo - IO user
on 16 July 2018
THE FOOD METABOLOME: A WINDOW OVER DIETARY EXPOSURE 1287
all metabolites directly derived from the digestion of foods, their with disease outcomes, or to monitor dietary changes in pop-
absorption in the gut, and biotransformation by the host tissues ulations. Dietary exposure has traditionally been measured with
and the microbiota as first proposed by one of the authors of this self-reported methods, namely dietary recalls or food-frequency
review in 2008 (7). Other authors have also proposed to define questionnaires (10). However, a number of random and sys-
the “food metabolome” as the whole set of food constituents in tematic errors are inherent in such methods, including recall
any foods (5, 8). A definition of the metabolome centered on bias and difficulty in assessing portion sizes (11). The resulting
biological species is preferred here. Humans consume as many misclassification of subjects, especially when sorting them
metabolomes as there are biological species making up our according to dietary intake, can influence observed associations
foods—for example, the tomato or beef metabolomes. There- between dietary exposures and disease outcomes and underlies
fore, the human metabolome contains fractions of these me- inconsistencies in published findings in the field of nutritional
tabolomes, partly transformed after ingestion, which constitute epidemiology (12).
the human food metabolome. To address these shortcomings, intense efforts have been di-
The various foods consumed by humans contain .25,000 rected toward statistical techniques to correct measurement errors
compounds, most of them being further metabolized in the human as well as toward developing new dietary assessment instruments.
body (9). The food metabolome is therefore highly complex and The application of dietary biomarkers as more objective mea-
also highly variable. This variability constitutes a unique and sures of dietary exposure in nutritional epidemiology has been
extremely rich source of information on the human diet that has particularly significant (13). These biomarkers have been used as
barely been exploited. Detailed characterization of the food measures of nutritional status and of exposure to bioactive
metabolome should permit accurate monitoring of dietary ex- molecules in foods, as surrogate indicators of food intake, and to
posure and identification of foods that influence disease risks in validate measures of dietary intake (14). Biomarkers are also
clinical and epidemiologic studies. This review describes the cur- useful when little or no data exist on food composition, as is often
rent knowledge on the food metabolome and discusses oppor- the case for bioactive molecules such as glucosinolates or food
tunities for nutrition research. It also makes recommendations to contaminants such as aflatoxins (15, 16).
move the field forward as discussed by the participants in the
First International Workshop on the Food Metabolome (4–5
June 2013, Glasgow, United Kingdom), which convened with 50 Dietary biomarkers measured in population studies
experts from Europe and North America (Supplemental Table 1 A variety of dietary biomarkers identified through the analysis
under “Supplemental data” in the online issue). of correlations with dietary intake have been measured in epi-
demiologic studies. Information on these biomarkers has been
systematically collected in the novel Exposome-Explorer data-
DIETARY BIOMARKERS IN THE PRE-OMICS ERA base (V Neveu, DS Wishart, and A Scalbert, unpublished data,
Studies of connections between the diet or specific dietary 2014); w100 biomarkers could be identified (Supplemental
factors and health status require accurate measurements of di- Table 2 under “Supplemental data” in the online issue). These
etary exposures. Such measurements can be used to evaluate biomarkers have been measured in plasma or serum (caroten-
compliance in dietary intervention studies, to find associations oids, fatty acids, vitamins, polyphenols, food contaminants, and
FIGURE 1. The human metabolomes. sp., species.

on 16 July 2018
1288 SCALBERT ET AL
enzymes), red blood cells (fatty acids, carotenoids, and hemo- in erythrocyte glutathione peroxidase show saturable effects and
globin adducts), and to a lesser extent in urine (polyphenols, may not be suitable for use at high levels of exposure (29, 42).
vitamins, inorganic compounds, and amino acids). Some of Conversely, some biomarkers are present at concentrations too low
these biomarkers correspond to nutrients and bioactive compounds to be reliably detected at low levels of exposure. For example,
and have been used to compare status or exposure. Some have been some biomarkers of alcohol abuse were not appropriate to evaluate
used as surrogate biomarkers of food intake, as follows: poly- low to moderate levels of alcohol consumption (43).
phenols, carotenoids, and vitamin C for fruit and vegetables (17, Specificity is another essential characteristic of biomarkers.
18); alkylresorcinols for whole-grain cereals (19, 20); isoflavones Some biomarkers can be highly specific for a particular food (Table
for soy (21); amino acids and fatty acids for meat (22, 23); fatty 1). Proline betaine and lycopene are well-established biomarkers
acids for dairy products and fish (22, 24); and polyphenols for tea for citrus fruit and tomato products, respectively (44, 45). Other
and wine (18, 25) (Table 1). Dietary biomarkers not only include biomarkers may be common to several foods or characteristic of an
natural food constituents but also certain food additives such as entire food group. Vitamin C and a number of carotenoids and
iodine in milk (26) or food contaminants such as polychlorinated flavonoids are common to many fruit and vegetables. Vitamin C or
biphenyls in fatty fish (27). These latter biomarkers are often the sum of carotenoids or flavonoids have been used as generic
specific to certain populations who consume these additives or biomarkers for fruit and vegetable intake (18, 45).
where consistent levels of contamination are observed.
Other biomarkers are directly derived from the digestion and gut
absorption of food constituents or are endogenous metabolites that Single biomarker or combinations of biomarkers
have been altered by exposure to specific nutrients. For instance, Traditionally, single biomarkers have been used to characterize
serotonin metabolism is altered by acute alcohol intake (28), the complex dietary exposures such as consumption of a whole food
activity of selenium-containing enzymes such as erythrocyte group or intake of a group of compounds with related biological
glutathione peroxidase depends on selenium intake, and ceramide activities. Two examples show the limits of such global assays.
synthase is inhibited by exposure to the mycotoxin fumonisins (29). Vitamin C used as a biomarker for fruit and vegetable intake is
present in a large number of fruit and vegetables, but its content
varies widely according to species, varieties, and food-processing
Pharmacokinetics and reliability of dietary biomarkers methods. It is also widely used as an additive and dietary sup-
Dietary biomarkers are not without their limitations. They may plement. The Folin assay, commonly used to estimate total
be altered because of possible interactions with genetic factors, polyphenols in foods (46), has also been applied to urine samples
physiologic or health status (ie, age or obesity) (30), dietary to compare polyphenol intake (47), but such use may be in-
factors such as fats for lipophilic biomarkers (31), and lifestyle appropriate because of the presence of interfering reducing
factors such as alcohol intake or smoking (32). Their concen- metabolites in such complex biological matrices (46).
trations also vary over time according to their pharmacokinetic In contrast to these global assays, analytic approaches based on
properties. A higher intraindividual variability is expected for the estimation of combinations of dietary constituents may pro-
biomarkers with a short half-life (20, 33). Intraindividual vari- vide more accurate measurements of dietary exposure. The ratios
ability leads to exposure measurement errors when the objective of 2 alkylresorcinols characteristic of whole-grain wheat or rye
is to characterize habitual exposure in epidemiologic studies and were found to be good indicators of the relative consumption of
small numbers of measurements are available across subjects. these cereals (20, 48). However, there are very few such examples
Some of the biomarkers listed in Table 1 have half-lives that do in which combinations of biomarkers were used to improve the
not exceed 24 h [polyphenols, alkylresorcinols, and amino acids specificity of dietary exposure measurements. Metabolomics
(34, 35)]. These biomarkers may thus be useful only in pop- constitutes a comprehensive approach to identify new panels of
ulations who regularly and frequently consume these dietary biomarkers that are specific or common to particular foods or food
sources. Lipophilic markers (carotenoids, lipids) (36) or bio- groups, as shown recently for citrus fruit (49). This should greatly
markers associated with erythrocytes (folate, fatty acids) (29) improve the assessment of exposure to classes of food bioactive
have longer half-lives (week to month) because of the equilibrium compounds, food groups, or dietary patterns.
of biomarkers between blood and fatty tissues, or because of their
integration into erythrocytes. Some dietary compounds such as
isothiocyanates and acrylamide also form adducts with blood THE FOOD METABOLOME IN THE OMICS ERA
albumin and hemoglobin (37, 38), with half-lives varying be- Metabolomics can be described as the application of high-
tween 3 and 8 wk, and may be used as longer-term biomarkers. throughput analytic chemistry technologies [liquid chromatography–
Protein adducts with dietary compounds have received limited mass spectrometry (LC-MS)4, nuclear magnetic resonance
attention thus far. Adductomics appears to be particularly
promising for the discovery of these adduct biomarkers (39, 40).
4
Abbreviations used: dbNP, Nutritional Phenotype Database; ECMDB,
E. coli Metabolome Database; FDR, false discovery rate; FooDB, Food Com-
Biomarker sensitivity and specificity ponent Database; GC-MS, gas chromatography–mass spectrometry; HMDB,
Human Metabolome Database; LC-MS, liquid chromatography–mass spec-
Dietary biomarkers should have sufficient sensitivity to measure
trometry; MS, mass spectrometry; MSI, Metabolomics Standards Initiative;
exposures within ranges commonly found in the populations of MWAS, metabolome-wide association study; NMR, nuclear magnetic reso-
interest. Intervention studies are essential to address this question nance spectroscopy; PCA, principal components analysis; PLS-DA, partial
and to evaluate the relation between exposure and biomarker least-squares discriminant analysis; TMAO, trimethylamine oxide-N-oxide;
concentrations (17, 41). Biomarkers such as vitamin C or selenium YMDB, Yeast Metabolome Database.

on 16 July 2018
TABLE 1
Biomarkers used as surrogate indicators of consumption of foods and food groups for which significant (r . 0.3) correlations have been reported1
Food category and food Biomarkers
Fruit
Apple Kaempferol, isorhamnetin, m-coumaric acid, phloretin
Orange Caffeic acid, hesperetin, proline betaine
Grapefruit Naringenin
Citrus fruit Ascorbic acid, b-cryptoxanthin, hesperetin, naringenin, proline betaine, vitamin A, zeaxanthin
Fruit (total) 4-O-Methylgallic acid, b-cryptoxanthin, carotenoids (mix), flavonoids (mix), gallic acid, hesperetin, isorhamnetin,
kaempferol, lutein, lycopene, naringenin, phloretin, vitamin A, vitamin C, zeaxanthin
Vegetables
Carrot a-Carotene
Tomato Carotenoids (mix), lycopene, lutein
Vegetables, leafy Ascorbic acid, b-carotene, carotenoids (mix)
Vegetables, root Ascorbic acid, a-carotene, b-carotene
Vegetables (total) Ascorbic acid, a-carotene, b-carotene, b-cryptoxanthin, carotenoids (mix), enterolactone, lutein, lycopene
Fruit and vegetables (total) a-Carotene, apigenin, ascorbic acid, b-carotene, b-cryptoxanthin, carotenoids (mix), eriodictyol, flavonoids (mix),
hesperetin, hippuric acid, lutein, lycopene, naringenin, phloretin, phytoene, zeaxanthin
Cereal products
Whole-grain rye 5-Heptadecylresorcinol, 5-pentacosylresorcinol, 5-tricosylresorcinol
Whole-grain wheat 5-Heneicosylresorcinol, 5-tricosylresorcinol, alkylresorcinols (mix)
Whole-grain cereals (total) 5-Heneicosylresorcinol, 3,5-dihydroxybenzoic acid, 3-(3,5-dihydroxyphenyl)-1-propanoic acid, 5-pentacosylresorcinol,
5-tricosylresorcinol, alkylresorcinols (mix)
Seeds
Soy products Daidzein, genistein, isoflavones (mix), O-desmethylangolensin
Meats
Meat 1-Hydroxypyrene glucuronide, 1-methylhistidine
Meat, beef Pentadecylic acid
Animal products (total) 1-Methylhistidine, 3-methylhistidine, margaric acid, pentadecylic acid, phytanic acid
Dairy products
Milk, dairy products Iodine, margaric acid, pentadecylic acid, phytanic acid
Fish
Fatty DHA, EPA, long-chain v-3 PUFAs, polychlorinated biphenyl toxic equivalents, pentachlorodibenzofuran,
polychlorinated biphenyl 126, polychlorinated biphenyl 153, v-3 PUFAs
Lean Long-chain v-3 PUFAs
Beverages (nonalcoholic)
Tea 4-O-Methylgallic acid, gallic acid, kaempferol
Coffee Chlorogenic acid
Beverages (alcoholic)
Wine 4-O-Methylgallic acid, caffeic acid, gallic acid, resveratrol metabolites
Beverages (alcoholic) (total) 5-Hydroxytryptophol/5-hydroxyindole-3-acetic acid, carbohydrate-deficient transferrin, ethyl glucuronide,
g-glutamyltransferase, aspartate aminotransferase, alanine aminotransferase
1
Data were extracted from the Exposome-Explorer database (V Neveu, DS Wishart, and A Scalbert, unpublished data, 2014).
spectroscopy (NMR), gas chromatography–mass spectrometry at characterizing the metabolic responses of humans to the in-
(GC-MS)] directed at characterizing the metabolome (ie, the take of various foods or food constituents such as soy (55), citrus
small molecules associated with metabolism). Its development fruit (44), nuts (56), meats (57), and tea (58).
follows that of genomics, transcriptomics, and proteomics. Al-
though not as rapid in development or as high-throughput as its
omics cousins, metabolomics led a sea change in how small The food metabolome as part of the human metabolome
molecules could and should be analyzed. Rather than being It was through these early metabolome studies that scientists
limited to measuring only one or a few compounds at a time, realized that the human metabolome was not as small or as simple
new metabolomic technologies allowed researchers to measure as first imagined. In particular, noticeable differences in human
hundreds or even thousands of metabolites at a time. This newly metabolomes could be detected that appeared to depend strongly
found capacity to measure so many chemicals at once led to on diet, sex, health status, genetics, kinetics, physiology, and
a number of metabolomic projects, all launched in the mid- age—with diet being most important (59–62). This dietary de-
2000s, aimed at identifying the metabolomes of microbes (50), pendence was not unexpected, but it was not anticipated to be so
plants (51), and humans (52–54). These projects typically used complicated. Unlike laboratory animals, humans are free-living
LC-MS, GC-MS, NMR, or a combination of all 3 techniques omnivores who, in fact, eat other metabolomes. Furthermore,
to identify and/or quantify as many metabolites as possible in humans are exposed to a huge variety of “chemical environ-
cells, tissues, and biofluids of the organisms of interest. These ments” associated with the various foods we consume. Thus, the
comprehensive metabolomic studies were also complemented human metabolome is not just a single entity but consists of
by a number of much more specific metabolomic studies aimed several components (Figure 1), including the following: 1) the

on 16 July 2018
1290 SCALBERT ET AL
endogenous metabolome (consisting of chemicals needed for, or essential fatty acids along with most vitamins, and minerals,
excreted from, cellular metabolism), 2) the food metabolome which cannot be produced by humans and must originate from
(consisting of essential and nonessential chemicals derived from external dietary sources.
foods after digestion and subsequent metabolism by the tissues The second way that food constituents can be metabolized is
and the microbiota), 3) other xenobiotics derived from drugs, through transformation by host tissues. Food compounds that are
and 4) xenobiotics derived from environmental or workplace not useful for basic metabolism or that do not correspond to fa-
chemicals. miliar endogenous metabolites are treated as “foreign” or as
The exact size and composition of these different human xenobiotics. Examples of exogenous food constituents include
metabolomes are difficult to ascertain. Minimally, the human polyphenols, alkaloids, carotenoids, chlorophylls, artificial colors,
metabolome contains 50,000 different detectable compounds (9, artificial flavors, natural volatiles for flavoring/aroma, and Mail-
63), but as instrument sensitivity and separation technologies lard reaction products formed during cooking. The human body
improve, this number is expected to increase. Up to 200,000 maintains a complex defense system consisting of dozens of en-
different metabolites are estimated to occur in the plant kingdom, zymes and membrane transporters to recognize these foreign and
and combinations of several hundreds of secondary metabolites potentially toxic chemicals and to neutralize them by rapid bio-
generally characterize each edible plant (6, 64, 65). Furthermore, transformation and/or elimination. Classically, the biotrans-
the composition often depends on the body compartment, tissue, formation process consists of 2 types of chemical reactions,
or biofluid to which one refers. For instance, many food or drug phase I and phase II transformations, both of which occur
constituents that might be found in the mouth or stomach are primarily in the liver, kidney, and intestine. Phase I trans-
chemically identical to the compounds isolated from the intact formations typically involve oxidation of compounds via
food or drug. On the other hand, food constituents found in blood, cytochrome P450 enzymes as well as hydrolysis by various
urine, or other excreta are often metabolically transformed in the dehydrogenases, esterases, and amidases. On the other hand,
liver, kidney, or intestine to metabolites that are very different phase II transformations consist of chemical modifications
from the parent compound. This adds greatly to the diversity of such as methylation (by methyltransferases), sulfation (by
the food metabolome. However, in some cases, the parent sulfotransferases), acetylation (by N-acetyltransferases), glu-
compounds are broken down to such an extent that their end curonidation (by UDP-glucuronyltransferases), and amino acid
products are actually identical to chemicals that the body pro- conjugation (by glutathione or glycyl transferases). A recent
duces naturally. The importance of the gut microbiota in con- meta-analysis (68) of the metabolic fate of .1000 xenobiotics
tributing metabolites to the human metabolome has also recently showed that cytochrome P450 catalyzed oxidations (40%) and
emerged (50, 66). Some microbial metabolites, typically vitamins, UDP-glucuronosyltransferase glucuronidations (14%) were the
certain essential amino acids, and a few fatty acids, are specific most common followed by reactions involving dehydrogenases
microbial metabolites (w100 compounds in total are known at (8%), hydrolases (7%), glutathione-S-transferases (6%), and sul-
this time). However, a large majority of the metabolites produced fatases (5%). In fact, there are .300 different empirical rules that
by the gut microbiota are derived from the biotransformation of allow one to predict the fate of metabolites on the basis of their
both the endogenous metabolome and the food metabolome and chemical structure (69). Many of the metabolites derived from the
are therefore an integral part of these 2 metabolomes. These biotransformation of food components have not been well char-
microbial metabolites include short-chain fatty acids, secondary acterized. For polyphenols, .230 phase I/II metabolites have
bile acids, protein and amino acid metabolites, as well as plant been identified and associated with the consumption of specific
polyphenol metabolites (67). polyphenol-containing foods (70). The yield of phase I/II reactions
are often very high (68, 71), and host-transformed metabolites re-
tain many of the features of their parent compounds. Consequently,
Metabolism of food constituents these exogenously derived metabolites can be quite useful as specific
Knowledge of the metabolism of food constituents is critical to food biomarkers.
understanding the origin of the biotransformed fraction of the The third way that food metabolites may be transformed is
food metabolome. It is also essential if we wish to use food through microbial metabolism. Microbes have a very different set
metabolites as nutritional biomarkers or as a means to monitor of enzymes from mammals, and given that there are .1000
food consumption. In this regard, it is useful to review how food different species of microbes in the human gut (72) there is an
chemicals can be metabolized. Food constituents can be me- enormous diversity of enzymatic processes that act on food-
tabolized in 3 different ways: 1) they can be digested in the derived compounds. The gut microbiota is particularly adept at
mouth, stomach, and small intestine into simple nutrients that processing polyphenols to phenolic breakdown products. For
can be absorbed through the gut barrier; 2) they can be further instance, depending on the predominant microbiota, polyphe-
transformed by host tissues, especially the liver and kidney; nols can be transformed by ring cleavage to a variety of aromatic
or 3) they can be processed by the gut microbiota in the large compounds such as benzoate and various derivatives of hy-
intestine. droxyphenylacetic and hydroxypropionic acids. These phenolic
The first category of food constituents are intermediary me- acids can be further conjugated to glycine as in hippurate. The
tabolites formed by digestion of lipids, polysaccharides, and gut microbiota also processes indigestible carbohydrates
proteins. Most of these compounds are common to all living through a variety of fermentative pathways yielding short-chain
organisms and identical to human endogenous metabolites. They fatty acids such as butyric acid and propionic acid. Certain
cannot generally be used as dietary biomarkers because of their microbial metabolites can be useful as food biomarkers, al-
common identity and the impossibility to trace their dietary though there is a complex relation between the food source, the
origin. The possible exceptions are the essential amino acids, predominant gut microbial species, and the resulting food

on 16 July 2018
metabolites (73). Consequently, weaker correlations with in- and ECMDB resources. Entries in each of these databases
takes of foods or of their constituents were observed for mi- mentioned here are linked to other online resources such as
crobial metabolites when compared with untransformed food PubMed, PubChem, Kyoto Encyclopedia of Genes and Ge-
compounds and host-transformed metabolites (41). This is most nomes, Chemical Entities of Biological Interest, ChemSpider,
probably a result of the large variability of the microbiota across and other widely used chemical resources. The establishment of
subjects (74). As a result, microbial metabolites should be these database resources along with the increasingly widespread
treated with some caution when used as food biomarkers. use of metabolomics in nutrient analysis has now moved the
field of food and nutrition science firmly into the modern
“omics” era.
Food metabolome and metabolite databases
Given the complexity of food constituents, the diversity of
known food metabolites, and the rapidly growing number of METABOLOMICS AND DISCOVERY OF NOVEL
studies on the food metabolome, it is becoming clear that well- DIETARY BIOMARKERS
curated databases are of utmost importance to keep track of this
information. These “omics era” databases are being developed to Study design
help researchers understand the origins and fate of many food As noted previously, metabolomics has emerged as a key tool
metabolites (Table 2). Some recent examples include the in the search for novel biomarkers of dietary intake. To date, the
Human Metabolome Database (HMDB) (9), the E. coli methods used for biomarker discovery can be divided into 2 main
Metabolome Database (ECMDB) (66), the Yeast Metabolome categories: hypothesis-driven and data-driven. In both cases,
Database (YMDB) (75), Food Component Database (FooDB) metabolomics-based approaches can be applied. In the hypothesis-
(76), Phenol-Explorer (70), and PhytoHub (77). HMDB is an driven approach, prior knowledge about the biomarker or a series
online database of all known and presumptive human metabo- of biomarker candidates is available from food composition
lites. This rapidly growing database currently contains .40,000 databases such as FooDB (78) and methods are developed to
metabolites including endogenous, microbial, biotransformed, measure the candidate biomarkers. So far, this approach has
and exogenous/xenobiotic compounds. ECMDB is another essentially been applied to specific families of food constituents
online database consisting of 2750 metabolites known to be such as fatty acids or carotenoids (45, 79).
produced by Escherichia coli. This resource provides a In the data-driven approach, there is no prior knowledge of the
representative estimate of the microbial metabolome that biomarker and a large number of metabolites are measured, with
exists within the human gut. YMDB is a database consisting of the main limitation being the capacity of the analytic instrument
1730 metabolites known to be produced by Saccharomyces to detect them. This approach has been used to discover novel
cerevisae. Given the number of food products (wine, beer, biomarkers for a number of foods, nutrients, or diets (Table 3).
bread) produced by yeast fermentation and given that yeast also The samples to be analyzed can be obtained from 1) controlled
lives in the human gut, this database can also provide some dietary interventions or 2) cross-sectional studies.
useful data with regard to food metabolites and their possible In controlled dietary interventions, subjects consume the food
origins and fate. FooDB is a database of .28,000 food con- items of interest in a single meal (acute study) or in repeated
stituents, including artificial food additives. Much of the meals over a given period of time (ranging from a few days to up
chemical data in FooDB is now in HMDB, but FooDB provides to 6 mo; short- to medium-term study). In acute studies, biofluids
additional information about food sources and food concentra- are collected postprandially over a time period of up to 24 h after
tions that is not in the HMDB. PhytoHub is an online database consumption of the food of interest. Ideally, any biomarker
dedicated to the phytochemicals present in plant foods (w1000 identified in these acute studies must be validated with an in-
compounds), their known human metabolites reported in the tervention study to ensure there is a dose response, which would
literature, and other potential metabolites predicted with in silico render the biomarker suitable for use over a range of intakes. In
expert systems. Phenol-Explorer is an online database providing short-term interventions, biofluids are collected at the end of the
detailed information on dietary polyphenols and polyphenol intervention period and compared in subjects consuming either
metabolites. These food-focused resources are particularly de- the test food or a control food. Biofluids can also be collected
tailed and provide substantially more in-depth information and before and after consumption of the test food. A limitation of
reference material than what is available in the HMDB, YMDB, these intervention studies is the fact that the biomarkers identified
TABLE 2
Metabolite databases related to the food metabolome and accessible online1
No. of
Database Metabolites metabolites Website address Reference
HMDB Endogenous, microbial, biotransformed, and exogenous/ .40,000 www.hmdb.ca (9)

xenobiotic compounds identified in humans
ECMDB Escherichia coli metabolites 2750 www.ecmdb.ca (66)
YMDB Saccharomyces cerevisiae metabolites 1730 www.ymdb.ca (75)
FooDB Food constituents and food additives 28,000 www.foodb.ca (76)
Phenol-Explorer Dietary polyphenols and their metabolites 502 www.phenol-explorer.eu (70)
PhytoHub Dietary phytochemicals and their metabolites 1500 www.phytohub.eu (77)
1
ECMDB, E. coli Metabolome Database; FooDB, Food Component Database; HMDB, Human Metabolome Database; YMDB, Yeast Metabolome Database.

on 16 July 2018
1292 SCALBERT ET AL
may not be sufficiently specific for the test food in population that useful in epidemiologic studies because both their parent
studies, because regular diets may include other foods containing metabolites (caffeic acid and epicatechin) have been described in
precursors of the same biomarkers. For instance, in a cross- a variety of foods of plant origin (70).
sectional analysis of a whole-diet intervention study it was only For this reason, it may be particularly advisable to look for
possible to verify 23% of potential biomarkers observed in characteristic dietary biomarkers directly in cross-sectional
previous-meal studies (81). studies. However, the chances to identify robust biomarkers will
Cross-sectional studies can therefore play an important role in rely both on the sensitivity of the analytic equipment used and on
biomarker discovery. Low and high consumers are selected from the quality of the dietary data against which metabolic profiles are
food intake data collected by using food-frequency questionnaires, correlated. Both 24-h dietary recalls and food-frequency ques-
food diaries, or other dietary assessment tools. Comparison of tionnaires have been used, and new biomarkers for citrus fruit
these groups can lead to the identification of biomarkers that are intake or coffee were successfully identified (49, 88) (Table 3).
reflective of habitual intake, provided that these biomarkers have The use of food-frequency questionnaires may directly lead to the
a sufficient half-life in the organism or that the foods are regularly identification of biomarkers of habitual dietary exposure, but the
consumed. Although these and other studies have shown the lower accuracy and lower number of foods documented may limit
potential of cross-sectional studies, care needs to be taken because their value for such discovery studies (105).
many of the foods consumed are highly correlated and there is With the exception of 2 studies on dietary fiber and milk protein
a risk of identifying biomarkers that are not specific to the par- diet, all discovery studies were conducted on urine samples as
ticular food of interest unless their identity and specific occurrence opposed to blood samples (Table 3). The reason for this is partly
in the considered foods are established. Notwithstanding, cross- technical because of the higher concentrations of food-derived
sectional studies are excellent resources that are currently un- metabolites in urine as compared with blood and because of the
derused for dietary biomarker discovery. lack of interfering proteins. This contrasts with the preferred use
of blood biospecimens to measure biomarkers of nutritional status
in epidemiologic studies. More metabolomic studies using blood
Novel dietary biomarkers identified through samples should be carried out because of the more common
a metabolomic approach availability of plasma or serum samples in biobanks. Also, li-
An extensive list of potential dietary biomarkers discovered by pophilic biomarkers, which may be more stable over time (see
metabolomics is presented in Table 3. Markers associated with Pharmacokinetics and reliability of dietary biomarkers section),
the consumption of foods, nutrients, or diets have been identified. are more likely to be found in blood. Regression analyses of the
Successful studies include the identification of proline betaine as concentrations of 363 metabolites in plasma with a number of
a marker of citrus intake (49, 80). This marker was first identified dietary variables measured with a food-frequency questionnaire
in small-scale acute feeding studies and validated in free-living showed the highest correlations with phospholipid concentra-
subjects in 2 independent studies (44, 80). It was confirmed in tions (109). Furthermore, chain length and degree of saturation
a cross-sectional study that used untargeted metabolomics (49) of fatty acids in glycerophosphatidylcholines were associated
and played an important role in discriminating noncompliant with intake of specific foods or nutrients such as fish and dietary
individuals in a dietary pattern study of Nordic compared with fiber.
habitual diets (106). In these same studies, screening of urinary It is important to point out that the identities of many of the
profiles for predicted metabolites of citrus fruit also led to the proposed biomarkers in Table 3 (marked with an asterisk) have
identification of some terpenoids and flavonoids as biomarkers of not been fully validated with proper chemical standards because
citrus food intake as well as of intake of citrus-flavored sweets. these standards are often not commercially available. In addition,
This shows well the importance of previous knowledge on food no standard yet exists to report chemical identification of bio-
composition and on metabolism of food constituents for anno- markers in metabolomic studies (110). For this reason, it is
tating unknown discriminating ions in untargeted metabolomic often difficult to evaluate the degree of confidence in biomarker
studies. identification.
Trimethylamine oxide-N-oxide (TMAO) was found to be
a putative biomarker for meat intake or for meat-containing diets
in several studies (102–104), but it has also been reported as Analysis of the food metabolome
a biomarker of fish intake by other authors (82, 107) and shown Analyzing the food metabolome is a particularly challenging
to be more responsive to intake of fish than meat (85). Several task for 3 reasons. First, it comprises a much greater chemical
dietary precursors of TMAO such as choline or carnitine have diversity than any other part of the metabolome (see Food me-
been described (108) and care should be paid when interpreting tabolome and metabolite databases section). A second feature of
variations in TMAO concentrations in populations. the food metabolome is the huge range of concentrations, from
The state of validation of biomarkers listed in Table 3 varies picomolar or nanomolar concentrations for some contaminants
widely. Proline betaine is a good example of a well-validated or phytochemical metabolites to millimolar concentrations for
citrus fruit biomarker. Other biomarkers, particularly those nutrients such as sugars. Third, many components of the food
identified in controlled intervention studies, may prove to be less metabolome are unknown. Indeed, the metabolism for a large
robust in populations because of the possible existence of a va- proportion of nonnutrients in humans has never been studied and
riety of precursors as seen for TMAO, or the occurrence of the the chemical structures of their circulating metabolites have not
same precursor in various foods. Food-derived biomarkers such been identified. Until recently, the food metabolome was typi-
as caffeic acid sulfate or methylepicatechin sulfate, which were cally analyzed through targeted methods optimized for specific
found to discriminate consumers of raspberries (82), may not be compounds or families of nutrients or nonnutrients, such as

on 16 July 2018
TABLE 3
on 16 July 2018
Tentative dietary biomarkers identified through untargeted metabolomic approaches in human dietary intervention studies and cross-sectional studies1
Dietary factor and No. of Dietary assessment Analytic
study type subjects Comparison tool Biospecimen technique Biomarker Reference
Fruit, fruit juices

Mixed-fruit meal
AI 8 Consumers/ NA U (spot) NMR Proline betaine (80)
control
Citrus fruit

CS 499 Consumers/ 24-h dietary record U (24-h) NMR Proline betaine (80)
nonconsumers
CS 12 H/M/L FFQ U (fasting) FIE-FTICR-MS Proline betaine, 4-hydroxyproline betaine (44)
Orange juice
AI 4 Consumers/ NA U (kinetics) LC-Q-Tof, Proline betaine, limonene-8,9-diol-glucuronide,* nootkatone-13, (49)
control LTQ-Orbitrap 14-diol-glucuronide,* hesperetin-3#- glucuronide, hydroxyproline
SMTI 12 Consumers/ NA U (24-h) LC-Q-Tof, betaine, N-methyltyramine-sulfate,* naringenin-7-O-glucuronide
control LTQ-Orbitrap
Citrus fruit
CS 80 H/L FFQ and 24-h U (spot) LC-Q-Tof,
dietary record LTQ-Orbitrap
CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof Proline betaine, hesperetin-3-glucuronide* (81)
nonconsumers
Raspberries
SMTI 24 Consumers/ NA U (kinetics) FIE-FTICR-MS, Caffeic acid-sulfate, methylepicatechin-sulfate (82)

control GC-Tof
Strawberries
CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof 2,5-Dimethyl-4-methoxy-3(2H)- (81)
nonconsumers furanone-sulfate*
Vegetables
Vegetables
CS 160 H/M/L Food diary U (fasting) NMR Phenylacetylglutamine (83)
Broccoli
SMTI 24 Consumers/ NA U (kinetics) FIE-FTICR-MS Tetronic acid,* xylonate/lyxonate,* threitol/erythritol* (82)
control
Cruciferous
vegetables
SMTI 20 Before/after NA U (kinetics) NMR S-Methyl-L-cysteine sulfoxide (84)
AI 17 Consumers/ NA U (kinetics) LC-Q-Tof Sulforaphane N-acetylcysteine, N-acetyl-(N#-benzylthiocarbamoyl)cysteine, (85)
THE FOOD METABOLOME: A WINDOW OVER DIETARY EXPOSURE
control sulforaphane N-cysteine,* N-acetyl-S-(N-3-methylthiopropyl)cysteine,*

N-acetyl-S-(N-allylthiocarbamoyl)cysteine,* iberin N-acetyl-cysteine,*
4-iminopentylisothiocyanate,* erucin N-acetylcysteine*
Red cabbage
CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof 3-Hydroxy-3-(methylsulfinyl)propanoic acid,* 3-hydroxyhippuric (81)
nonconsumers acid-sulfate,* 3-hydroxyhippuric acid,* iberin N-acetyl-cysteine,*
N-acetyl-S-(N-3-methylthiopropyl)cysteine,* N-acetyl-S-
(N-allylthiocarbamoyl)cysteine,* sulforaphane N-acetylcysteine*
Beetroot
(Continued)
1293
on 16 July 2018
1294
TABLE 3 (Continued )

CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof 4-Ethyl-5-aminopyrocatechol sulfate,* 4-ethyl-5-methylaminopyrocatechol- (81)

nonconsumers sulfate,* 4-ethylpyridine-2-carboxylic acid glycine conjugate
Cereals
Whole-grain
rye bread
SMTI 20 Consumers/control NA U (24-h) LC-Q-Tof 3-(3,5-Dihydroxyphenyl)-1-propanoic acid-sulfate* and -glucuronide,* (86)
enterolactone- glucuronide,* azelaic acid,* 2-aminophenol-sulfate,*
2,4-dihydroxy-1,4-benzoxazin-3-one,* 2-aminophenol-sulfate,*
2-4-dihydroxy-1,4-benzoxazin-3-one-sulfate,* indolylacryloylglycine,*
ferulic acid-sulfate,* 3,5-dihydroxyphenylethanol-sulfate,*
3,5-dihydroxycinnamic acid-sulfate*
Meat and fish
Red meat
CS 160 H/M/L Food diary U (fasting) NMR O-Acetylcarnitines (83)
Salmon
SMTI 24 Consumers/control NA U (kinetics) FIE-FTICR-MS Anserine, methylhistidine, trimethylamine-N-oxide (82)

Oily fish
CS 68 H/M/L FFQ U (spot, 24-h, FIE-FTICR-MS Methylhistidine (87)
fasting)
Beverages
SCALBERT ET AL
Coffee
CS 18 Consumers/ U (fasting) LC-Q-Tof N-Methylpyridinium, trigonelline (88)
nonconsumers
AI 9 Before/after NA U (kinetics) LC-Q-Tof N-Methylpyridinium, trigonelline (88)
CS 68 H/M/L FFQ U (spot, 24-h, FIE-FTICR-MS Dihydrocaffeic acid (87)
fasting)
Chamomile tea
SMTI 14 Before/after NA U (spot) NMR Hippuric acid* (89)
Black tea
AI 3 Before/after NA U (24-h) NMR Hippuric acid,* gallic acid, 1,3-dihydroxyphenyl-2-O-sulfate* (90)
Tea (black and green)
STI 17 Consumers/control NA U (24-h) NMR Hippuric acid.* 1,3-dihydrophenyl-2-O-sulfate* (58)
Green tea
AI 8 Before/after NA U (kinetics) NMR Hippuric acid* (91)
Black tea
AI 20 Consumers/control NA U (kinetics) NMR Hippuric acid,* 4-hydroxyhippuric acid,* 1,3-dihydrophenyl-2-O- (92)
sulfate,* allic acid, 4-O-methylgallic acid*
(Continued)
on 16 July 2018

Mixed red wine/grape

juice extracts
SMTI 35 Consumers/control NA U (24-h) GC-MS, Hippuric acid,* 3-hydroxyhippuric acid,* 4-hydroxyhippuric acid,* (93, 94)

LC-MS/MS 4-hydroxybenzoic acid,* 1,2,3-trihydroxybenzene,* vanillic acid,*
isovanillic acid,* syringic acid,* 3-hydroxyphenylacetic acid,*
4-hydroxymandelic acid,* vanilmandelic acid,* ferulic acid,*
3-hydroxyphenylpropionic acid,* 3,4-dihydroxyphenylpropionic acid,*
3-(3-hydroxyphenyl)-3-hydroxypropionic acid,* catechol,* pyrogallol,*
citrate,* betaine*
Wine
SMTI 61 Consumers/control NA U (24-h) NMR Tartrate,* 4-hydroxyphenylacetate,* mannitol,* ethanol* (95)
Other foods
Cocoa powder
AI 10 Consumers/control NA U (kinetics) LC-Q-Tof Vanilloylglycine,* 6-amino-5-(N-methylformylamino)-1-methyluracil,* (96)
3-methyluric acid,* 7-methyluric acid,* 3-methylxanthine,*
7-methylxanthine,* dimethyluric acid,* theobromine, caffeine, trigonelline,*
hydroxynicotinic acid,* tyrosine, 3,5-diethyl-2-methylpyrazine,*
hydroxyacetophenone,* diketopiperazines,* epicatechin-sulfate,*

O-methylepicatechin,* vanillic acid,* phenylvaleric acid* and
phenylvalerolactone* derivatives, furoylglycine,* xanthurenic acid*
SMTI 20 Consumers/control NA U (24-h) LC-Q-Tof Hydroxynicotinic acid,* 6-amino-5-(N-methylformylamino)- (97)
and before/after 1-methyluracil,* 7- and 3-methyluric acid,* 7- and 3-methylxanthine,*
3,7-dimethylruric acid,* cyclo(propylalanyl),* 3,5-diethyl-
2-methylpyrazine,* theobromine,* vanillic acid-glucuronide*
and -sulfate- glucuronide,* vanilloylglycine,* 4-hydroxy-
5-(dihydroxyphenyl)-valeric acid-glucuronide* and -sulfate,*
3#-methoxy-4#-hydroxyphenylvalerolactone,* 4#-hydroxy-5-
(hydroxymethoxyphenyl)valeric acid-glucuronide,* 5-(3#,4#-
dihydroxyphenyl)-g-valerolactone-glucuronide* and -sulfate*
and -sulfate glucuronide,* (epi)catechin- glucuronide* and -sulfate
glucuronide,* methyl-(epi)catechin-sulfate,* N-(4#-hydroxy-3#-methoxy-E-
cinnamoyl)-L-aspartic acid,* N-(4#-hydroxycinnamoyl]-L-aspartic acid,*
THE FOOD METABOLOME: A WINDOW OVER DIETARY EXPOSURE
methoxyhydroxyphenylvalerolactone-glucuronide,*
hydroxyphenylvalerolactone-glucuronide* and -sulfate,*
5-(hydroxymethoxyphenyl)valeric acid-sulfate,* 4-hydroxy-
5-(phenyl)valeric acid-sulfate*
Chocolate (solid or
drink)
CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof 6-Amino-5-(N-methylformylamino)-1-methyluracil,* theobromine, (81)
nonconsumers 7-methyluric acid
(Continued)
1295
on 16 July 2018
1296

Almond-skin extract
AI 24 Before/after NA U (kinetics) LC-Q-Tof (Epi)catechin-sulfate,* O-methyl-(epi)catechin-sulfate,* naringenin- (98)
O-glucuronide,* 5-(hydroxyphenyl)-g-valerolactone-glucuronide*
and -sulfate,* 5-(dihydroxyphenyl)-g-valerolactone- glucuronide,* -sulfate
glucuronide* and -sulfate,* 5-(trihydroxyphenyl)-g-valerolactone-

glucuronide,* 5-(hydroxymethoxyphenyl)-g-valerolactone-glucuronide*
and sulfate,* 4-hydroxy-5-(dihydroxyphenyl)-valeric acid-glucuronide*
and sulfate,* 4-hydroxy-5-(hydroxymethoxyphenyl)valeric acid-
glucuronide,* 4-hydroxy-5-(methoxyphenyl)valeric acid-glucuronide,*
4-hydroxy-5-(hydroxyphenyl)valeric acid-glucuronide and -sulfate,*
4-hydroxy-5-(phenyl)valeric acid-sulfate,* 2-(dihydroxyphenyl)acetic
acid-glucuronide,* -sulfate glucuronide* and -sulfate,*
2-(hydroxymethoxyphenyl)acetic acid-glucuronide,*
2-(hydroxyphenyl)acetic acid-sulfate,* 3-(hydroxyphenyl)propionic
acid-glucuronide,* 3-(dihydroxyphenyl)propionic acid-sulfate,*
vanillic acid-glucuronide,* hydroxyhippuric acid,* ferulic
acid-glucuronide*
Nuts
SMTI 42 Consumers/control NA U (24-h) LC-Q-Tof, 10-Hydroxydecene-4,6-diynoic acid-sulfate,* tridecadienoic/tridecynoic acid- (56)
LTQ-Orbitrap glucuronide,* dodecanedioic acid,* 1,3-dihydroxyphenyl-2-O-

sulfate,* p-coumaroyl alcohol-glucuronide* and -sulfate,*
N-acetylserotonine-sulfate,* 5-hydroxyindoleacetic acid,* urolitin A-
glucuronide, sulfate* and sulfate glucuronide*
Walnuts
SCALBERT ET AL
CS 107 Consumers/ 24-h dietary record U (24-h) LC-Q-Tof 5-Hydroxyindole-3-acetic acid (81)
nonconsumers
Nutrients
Dietary fiber
SMTI 77 H/L Dietary record U (24-h) NMR Hippuric acid* (99)
SMTI 25 Consumers/control NA P (fasting) LC-Q-Tof 2-Aminophenol-sulfate, 2,6-dihydroxybenzoic acid, hydroxynuategenin- (100)
glucuronide*
Whey protein isolate
SMTI 12 Consumers/control NA P (sequential) LC-Q-Tof Tryptophan, phenylalanine, kynurenine, g-Glu-Leu (101)
Whey hydrolysate
SMTI 12 Consumers/control NA P (sequential) LC-Q-Tof Methionine sulphoxide, cyclo(Pro-Thr), cyclo(Ala-Ile), cyclo(Phe-Val), (101)
b-Asp-Leu, pGlu-Pro,
Diets
Omnivorous diet
SMTI 12 Consumers/control NA U (24-h) NMR Taurine,* carnitine,* acetylcarnitine,* 1-methylhistidine,* (102)
3-methylhistidine,* trimethylamine-N-oxide*
Vegetarian diet
SMTI 12 Consumers/control NA U (24-h) NMR p-Hydroxyphenylacetate* (102)
Meat protein diet
SMTI 24 Before/after NA U (24-h) NMR Trimethylamine-N-oxide,* histidine* (103)
Seafood
AI 17 Consumers/control NA U (kinetics) LC-Q-Tof Trimethylamine-N-oxide (85)
(Continued)
*No standard was used to confirm the identity of the biomarker. AI, acute intervention; CS, cross-sectional; FFQ, food-frequency questionnaire; FIE, flow injection electrospray; FTICR, Fourier transform
Reference
ion cyclotron resonance; GC, gas chromatography; H/L, high and low (intake); H/M/L, high, medium, and low (intake); LC, liquid chromatography; MS, mass spectrometry; NA, not applicable; NMR, nuclear
lipids, organic acids, sugars, flavonoids, or carotenoids. How-
(104)
(103)
(104)
(105)
(105)
(106)
ever, the combination of available targeted analysis methods is
still far from covering the whole chemical space of the food
metabolome. In principle, untargeted metabolomics provides
equol,* glycitein,* O-desmethylangolensin,* enterolactone,* trigonelline*

Trimethylamine-N-oxide,* dimethylamine,* phenylalanine,* methylhistidine*
Sulforaphane,* proline betaine,* hippuric acid,* genistein,* daidzein,*
(2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid, 3,4,5,6-tetrahydrohippurate*

a wider coverage and is likely to show the presence of new
Trimethylamine-N-oxide, hydroquinone-glucuronide, hippuric acid,

metabolites in biofluids and tissues.
As is the case for the other parts of the metabolome, mass
spectrometry (MS) coupled with gas chromatography or liquid
chromatography and NMR are currently the most widely used
technologies for food metabolome analysis (Table 3). The ad-
vantages and disadvantages of these techniques have been ex-
tensively discussed elsewhere and are beyond the scope of the
present review (111–113). Briefly, NMR is robust, nondestructive,
Biomarker
and quantitative but has a relatively low sensitivity, which narrows

its coverage of the food metabolome to predominant nutrients,
sugars, and microbial metabolites present at millimolar to mi-
cromolar concentrations. MS is by far the most sensitive tech-
nique and the only method able to cover the nonnutrient
magnetic resonance spectroscopy; P, plasma; Q, quadrupole; S, serum; SMTI, short- and medium-term intervention; Tof, time-of-flight; U, urine.
Short-chain fatty acids*
metabolites of the food metabolome occurring at low concen-

trations in biological samples. GC-MS combined with chemical
Proline betaine*
derivatization has been used to analyze constituents of the food

metabolome such as phenolic acids or fatty acids (79, 93, 94).
However, to date, most studies on the food metabolome have
Citrate*
been performed by using high-resolution liquid chromatography-

quadrupole-time-of-flight MS with electrospray ionization
(Table 3). This technique has been successful in detecting
LC-FTICR-MS
LC-FTICR-MS
compounds such as terpene metabolites, diketopiperazine me-

technique
Analytic
tabolites, phenylvalerolactones, and benzoxazinoid metabolites,

LC-Q-Tof
which are interesting candidate biomarkers of food intake that

NMR
NMR
NMR
would not be easily detected in biofluids by NMR or GC-MS

(49, 86, 96). No single chromatographic method is able to cover
the wide range of polarity existing for the food metabolome
Biospecimen
compounds. Highly polar compounds may have to be analyzed

U (fasting)
U (fasting)
U (fasting)
S (fasting)
U (spot)
U (spot)
by using hydrophilic interaction chromatography, whereas spe-

cific methods with atmospheric pressure chemical ionization
may be developed for profiling apolar plasma metabolites. Di-
rect flow injection-MS has also been used (82, 114), which of-
supermarket records
Dietary assessment
fers the advantage of high-throughput analysis, as would be

required for large-scale epidemiologic studies. However, ion
24-h recall and
Dietary record
Questionnaire
Questionnaire
suppression effects, due to inefficient ionization of certain ions

tool
in complex matrices and the inability to discriminate between

isomers, limit the use of this approach.
NA
NA
The main current limitation of MS is the very challenging and

burdensome task of the structural elucidation of the detected ions
Consumers/control
Consumers/control
Consumers/control
Consumers/control
(see below). However, because of its sensitivity and breadth of

Comparison
coverage, LC-MS has certainly become the method of choice for

Before/after
untargeted analysis of the food metabolome. Rapid advances in

technology have led to a new generation of much more efficient
H/L
time-of-flight and single-stage Orbitrap (Exactive; Thermo Sci-

entific) instruments, offering improved linearity, resolution, and
subjects
mass accuracy, which will be critically important for the analysis

No. of
161
161
107
24
10
60
of the food metabolome (115). As with any experimentally based

analytic method, multiple variables can substantially affect the
vegetables, soy)
Lactovegetarian diet
final data set. These include the mode of sample preparation,

Phytochemical-rich
Milk protein diet
method of chromatography, mode of detection, and the choice of

Omnivorous diet
diet (citrus,
cruciferous
Dietary factor and
data reduction methods (116, 117). No standardized method

Nordic diet
exists yet, and the need for improved harmonization is certainly

SMTI
SMTI
SMTI
study type
desirable for further progress on the food metabolome.

CS
CS
CS
Achieving absolute quantification rather than relative quantifi-

cation of food metabolome metabolites via untargeted methods

on 16 July 2018
1298 SCALBERT ET AL
remains a continuing challenge. It is essentially impossible to use compounds and structures in the samples and is therefore partic-
standards or isotopically labeled references to quantify the thou- ularly important for characterizing the food metabolome.
sands of compounds in the food metabolome. New approaches are Metabolic profiling data may be analyzed by using univariate or
being developed with isotope labeling and multiple reaction multivariate statistical methods. Statistical analysis of untargeted
monitoring–based profiling for families of compounds sharing metabolomic data is often an initial step in the biomarker discovery
distinctive chemical functionalities (118). Labeled reagents tar- process that should not be confused with hypothesis testing, be-
geted at these functionalities or particular multiple reaction cause there is no a priori hypothesis. In dietary intervention studies
monitoring transitions could be used to specifically measure se- with single foods, the contrast observed for a good biomarker can be
lected fractions of the food metabolome such as amines, phenols, large, sometimes even infinite, making it possible to work robustly
glucuronides, or mercapturic acid derivatives. These advances may with small sample sets and discriminate potential intake biomarkers
allow researchers to target larger areas of the food metabolome from more subtle changes in endogenous metabolites (126). In
chemical space with the use of standardized quantitative methods. cross-sectional studies this large contrast seldom applies, but ap-
proximate dose-response relations from food-frequency question-
naires may help in the identification of food intake biomarkers.
Analysis of metabolomic data Multivariate analysis is most commonly used for explorative
The metabolic profile of raw data generated by the spectro- analysis of metabolic profiling data (127). As opposed to uni-
metric analysis of biological samples can be analyzed in several variate analysis, multivariate analysis can be performed in an
steps (119, 120). These include data preprocessing, data align- unsupervised manner (ie, without including information on group
ment, data normalization, and signal correction followed by the assignment for the analysis). This provides an objective as-
analysis through various statistical methods. There are a number sessment of the principal patterns in the data set (eg, intake or no
of different software tools available for these tasks; most vendors intake of a specific food component or diet). Unsupervised
have their proprietary software but highly efficient freeware analysis such as principal components analysis (PCA) should
programs, Web servers, or add-on softwares exist. For NMR, an always be the starting point for explorative multivariate analysis
example is the Interval Correlation Optimized shift algorithm to ascertain that there is an overall segregation into a food-related
produced for Matlab (121), and for LC-MS data alignment pattern. The features associated with any pattern can be shown by
freeware such as XCMS (122), MZmine (119, 123), and Met- the loadings in a PCA plot; however, PCA is generally not well
Align (124) are widely used. suited to identify the most prominent part of the pattern. Sparse
The preprocessing step is software dependent and typically PCA overcomes this limitation (128, 129). Clustering methods
includes data reduction methods such as centroiding of mass are also widely used for subdividing and ordering a data set into
spectra or analog-to-digital conversion of NMR, infrared, or UV/ groups of data with a high degree of similarity. Hierarchical
visible spectra. Preprocessing also includes translation of data clustering generates a dendrogram in which neighboring samples
formats and data export. The next step is data alignment. It is share the greatest similarity and neighboring features are those
crucial to align the different sample profiles, which do not match most closely related. This provides useful biological information
exactly because of small variations in retention times, masses, or and unsupervised groupings of the data set (130).
chemical shifts. All available software tools differ in their peak Supervised multivariate analysis is commonly the next step in
picking algorithms. There is only a 50–70% overlap between the many data analysis methods but has a strong tendency to overfit
peaks detected by different packages from the same raw data set, the data. Even random data will usually segregate and show
even with similar settings (125). Additional markers may be a “marker pattern” after supervised analysis (131). Careful
observed by using additional softwares or simply by altering validation with the use of techniques such as permutation testing
software settings. Another major difference between packages is and cross-validation is therefore always necessary. There are
the presence or absence of so-called gap filling, a routine to a large number of supervised methods (120, 127), with the most
revisit the raw data for any peak that has not been detected in commonly used analysis for comparing 2 groups being partial
a sample when it was found in others. The lack of a gap-filling least-squares discriminant analysis (PLS-DA) (132) or one of its
algorithm creates major problems for normalization and for several variants. In complex nutritional studies it may be useful
statistical analysis. An ideal food intake marker would have to combine ANOVA separations of factors with PLS-DA (133,
a zero value in control samples from volunteers who did not 134) or use multilevel PLS-DA to reduce the influence of in-
consume the food; in this case, the gap-filling routine helps to terindividual variation (135). Some multivariate methods such as
estimate the background noise in the peak area. PLS are mainly used to fit the data to a continuous variable. This
The output from the peak detection and data alignment steps is is useful to explore the relation of any features in the profiling
typically a matrix of samples and features with the intensity as the data set with an external variable (eg, intake of a specific food
values within the matrix structure. A feature here denotes any based on a questionnaire or any biological outcome marker)
distinct peak in the data set, regardless of whether it represents (121). In addition, for these prediction models very careful
a known, unknown, or even an artifact ion. In LC-MS profiling, validation is required and their global ability to predict a specific
the features are characterized by a retention time and a mass (m/z) food intake has to be assessed in separate studies.
value. Such a feature may be a compound’s parent ion, but just Univariate analysis is supervised—that is, a hypothesis re-
as frequently it represents an adduct ion or a fragment from garding a difference between groups is implicit. Any marker
a compound. In NMR and in most other digitized spectral data the identified by this approach should therefore also be in-
single features are part of spectral shapes that usually have local dependently validated in a separate study. For univariate analysis
maxima and minima. For both kinds of data the fine structure of the used in exploration of new food intake biomarkers it is impor-
data contains additional information that is useful for identifying tant to set a reasonable threshold for false discovery rates

on 16 July 2018
(FDRs) (136, 137). In explorative science there is no fixed rule existing spectral data are still scattered over numerous Web-based
for the acceptability level of the FDR, and any level from 5% to (searchable) databases, printed tables in scientific journals, Excel
50% may be useful, depending on further data analysis steps. files in supporting information, and scientific books (140, 149,
If no additional data analysis is planned as, for instance, in 150). As described earlier, the major online chemical resources
metabolome-wide association studies (MWASs), the FDR should (typified by PubChem, Kyoto Encyclopedia of Genes and Ge-
generally be selected in the lower end of this range. If the nomes, and ChemSpider) contain limited information on human
univariate data step is used for selection of features that will be metabolites derived from food compounds. Although they are not
analyzed further (eg, by multivatiate models), it may be more specific to the food metabolome, these resources are useful for
appropriate to use a higher FDR. In any case, the markers found metabolite identification because fragmentation data or NMR
must be validated in subsequent independent studies. signals of known metabolites can be compared with the unknown
Overall, the field of metabolomics is rich with data analysis query to gain structural information. The most comprehensive
options, and the challenge in the future will be to optimally apply and best-curated chemical (commercial) database is currently
these to food metabolomic studies. Useful resources exist to help SciFinder, which includes many food metabolome compounds
in selecting and using in the most rigorous way appropriate tools collected from the literature (151). Recently, a large number of
for data analysis in a particular project (138). food compounds have been added to the HMDB, which makes
searches on the basis of their accurate masses possible (9);
however, to date it contains few mass fragmentation spectra
Metabolite identification useful for food metabolite identification.
Metabolite identification in metabolomic studies relies on the The robust and reproducible fragmentation patterns and re-
comparison of generated spectra with those in curated metabolite tention times of volatile metabolites in GC-MS have successfully
databases. However, the vast majority of the food metabolome been used to set up metabolomic workflows that search for
components are not yet represented in these databases, which possible candidate metabolites in the National Institutes of
makes the elucidation of their structure difficult. As previously Standards and Technology library or in-house libraries (152).
described, the identification of candidate dietary biomarkers is Recently, similar approaches have been proposed for LC-MS–
complicated by the fact that the majority of food compounds are and NMR-based metabolomic data sets. Spectral databases
treated as xenobiotics by the human body in phase I and phase II contain fragmentation spectra obtained in different experimental
reactions or undergo fermentation in the colon by the gut conditions (eg, several collision energies and different mass
microbiota (139). Despite some increase in their availability over spectrometers) to facilitate direct comparison with experimental
the past few years, these highly diverse metabolites are largely data (141). Also, the number of metabolite spectra in Chem-
absent from most databases. One exception is Phenol-Explorer, spider and HMDB is increasing. Even though not specific to the
which gives a comprehensive overview of the human and animal food metabolome, these resources are particularly useful for
metabolites formed from polyphenols (70). metabolite identification because fragmentation data or NMR
NMR spectroscopy and MS are the 2 essential tools for elu- signals of known metabolites can give structural hints for the
cidation of the structure of unknown metabolites in metabolomic unknown query.
studies (140, 141). Metabolites such as S-methyl-L-cysteine
sulfoxide or proline betaine as biomarkers of cruciferous vege-
tables or citrus fruit, respectively, could be identified in NMR Software tools for annotation of the food metabolome
studies on the basis of their characteristic chemical shifts (Table Software tools such as MetFrag, MyCompoundID, MetiTree,
3) (80, 84). More markers of food intake have been identified in and Mass Frontier can handle metabolite fragmentation data and
MS-based metabolomic studies on the basis of their accurate permit library searches for potential candidates using in silico
mass and mass fragmentation spectra (142–144). fragmentation predictions of metabolites or comparisons to
A number of commercial and “in house” software tools have previously fragmented metabolites or standards (146, 153–155).
been developed recently and used to recognize and identify MetFusion combines knowledge from spectral databases such as
fragments and adducts derived from one food metabolite (97, MassBank with the multitude of candidates generated by frag-
114, 145). These tools are particularly useful to identify phase menters such as MetFrag (156).
II conjugates, common constituents of the food metabolome, Software tools have also been developed that integrate me-
which show characteristic neutral losses (eg, 79.957 amu for tabolite annotation directly within the processing pipeline of LC-
sulfate conjugates and 176.032 amu for glucuronides) (44, 114, MS data (157). For example, CAMERA is a pipeline for the
140). Customized in-house databases on the most likely phase I annotation and analysis of LC-MS data in cooperation with
and phase II metabolites have also been developed based on in XCMS (158, 159). Online MS/MS fragmentation, UV spectra,
silico prediction with expert systems such as Meteor (49, 146– and estimates of partition coefficients based on retention time
148). An important challenge for the future will be the de- have been used to further investigate metabolite structures (157,
velopment of a coordinated international effort to extend existing 160, 161). The MagMA software package recently launched is
and develop novel software tools and databases allowing the more able to read multistage tandem mass spectral data to add potential
“intelligent” prediction of the metabolic fate of food constituents. candidates based on in silico–predicted fragmentation (162). In
particular, the use of accurate fragmentation mass data as input
can enhance the metabolite identification process by selecting
Spectral databases for the food metabolome the most likely candidates on the basis of similarities in frag-
Despite the many initiatives to make spectral data sets mentation pathways and their readily assigned elemental for-
available to the scientific community, the publicly accessible mula with the unknown query metabolite as exemplified by

on 16 July 2018
1300 SCALBERT ET AL
dietary polyphenols (144). A large number of polyphenol me- acid, and di-homo-g-linolenic acid—were found to be associ-
tabolites such as glucuronides of 5-(3#,4#-dihydroxyphenyl)- ated with the risk of gastric cancer (169). These associations
g-valerolactone and sulfate esters of methylated (epi)catechin were tentatively explained by either different amounts of dietary
could thus be easily annotated and some fully structurally elu- intake or differential fatty acid metabolism in cases and controls.
cidated by using a combination of MS fragmentation and NMR The alternative untargeted approach makes no a priori as-
(163). sumptions regarding sources of exposure that are causal for
Moreover, recently developed bioinformatics approaches aim a particular disease but instead relies on comparisons of com-
to narrow the number of possible candidate structures that match prehensive profiles of metabolomic features between cases and
with an unknown query metabolite by taking into account the controls to find discriminating exposure biomarkers. Once these
chemical and biological background of the sample (164). For exposure biomarkers have been identified, follow-up studies are
example, it is more likely that a metabolite excreted in urine is performed to determine their sources (167), and those related to
more polar as a result of phase II reactions. This has predictable dietary factors would be regarded as disease-associated dietary
consequences for its expected mass and chromatographic be- biomarkers (Figure 2). The agnostic nature of the untargeted
havior, which can be used to mine metabolomic data sets. It is design allows all potentially useful biomarkers to be identified,
expected that these various software tools will be beneficial in the including not only dietary biomarkers but also those related to
hunt for metabolite entities represented by the food metabolome. endogenous factors (including the microbiota), pollution, and
drugs as well as biomarkers of disease progression. A good
example of the untargeted approach is given by Holmes et al (59)
PERSPECTIVES FOR FUTURE APPLICATIONS OF THE and Bictash et al (166) who used untargeted NMR of .4000
FOOD METABOLOME urine specimens from the INTERMAP study to investigate po-
tentially causal factors for high blood pressure across geo-
Discovering disease-related dietary factors graphically diverse populations. The investigators showed that
MWASs have been proposed as useful tools for discovering metabolite concentrations differed substantially between Asian
low-molecular-weight biomarkers that are predictive of either and Western populations, suggesting important effects of diet
causal exposures or disease progression (59, 165, 166). In fact, and related risk factors, including the microbiota, on the risk of
MWASs can be regarded as a special case of the exposome-wide coronary artery disease and stroke. Three highly discriminating
association study, which investigates disease associations with all biomarkers were identified, namely alanine, which was directly
exposures to low- and high-molecular-weight compounds (167). correlated with blood pressure, and formate and hippurate, both
Given the thousands of potentially important exposures to con- of which were inversely correlated with blood pressure. All of
sider, MWASs and exposome-wide association studies move these discriminatory biomarkers point to dietary sources, some-
away from knowledge-driven designs that focus on a priori times in combination with cometabolism by gut microbiota. For
hypotheses about particular exposures toward data-driven de- example, alanine is associated with diets that emphasize animal
signs using untargeted or semitargeted sets of analytes (167). In products rather than vegetables, and hippurate has been associated
either case, potentially useful biomarkers may be identified with microbiota colonization of the gut (170).
through rigorous comparisons of quantitative or semiquantitative A more recent example of the untargeted approach is provided
profiles of biospecimens obtained from subjects with and without by a series of articles from Stanley Hazen’s group at the
a particular disease (59). Because diets and lifestyle strongly Cleveland Clinic (108, 171, 172). In their initial untargeted
affect the metabolome, any pending disease may lead to reverse LC-MS/MS investigation (171), the authors showed that the nutrient
causation in MWASs; study design and interpretation must choline, along with its major metabolites, betaine and TMAO,
therefore take into account the common responses to early signs were associated with risks of cardiovascular disease, particularly
of disease in the population under study and other potential TMAO. Then, by using an elegant set of targeted follow-up
confounders.
This biomarker discovery process is shown in Figure 2. With
a focus on the food metabolome and associated biomarkers of
potentially causal dietary exposures, the figure includes both
semitargeted and untargeted designs. In the semitargeted ap-
proach, preliminary cross-sectional studies are developed to
connect dietary records with the food metabolome and thereby
identify dietary biomarkers that are highly correlated with the
consumption of particular foods. A good example of this ap-
proach is given by Saadatian-Elahi et al (168), who correlated
food consumption, as determined by 24-h dietary recall, with
plasma concentrations of 22 fatty acids determined by gas
chromatography in 3000 subjects from the European Prospective
Investigation into Cancer and Nutrition cohort. Strong correla-
tions between regional dietary factors and fatty acid concen-
trations allowed components of the food metabolome to be used
as predictor variables in a prospective investigation of gastric FIGURE 2. The food metabolome and discovery of food-related bio-
cancer in the European Prospective Investigation into Cancer markers associated with diseases. Both semitargeted and untargeted ap-
and Nutrition cohort. Three fatty acids—oleic acid, a-linolenic proaches are shown. Disease-validated biomarkers are shown in bold letters.

on 16 July 2018
studies with the use of a choline challenge as well as charac- diseases. A number of loci associated with variations in the
terization and manipulation of microbiota, Hazen and coworkers concentration of endogenous metabolites could be identified in
showed that consumption of foods rich in choline or carnitine, genome-wide analysis studies, and many of these genes were
such as eggs, milk, liver, meat, or fish, produced high concen- coding for metabolic enzymes (180–182). Various enzymes in-
trations of TMAO in both humans and animals who possessed volved in the biotransformation of xenobiotics and dietary com-
the requisite microbiota for metabolizing choline or carnitine to pounds also show genetic polymorphisms (183, 184). The analysis
trimethylamine, the immediate precursor of TMAO (108, 171, of their variants combined with that of the food metabolome in
172). Subjects from a cohort of .2000 patients with cardio- MWASs may reinforce the associations observed between food-
vascular disease, who were in the highest quartile for plasma derived metabolites and disease risk as has been previously found
TMAO concentrations, had a .2-fold risk of a heart attack or for alcohol or folate as disease risk factors (185, 186). A deeper
stroke compared with subjects from the lowest quartile (108, 172). knowledge of the enzymes involved in the biotransformation of
dietary compounds is, however, needed to warrant success of this
approach.
Identification of new potentially bioactive food–derived Another possible approach to identify food compounds po-
metabolites tentially responsible for the activity is the study of longitudinal
The application of metabolomics to foods has allowed the variations in their concentrations and their associations with
identification of a large variety of novel food constituents that are particular health outcomes or surrogate health markers in pop-
either naturally present in the food species or formed during food ulation studies or clinical trials. The kinetics of a metabolite’s
processing (65, 173, 174). Similarly, the exploration of the food appearance in plasma after a meal can be related to the kinetics
metabolome in human biofluids by means of wide-coverage of associated physiologic events. Epicatechin metabolite con-
profiling methods and intermetabolite correlation analysis (175) centrations in plasma after cocoa intake paralleled the increase
should show exposures to many nonnutrient food compounds and of plasma nitroso species concentrations and the vascular re-
their metabolites whose presence has not been previously sponse (187). Overall, the study of the variability in the food
identified. These compounds could also be new bioactive com- metabolome (which permeates all human tissues) and its asso-
pounds. As an example, the recent description of benzoxazinoids ciation with health outcomes should greatly contribute to the
in rye facilitated the identification of some of their metabolites identification of the food metabolites responsible for the effects
(2,4-dihydroxy-1,4-benzoxazin-3-one, 2-aminophenol sulfate, and of diet on health and diseases.
hydroxylated phenylacetamides) in urinary metabolic profiles
observed after rye bread consumption (86, 114). These ben-
zoxazinoid metabolites certainly deserve further investigation as NETWORKING AND RECOMMENDATIONS TO MOVE
potential contributors to the health effects of rye products because THE FIELD FORWARD
of some documented anti-inflammatory, immunoregulatory, and As detailed in the previous sections, food metabolomics re-
appetite-suppressing properties (176). This example shows that quires inputs from specialists from various disciplines, including
a better characterization of chemicals contained in a given food analytic chemistry, chemometrics, statistics, bioinformatics,
should markedly improve our understanding of food-derived nutritional science, and biology. Within one group, it is difficult to
exposures and their biological effects. cover all the techniques and methods required to perform a
Metabolomics will help nutrition researchers move away from comprehensive metabolomic study. Several networking initia-
the reductionist views on health effects of foods that have largely tives may help in this respect by providing rapid access to new
prevailed until today. For many years, health effects associated information and tools. The rapid pace of development in
with a particular food have often been attributed to just 1 or 2 of metabolomic profiling techniques makes the role of networks
their constituents on the basis of certain biological properties even more important to help absorb and facilitate the use of all of
observed in vitro. Examples include lycopene in tomato, which is the information. This is supported by creating databases for
thought to prevent prostate cancer; isoflavones in soy products, compound information and spectral data, libraries of chemical
which may prevent hormone-dependent cancers; and catechins in standards, algorithms for data analysis, repositories for raw data
tea or flavanones in citrus, which may play a role in the pre- and metadata, and standardization initiatives to define current
vention of cardiovascular diseases. Although these compounds good practices. The Metabolomics Standards Initiative (MSI)
may actually contribute to the health effects of the food, as has launched by the Metabolomics Society is an example of such an
been well demonstrated in intervention studies in which a whole initiative, and the MSI has already had significant impact on
food has been compared with one of its bioactive constituents reporting formats in metabolomics (110, 188).
(177), their popularity may have overshadowed the contribution Further networking initiatives to share knowledge in open dis-
of other, lesser known constituents also present in the same food. cussion or workshops, the sharing of data and standard operating
Metabolomics could potentially reveal these other bioactive protocols, as well as starting common training initiatives will be
constituents, and the approach is already being used in the important to accelerate progress in the field. A good example of such
characterization of multicomponent drugs and herbal medicines a sharing network is the European Nutrigenomics Organization,
(178). Knowledge of all circulating metabolites is essential to a not-for-profit private organization with academic and private in-
understand the effects of the diet on health, and new metabolites stitutional members from all over the world. None of these efforts
formed from nutrients and other food constituents are continuously should be seen as static but rather as a current collective instrument
being identified, even for widely studied compounds (101, 179). to help in the release of biological information at the level of the
The combining of metabolomic with genomic data will also be metabolome. There are several open-user forums working with the
important to identify dietary compounds causally related to development and application of metabolomic software and

on 16 July 2018
1302 SCALBERT ET AL
standards in general, such as the MSI working groups (189), the by the gut microbiota, so these metabolic pathways need to be
Metabolomics Forum (190), and several others, but none of these covered as well. This work will require a large community effort
relate specifically to the food metabolome. The First International to develop software to predict structures from all possible me-
Workshop on the Food Metabolome was a first occasion for all tabolites from any food compound, including their conjugates;
researchers active in the field to meet and make propositions for such a tool could be further combined with software that performs
future research. These propositions are summarized here. in silico fragmentation to predict daughter ions and additional
prediction tools for predicting physicochemical properties such as
Coordination of dietary studies polarity and hence retention time. Prediction of absorption, dis-
tribution, and excretion of the food compounds and of their me-
The food metabolome is exceedingly complex because it en-
tabolites would be an additional area that would help the food
compasses metabolites derived from as many metabolomes as there
metabolome community. Systematic in silico–predicted metabo-
are edible species. Therefore, a particularly focused community
lites could also be stored in food metabolome databases.
effort is necessary to reach our ultimate goal of full coverage for all
foods and all food metabolites. A large number of studies with
different designs will be necessary to validate each dietary marker. Databases
For example, many studies have been conducted with oranges
The human metabolome database has recently expanded to
(Table 3), but a broad coverage of all citrus and many other fruit as
include compounds found in common foods because these are, at
well as kinetic studies have been necessary to interpret proline
least initially before metabolism, also present within the human
betaine as a short-term marker of citrus that is dominated by orange
body (9). Databases specific for the food metabolome are still
and orange juice intake (80). Similar work is needed and could be
largely missing apart from Phenol-Explorer, a database on all
a shared effort for many other food groups, including cruciferous
known polyphenol metabolites (70). The development of similar
and apiaceous vegetables, pomes, cheeses, meats, fish, and others.
databases for other classes of food compounds will likely require
A large concerted action or open-project network would be
a coordinated effort from many researchers active in various
needed to help prioritize needs for novel markers and focus on areas
fields. These databases should provide spectral data for the food-
in which drugs have largely failed and where diet and nutrition
derived metabolites in each class and any information useful for
show promise to prevent or cure diseases. More discussion is clearly
their identification. When not available, in silico–predicted mass
needed between laboratory scientists, nutritionists, and epidemi-
fragmentation spectra could be calculated and also stored, as is
ologists to address this question in a rational way. Such a network
done in SciFinder (151). The same databases could additionally
might share information on current research plans to avoid re-
allow metabolites to be linked with their food precursors, as well
dundancy, share known as well as unidentified markers related to
as with their possible dietary sources (70). The involvement of
specific foods, or even form a shared workflow pipeline for dietary
food scientists will be essential to provide this information.
studies, data analysis, and metabolite identification. In addition, the
constitution of a database describing resources of high-quality
human samples collected in various dietary intervention studies Study repositories with processed metabolomic data
developed for other purposes would also be extremely useful. This
To shape consensus and create openness in the evolving field of
information is partly accessible in a database such as ClinicalTrials.
metabolomics, it is important to share data and information on
gov (191), but no indication is given on the availability of bio-
food metabolome studies, as is done in many other biomedical
specimens. These samples would prove very useful for biomarker
fields (194–196). Indeed, for many funding agencies, this is
validation purposes and would save a lot of effort and money
becoming a key condition of funding. One such initiative is the
otherwise needed to replicate such clinical studies. An example of
Metabolights database, which aims to shape a fully open-access,
a local, but open, sample repository for experimental studies in-
shared database for metabolomic studies (197). Raw and pro-
cluding nutrition is the CUBE biobank, which covers samples from
cessed data and metadata can be uploaded and curated before
a single university (www.cube.ku.dk). An umbrella of such local
deposition into the Metabolights core database, which then
repositories could be one possible way forward to improve reuse of
makes the information accessible through the Internet. A similar
samples for biomarker validation studies.
ongoing but conceptually broader initiative is the Nutritional
Phenotype Database (dbNP) (198), initiated by the Nu-
Software tools trigenomics Organization. The dbNP can hold data from several
A comprehensive set of software tools has been developed and omics platforms, including metabolomics, together with study
shared to help the scientific community that covers every step in metadata in a searchable format. It is open access and builds on
data processing and analysis. Most of these are not specific to the private accounts for uploading and analyzing data with the
food metabolome analysis (see Analysis of metabolomic data possibility of open sharing when data can be released for others.
and Software tools for annotation of the food metabolome sec- Both dbNP and Metabolights provide several online software
tions). However, for the identification of food-derived metabo- tools to help in data curation and analysis.
lites, additional software developments are needed, particularly The storage of searchable, annotated, raw analytic data files
for in silico prediction of the metabolism of compounds found in with well-documented dietary metadata from human intervention
foods. Some commercial software exists for the pharmaceutical or cross-sectional studies will facilitate the comparison of raw or
area (192, 193) and covers many phase I and II reactions. How- preprocessed data with previously obtained spectral data of food-
ever, many compounds in foods have structures that are un- derived metabolites. Such a repository that contains all unknowns
common in pharmaceuticals. Food constituents may be degraded detected in previous food metabolome studies would be a pre-
by specialized enzymes and may also be extensively metabolized cious aid to identify the most robust dietary biomarkers. The

on 16 July 2018
format of raw analytic data concerning the food metabolome as contribute to future progress in nutrition research. Propositions
well as that of the dietary metadata will have to be defined. made here to define common objectives and priorities, optimize
study designs, develop databases and software tools, and promote
Food metabolome reference library sharing of data and resources should contribute to bringing this
emerging field to maturity. A dialogue between nutritionists,
The definitive identification of biomarkers is often hampered epidemiologists, analysts, chemometricians, statisticians, and
by the lack of available chemical standards. The large majority of bioinformaticians has just begun. It will be essential to build
the components of the food metabolome are not commercially multidisciplinary projects and make sure that the design of future
available. The development of a resource to synthesize and studies is defined and optimized to answer to nutritionists’ and
distribute chemical standards should be a priority. The de- epidemiologists’ most urgent needs for biomarkers. Major
velopment of a shared or federated resource of chemical stan- progress in assessing complex dietary exposures at the indi-
dards for dietary metabolites will allow researchers to confirm or vidual level is expected from these biomarkers. They should also
validate compound identifications. Food scientists and natural significantly contribute to a better understanding of the complex
product chemists who have isolated from various foods and interactions between diet and human health.
related products or synthesized these chemicals should be as-
sociated with this effort. Biotransformation routes (enzymes, We thank Mazda Jenab (International Agency for Research on Cancer,
microorganisms) could also be better exploited particularly to Lyon) for helpful comments on the manuscript. We also thank all of the par-
ticipants in the First International Workshop on the Food Metabolome for
synthesize conjugated metabolites. their active participation in the discussions from which many of the recom-
mendations presented in this article were derived.
Standardization initiatives The authors’ responsibilities were as follows—AS, CM, JD, and LB:
contributed to the conception and design of the manuscript; and AS provided
The MSI, initiated by the Metabolomics Society, has already extensive feedback concerning all versions of the manuscript and had pri-
issued several reference articles on good practice for metab- mary responsibility for final content. All of the authors contributed to the
olomic research. The MSI is broad and includes activities by writing of separate sections of the manuscript and reviewed and edited all
several working groups covering many aspects of metabolomics versions of the manuscript. All of the authors read and approved the final
(189). However, there is no current standardization initiative for manuscript. None of the authors had a conflict of interest.
the food metabolome, and the current article is launched as
a starting signal for such an initiative to share tools, information,
and data sets to help encourage a community-driven advancement REFERENCES
of research on the food metabolome. 1. Doets EL, de Wit LS, Dhonukshe-Rutten RAM, Cavelaars A, Raats
One of the most needed initiatives is a strategy with associated MM, Timotijevic L, Brzozowska A, Wijnhoven TMA, Pavlovic M,
Totland TH, et al. Current micronutrient recommendations in Europe:
tools for the validation of food intake biomarkers. In particular,
towards understanding their differences and similarities. Eur J Nutr
a reference database could integrate all potential markers that can 2008;47:17–40.
be included into targeted multimetabolite methods; each marker 2. Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL.
listed could be graded indicating the level of validation: for ex- Systems level studies of mammalian metabolomes: the roles of mass
ample, “0” for a newly discovered putative biomarker, “1” for spectrometry and nuclear magnetic resonance spectroscopy. Chem
Soc Rev 2011;40:387–426.
a biomarker with analytic validation including kinetics in the 3. Wild CP, Scalbert A, Herceg Z. Measuring the exposome: a powerful
sample type of interest, “2” for a biomarker also validated in a basis for evaluating environmental exposures and cancer risk. Environ
controlled dietary intervention studies as well as in cross-sectional Mol Mutagen 2013;54:480–99.
studies, and “3” for a biomarker also confirmed to be in ac- 4. Rezzi S, Ramadan Z, Fay LB, Kochhar S. Nutritional metabonomics:
cordance with other markers for the same food or foods. applications and perspectives. J Proteome Res 2007;6:513–25.
5. Wishart DS. Metabolomics: applications to food science and nutrition
research. Trends Food Sci Technol 2008;19:482–93.
Training 6. Manach C, Hubert J, Llorach R, Scalbert A. The complex links be-
tween dietary phytochemicals and human health deciphered by me-
Finally, education and training in the food metabolome also tabolomics. Mol Nutr Food Res 2009;53:1303–15.
represent an effort that needs to be shared at all levels, from 7. Fardet A, Llorach R, Orsoni A, Martin JF, Pujos-Guyot E, Lapierre C,
creating the basic training texts to specialized courses at several Scalbert A. Metabolomics provide new insights on the metabolism of
dietary phytochemicals in rats. J Nutr 2008;138:1282–7.
academic levels. Several training workshops on metabolomics 8. Cevallos-Cevallos JM, Reyes-De-Corcuera JI, Etxeberria E, Danyluk
and nutrition were supported by the Nutrigenomics Organization MD, Rodrick GE. Metabolomic analysis in food science: a review.
(112). However, more sustained and focused support is needed to Trends Food Sci Technol 2009;20:557–66.
bring the field of food metabolome research to maturity. 9. Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y,
Djoumbou Y, Mandal R, Aziat F, Dong E, et al. HMDB 3.0—the
Human Metabolome Database in 2013. Nucleic Acids Res 2013;41
CONCLUSIONS (Database issue):D801–7.
10. Rutishauser IHE. Dietary intake measurements. Public Health Nutr
Recent analyses of the food metabolome with modern analytic 2005;8:1100–7.
and bioinformatic tools have shown the considerable extent of 11. Bingham S, Luben R, Welch A, Tasevska N, Wareham N, Khaw KT.
information on dietary exposure contained in human biospeci- Epidemiologic assessment of sugars consumption using biomarkers:
mens. Some proof-of-principle studies have established the comparisons of obese and nonobese individuals in the European
Prospective Investigation of Cancer Norfolk. Cancer Epidemiol Bio-
feasibility of metabolomic approaches to identify novel dietary markers Prev 2007;16:1651–4.
biomarkers and suggest that these approaches could greatly 12. Marshall JR, Chen Z. Diet and health risk: risk patterns and disease-
expand the field of molecular nutritional epidemiology and specific associations. Am J Clin Nutr 1999;69:1351S–6S.

on 16 July 2018
1304 SCALBERT ET AL
13. Jenab M, Slimani N, Bictash M, Ferrari P, Bingham SA. Biomarkers 31. Brown MJ, Ferruzzi MG, Nguyen ML, Cooper DA, Eldridge AL,
in nutritional epidemiology: applications, needs and new horizons. Schwartz SJ, White WS. Carotenoid bioavailability is higher from salads
Hum Genet 2009;125:507–25. ingested with full-fat than with fat-reduced salad dressings as measured
14. Potischman N, Freudenheim JL. Biomarkers of nutritional exposure with electrochemical detection. Am J Clin Nutr 2004;80:396–403.
and nutritional status: an overview. J Nutr 2003;133(suppl):873S– 32. Albanes D, Virtamo J, Taylor PR, Rautalahti M, Pietinen P, Heinonen
4S. OP. Effects of supplemental beta-carotene, cigarette smoking, and al-
15. London SJ, Yuan JM, Chung FL, Gao YT, Coetzee GA, Ross RK, Yu cohol consumption on serum carotenoids in the Alpha-Tocopherol, Beta-
MC. Isothiocyanates, glutathione S-transferase M1 and T1 poly- Carotene Cancer Prevention Study. Am J Clin Nutr 1997;66:366–72.
morphisms, and lung-cancer risk: a prospective study of men in 33. Zamora-Ros R, Touillaud M, Rothwell JA, Romieu I, Scalbert A.
Shanghai, China. Lancet 2000;356:724–9. Measuring exposure to the polyphenol metabolome in epidemiolog-
16. Kensler TW, Roebuck BD, Wogan GN, Groopman JD. Aflatoxin: ical studies: current tools, applications and their limits. Am J Clin
a 50-year odyssey of mechanistic and translational toxicology. Tox- Nutr (in press).
icol Sci 2011;120:S28–48. 34. Manach C, Williamson G, Morand C, Scalbert A, Remesy C. Bio-
17. Baldrick FR, Woodside JV, Elborn JS, Young IS, McKinley MC. availability and bioefficacy of polyphenols in humans. I. Review of 97
Biomarkers of fruit and vegetable intake in human intervention bioavailability studies. Am J Clin Nutr 2005;81:230S–42S.
studies: a systematic review. Crit Rev Food Sci Nutr 2011;51: 35. Söderholm PP, Koskela AH, Lundin JE, Tikkanen MJ, Adlercreutz
795–815. HC. Plasma pharmacokinetics of alkylresorcinol metabolites: new
18. Mennen LI, Sapinho D, Ito H, Galan P, Hercberg S, Scalbert A. candidate biomarkers for whole-grain rye and wheat intake. Am J
Urinary flavonoids and phenolic acids as biomarkers of intake for Clin Nutr 2009;90:1167–71.
polyphenol-rich foods. Br J Nutr 2006;96:191–8. 36. Burri BJ, Neidlinger TR, Clifford AJ. Serum carotenoid depletion
19. Ross AB, Bourgeois A, Macharia HN, Kochhar S, Jebb SA, Brownlee follows first-order kinetics in healthy adult women fed naturally low
IA, Seal CJ. Plasma alkylresorcinols as a biomarker of whole-grain carotenoid diets. J Nutr 2001;131:2096–100.
food consumption in a large population: results from the WHOLE- 37. Kumar A, Vineis P, Sacerdote C, Fiorini L, Sabbioni G. De-
heart Intervention Study. Am J Clin Nutr 2012;95:204–11. termination of new biomarkers to monitor the dietary consumption of
20. Andersson A, Marklund M, Diana M, Landberg R. Plasma alkylre- isothiocyanates. Biomarkers 2010;15:739–45.
sorcinol concentrations correlate with whole grain wheat and rye in- 38. Outzen M, Egeberg R, Dragsted L, Christensen J, Olesen PT, Frandsen
take and show moderate reproducibility over a 2-to 3-month period in H, Overvad K, Tjonneland A, Olsen A. Dietary determinants for Hb-
free-living Swedish adults. J Nutr 2011;141:1712–8. acrylamide and Hb-glycidamide adducts in Danish non-smoking
21. Verkasalo PK, Appleby PN, Allen NE, Davey G, Adlercreutz H, Key women. Br J Nutr 2011;105:1381–7.
TJ. Soya intake and plasma concentrations of daidzein and genistein: 39. Grigoryan H, Li H, Iavarone AT, Williams ER, Rappaport SM. Cys34
validity of dietary assessment among eighty British women (Oxford adducts of reactive oxygen species in human serum albumin. Chem
arm of the European Prospective Investigation into Cancer and Nu- Res Toxicol 2012;25:1633–42.
trition). Br J Nutr 2001;86:415–21. 40. Rappaport SM, Li H, Grigoryan H, Funk WE, Williams ER. Ad-
22. Allen NE, Grace PB, Ginn A, Travis RC, Roddam AW, Appleby PN, ductomics: characterizing exposures to reactive electrophiles. Toxicol
Key T. Phytanic acid: measurement of plasma concentrations by Lett 2012;213:83–90.
gas-liquid chromatography-mass spectrometry analysis and associ- 41. Pérez-Jiménez J, Hubert J, Ashton K, Hooper L, Cassidy A, Manach
ations with diet and other plasma fatty acids. Br J Nutr 2008;99: C, Williamson G, Scalbert A. Urinary metabolites as biomarkers of
653–9. polyphenol intake in humans—a systematic review. Am J Clin Nutr
23. Myint T, Fraser GE, Lindsted KD, Knutsen SF, Hubbard RW, Bennett 2010;92:801–9.
HW. Urinary 1-methylhistidine is a marker of meat consumption in 42. Levine M, Conry-Cantilena C, Wang Y, Welch RW, Washko PW,
black and in white California Seventh-day Adventists. Am J Epi- Dhariwal KR, Park JB, Lazarev A, Graumlich JF, King J, et al. Vitamin
demiol 2000;152:752–5. C pharmacokinetics in healthy volunteers: evidence for a recommended
24. Arsenault LN, Matthan N, Scott TM, Dallal G, Lichtenstein AH, dietary allowance. Proc Natl Acad Sci USA 1996;93:3704–9.
Folstein MF, Rosenberg I, Tucker KL. Validity of estimated dietary 43. Pirro V, Valente V, Oliveri P, De Bernardis A, Salomone A, Vincenti
eicosapentaenoic acid and docosahexaenoic acid intakes determined M. Chemometric evaluation of nine alcohol biomarkers in a large
by interviewer-administered food frequency questionnaire among population of clinically-classified subjects: pre-eminence of ethyl
older adults with mild-to-moderate cognitive impairment or dementia. glucuronide concentration in hair for confirmatory classification. Anal
Am J Epidemiol 2009;170:95–103. Bioanal Chem 2011;401:2153–64.
25. Hodgson JM, Chan SY, Puddey IB, Devine A, Wattanapenpaiboon N, 44. Lloyd AJ, Beckmann M, Fave G, Mathers JC, Draper J. Proline be-
Wahlqvist ML, Lukito W, Burke V, Ward NC, Prince RL, et al. taine and its biotransformation products in fasting urine samples are
Phenolic acid metabolites as biomarkers for tea- and coffee-derived potential biomarkers of habitual citrus fruit consumption. Br J Nutr
polyphenol exposure in human subjects. Br J Nutr 2004;91:301–6. 2011;106:812–24.
26. Brantsaeter AL, Haugen M, Julshamn K, Alexander J, Meltzer HM. 45. Al-Delaimy WK, Ferrari P, Slimani N, Pala V, Johansson I, Nilsson S,
Evaluation of urinary iodine excretion as a biomarker for intake of Mattisson I, Wirfalt E, Galasso R, Palli D, et al. Plasma carotenoids as
milk and dairy products in pregnant women in the Norwegian Mother biomarkers of intake of fruits and vegetables: individual-level corre-
and Child Cohort Study (MoBa). Eur J Clin Nutr 2009;63:347–54. lations in the European Prospective Investigation into Cancer and
27. Turunen AW, Mannisto S, Kiviranta H, Marniemi J, Jula A, Tiittanen P, Nutrition (EPIC). Eur J Clin Nutr 2005;59:1387–96.
Suominen-Taipale L, Vartiainen T, Verkasalo PK. Dioxins, polychlori- 46. Scalbert A, Manach C, Morand C, Rémésy C, Jiménez L. Dietary
nated biphenyls, methyl mercury and omega-3 polyunsaturated fatty acids polyphenols and the prevention of diseases. Crit Rev Food Sci Nutr
as biomarkers of fish consumption. Eur J Clin Nutr 2010;64:313–23. 2005;45:287–306.
28. Kroke A, Klipstein-Grobusch K, Hoffmann K, Terbeck I, Boeing H, 47. Medina-Remón A, Zamora-Ros R, Rotchés-Ribalta M, Andres-Lacueva
Helander A. Comparison of self-reported alcohol intake with C, Martı́nez-González MA, Covas MI, Corella D, Salas-Salvadó J,
the urinary excretion of 5-hydroxytryptophol: 5-hydroxyindole-3- Gómez-Gracia E, Ruiz-Gutiérrez V, et al. Total polyphenol excretion
acetic acid, a biomarker of recent alcohol intake. Br J Nutr 2001;85: and blood pressure in subjects at high cardiovascular risk. Nutr Metab
621–7. Cardiovasc Dis 2011;21:323–31.
29. Crews H, Alink G, Andersen R, Braesco V, Holst B, Maiani G, 48. Ross AB, Shepherd MJ, Schupphaus M, Sinclair V, Alfaro B,
Ovesen L, Scotter M, Solfrizzo M, van den Berg R, et al. A critical Kamal-Eldin A, Aman P. Alkylresorcinols in cereals and cereal
assessment of some biomarker approaches linked with dietary intake. products. J Agric Food Chem 2003;51:4111–8.
Br J Nutr 2001;86(suppl 1):S5–35. 49. Pujos-Guillot E, Hubert J, Martin J-F, Lyan B, Quintana M, Claude S,
30. Vioque J, Weinbrenner T, Asensio L, Castello A, Young IS, Fletcher Chabanas B, Rothwell JA, Bennetau-Pelissero C, Scalbert A, et al.
A. Plasma concentrations of carotenoids and vitamin C are better Mass spectrometry-based metabolomics for the discovery of bio-
correlated with dietary intake in normal weight than overweight and markers of fruit and vegetable intake: citrus fruit as a case study.
obese elderly subjects. Br J Nutr 2007;97:977–86. J Proteome Res 2013;12:1645–59.

on 16 July 2018
50. van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier 72. Peris-Bondia F, Latorre A, Artacho A, Moya A, D’Auria G. The
T. Microbial metabolomics: toward a platform with full metabolome active human gut microbiota differs from the total microbiota. PLoS
coverage. Anal Biochem 2007;370:17–25. ONE 2011;6:e22448.
51. Bais P, Moon SM, He K, Leitao R, Dreher K, Walk T, Sucaet Y, 73. Moco S, Martin F-P, Rezzi S. A metabolomics view on gut micro-
Barkan L, Wohlgemuth G, Roth MR, et al. PlantMetabolomics.org: biome modulation by polyphenol-rich foods. J Proteome Res 2012;
a web portal for plant metabolomics experiments. Plant Physiol 2010; 11:4781–90.
152:1807–16. 74. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende
52. Wishart DS. Human Metabolome Database: completing the ’human DR, Fernandes GR, Tap J, Bruls T, Batto J-M, et al. Enterotypes of the
parts list’. Pharmacogenomics 2007;8:683–6. human gut microbiome. Nature 2011;473:174–80.
53. Takeda I, Stretch C, Barnaby P, Bhatnager K, Rankin K, Fu H, Weljie 75. Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P,
A, Jha N, Slupsky C. Understanding the human salivary metabolome. Mandal R, Krishnamurthy R, Sinelnikov I, et al. YMDB: the Yeast
NMR Biomed 2009;22:577–84. Metabolome Database. Nucleic Acids Res 2012;40:D815–20.
54. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, 76. Wishart DS. Systems biology resource arising from the Human Me-
Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, et al. The human tabolome Project. In: Suhre K, ed. Genetics meets metabolomics.
serum metabolome. PLoS ONE 2011;6:e16957. New York, NY: Springer, 2012:157–75.
55. Solanky KS, Bailey NJ, Beckwith-Hall BM, Bingham S, Davis A, 77. Institut National de la Recherche Agronomique. PhytoHub. Available
Holmes E, Nicholson JK, Cassidy A. Biofluid 1H NMR-based me- from: www.phytohub.eu (cited 3 September 2013).
tabonomic techniques in nutrition research—metabolic effects of di- 78. University of Alberta. FooDB: the food component database. Avail-
etary isoflavones in humans. J Nutr Biochem 2005;16:236–44. able from: http://www.foodb.ca/ (cited 3 September 2013).
56. Tulipani S, Llorach R, Jáuregui O, López-Uriarte P, Garcia-Aloy M, 79. Chajès V, Biessy C, Byrnes G, Deharveng G, Saadatian-Elahi M,
Bullo M, Salas-Salvadó J, Andrés-Lacueva C. Metabolomics unveils Jenab M, Peeters PHM, Ocke M, Bueno-de-Mesquita HB, Johansson
urinary changes in subjects with metabolic syndrome following I, et al. Ecological-level associations between highly processed food
12-week nut consumption. J Proteome Res 2011;10:5047–58. intakes and plasma phospholipid elaidic acid concentrations: results
57. Cross AJ, Major JM, Sinha R. Urinary biomarkers of meat con- from a cross-sectional study within the European Prospective In-
sumption. Cancer Epidemiol Biomarkers Prev 2011;20:1107–11. vestigation into Cancer and Nutrition (EPIC). Nutr Cancer 2011;63:
58. Van Dorsten FA, Daykin CA, Mulder TPJ, Van Duynhoven JPM. 1235–50.
Metabonomics approach to determine metabolic differences between 80. Heinzmann SS, Brown IJ, Chan Q, Bictash M, Dumas M-E, Kochhar
green tea and black tea consumption. J Agric Food Chem 2006;54: S, Stamler J, Holmes E, Elliott P, Nicholson JK. Metabolic profiling
6929–38. strategy for discovery of nutritional biomarkers: proline betaine as
59. Holmes E, Loo RL, Stamler J, Bictash M, Yap IKS, Chan Q, Ebbels T, a marker of citrus consumption. Am J Clin Nutr 2010;92:436–43.
De Iorio M, Brown IJ, Veselkov KA, et al. Human metabolic phe- 81. Andersen MB, Kristensen M, Manach C, Pujos-Guillot E, Poulsen
SK, Larsen TM, Astrup A, Dragsted L. Discovery and validation of
notype diversity and its association with diet and blood pressure.
urinary exposure markers for different plant foods by untargeted
Nature 2008;453:396–400.
metabolomics. Anal Bioanal Chem 2014;406:1829–44.
60. Slupsky CM, Rankin KN, Wagner J, Fu H, Chang D, Weljie AM,
82. Lloyd AJ, Favé G, Beckmann M, Lin W, Tailliart K, Xie L, Mathers
Saude EJ, Lix B, Adamko DJ, Shah S, et al. Investigations of the
JC, Draper J. Use of mass spectrometry fingerprinting to identify
effects of gender, diurnal variation, and age in human urinary me-
urinary metabolites after consumption of specific foods. Am J Clin
tabolomic profiles. Anal Chem 2007;79:6995–7004.
Nutr 2011;94:981–91.
61. Krug S, Kastenmueller G, Stueckler F, Rist MJ, Skurk T, Sailer M,
83. O’Sullivan A, Gibney MJ, Brennan L. Dietary intake patterns are
Raffler J, Roemisch-Margl W, Adamski J, Prehn C, et al. The dynamic
reflected in metabolomic profiles: potential role in dietary assessment
range of the human metabolome revealed by challenges. FASEB J
studies. Am J Clin Nutr 2011;93:314–21.
2012;26:2607–19. 84. Edmands WMB, Beckonert OP, Stella C, Campbell A, Lake BG,
62. Heinzmann SS, Merrifield CA, Rezzi S, Kochhar S, Lindon JC, Lindon JC, Holmes E, Gooderham NJ. Identification of human uri-
Holmes E, Nicholson JK. Stability and robustness of human meta- nary biomarkers of cruciferous vegetable consumption by metabo-
bolic phenotypes in response to sequential food challenges. J Pro- nomic profiling. J Proteome Res 2011;10:4513–21.
teome Res 2012;11:643–55. 85. Andersen M-B, Reinbach H, Rinnan A, Barri T, Mithril C, Dragsted
63. Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, L. Discovery of exposure markers in urine for Brassica-containing
Custodio DE, Abagyan R, Siuzdak G. METLIN—a metabolite mass meals served with different protein sources by UPLC-qTOF-MS un-
spectral database. Ther Drug Monit 2005;27:747–51. targeted metabolomics. Metabolomics 2013;9:984–97.
64. Fiehn O. Metabolomics—the link between genotypes and phenotypes. 86. Bondia-Pons I, Barri T, Hanhineva K, Juntunen K, Dragsted LO,
Plant Mol Biol 2002;48:155–71. Mykkänen H, Poutanen K. UPLC-QTOF/MS metabolic profiling un-
65. Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki veils urinary changes in humans after a whole grain rye versus refined
T, Suzuki H, Okazaki K, Kitayama M, et al. Metabolite annotations based wheat bread intervention. Mol Nutr Food Res 2013;57:412–22.
on the integration of mass spectral information. Plant J 2008;54:949–62. 87. Lloyd AJ, Beckmann M, Haldar S, Seal C, Brandt K, Draper J. Data-
66. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, driven strategy for the discovery of potential urinary biomarkers of
Mandal R, Krishnamurthy R, Wishart DS. ECMDB: the E-coli Me- habitual dietary exposure. Am J Clin Nutr 2013;97:377–89.
tabolome Database. Nucleic Acids Res 2013;41:D625–30. 88. Lang R, Wahl A, Stark T, Hofmann T. Urinary N-methylpyridinium
67. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, and trigonelline as candidate dietary biomarkers of coffee consump-
Pettersson S. Host-gut microbiota metabolic interactions. Science tion. Mol Nutr Food Res 2011;55:1613–23.
2012;336:1262–7. 89. Wang Y, Tang H, Nicholson JK, Hylands PJ, Sampson J, Holmes E. A
68. Testa B, Pedretti A, Vistoli G. Foundation review: reactions and en- metabonomic strategy for the detection of the metabolic effects of
zymes in the metabolism of drugs and other xenobiotics. Drug Discov chamomile (Matricaria recutita L.) ingestion. J Agric Food Chem
Today 2012;17:549–60. 2005;53:191–6.
69. Langowski J, Long A. Computer systems for the prediction of xe- 90. Daykin CA, Van Duynhoven JP, Groenewegen A, Dachtler M, Van
nobiotic metabolism. Adv Drug Deliv Rev 2002;54:407–15. Amelsvoort JM, Mulder TP. Nuclear magnetic resonance spectro-
70. Rothwell JR, Urpi-Sarda M, Boto-Ordonez M, Knox C, Llorach R, scopic based studies of the metabolism of black tea polyphenols in
Eisner R, Cruz J, Neveu V, Wishart D, Manach C, et al. Phenol-Explorer humans. J Agric Food Chem 2005;53:1428–34.
2.0: a major update of the Phenol-Explorer database integrating data 91. Law WS, Huang PY, Ong ES, Ong CN, Li SF, Pasikanti KK, Chan
on polyphenol metabolism and pharmacokinetics in humans and ex- EC. Metabonomics investigation of human urine after ingestion of
perimental animals. Database 2012;2012:bas031. green tea with gas chromatography/mass spectrometry, liquid chro-
71. Silberberg M, Morand C, Mathevon T, Besson C, Manach C, Scalbert matography/mass spectrometry and (1)H NMR spectroscopy. Rapid
A, Remesy C. The bioavailability of polyphenols is highly governed Commun Mass Spectrom 2008;22:2436–46.
by the capacity of the intestine and of the liver to secrete conjugated 92. van Velzen EJ, Westerhuis JA, van Duynhoven JP, van Dorsten FA,
metabolites. Eur J Nutr 2006;45:88–96. Grun CH, Jacobs DM, Duchateau GS, Vis DJ, Smilde AK.

on 16 July 2018
1306 SCALBERT ET AL
Phenotyping tea consumers by nutrikinetic analysis of polyphenolic 111. Theodoridis G, Gika HG, Wilson ID. LC-MS-based methodology for
end-metabolites. J Proteome Res 2009;8:3317–30. global metabolite profiling in metabonomics/metabolomics. Trends
93. van Dorsten FA, Grun CH, van Velzen EJJ, Jacobs DM, Draijer R, van Analyt Chem 2008;27:251–60.
Duynhoven JPM. The metabolic fate of red wine and grape juice 112. Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS,
polyphenols in humans assessed by metabolomics. Mol Nutr Food van Ommen B, Pujos-Guyot E, Verheij E, Wishart D, Wopereis S.
Res 2010;54:897–908. Mass-spectrometry-based metabolomics: limitations and recommen-
94. Jacobs DM, Fuhrmann JC, van Dorsten FA, Rein D, Peters S, van dations for future progress with particular focus on nutrition research.
Velzen EJJ, Hollebrands B, Draijer R, van Duynhoven J, Garczarek U. Metabolomics 2009;5:435–58.
Impact of short-term intake of red wine and grape polyphenol extract 113. Issaq HJ, Van QN, Waybright TJ, Muschik GM, Veenstra TD. Ana-
on the human metabolome. J Agric Food Chem 2012;60:3078–85. lytical and statistical approaches to metabolomics research. J Sep Sci
95. Vázquez-Fresno R, Llorach R, Alcaro F, Rodriguez MA, Vinaixa M, 2009;32:2183–99.
Chiva-Blanch G, Estruch R, Correig X, Andres-Lacueva C. 1H-NMR- 114. Beckmann M, Lloyd AJ, Haldar S, Seal C, Brandt K, Draper J.
based metabolomic analysis of the effect of moderate wine con- Hydroxylated phenylacetamides derived from bioactive benzox-
sumption on subjects with cardiovascular risk factors. Electrophoresis azinoids are bioavailable in humans after habitual consumption of
2012;33:2345–54. whole grain sourdough rye bread. Mol Nutr Food Res 2013;57:
96. Llorach R, Urpi-Sarda M, Jauregui O, Monagas M, Andres-Lacueva 1859–73.
115. He X, Kozak M, Nimkar S. Ultra-sensitive measurements of
C. An LC-MS-based metabolomics approach for exploring urinary
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid in oral fluid
metabolome modifications after cocoa consumption. J Proteome Res
by microflow liquid chromatography-tandem mass spectrometry us-
2009;8:5060–8.
ing a benchtop quadrupole/Orbitrap mass spectrometer. Anal Chem
97. Llorach R, Urpi-Sarda M, Tulipani S, Garcia-Aloy M, Monagas M,
2012;84:7643–7.
Andres-Lacueva C. Metabolomic fingerprint in patients at high risk of 116. Barri T, Holmer-Jensen J, Hermansen K, Dragsted LO. Metabolic
cardiovascular disease by cocoa intervention. Mol Nutr Food Res fingerprinting of high-fat plasma samples processed by centrifuga-
2013;57:962–73. tion- and filtration-based protein precipitation delineates significant
98. Llorach R, Garrido I, Monagas MA, Urpi-Sarda M, Tulipani S, differences in metabolite information coverage. Anal Chim Acta
Bartolome BA, Andres-Lacueva C. Metabolomics study of human uri- 2012;718:47–57.
nary metabolome modifications after intake of almond (Prunus dulcis 117. Gika HG, Theodoridis GA, Earll M, Snyder RW, Sumner SJ, Wilson
(Mill.) D.A. Webb) skin polyphenols. J Proteome Res 2010;9:5859–67. ID. Does the mass spectrometer define the marker? A comparison of
99. Rasmussen LG, Winning H, Savorani F, Ritz C, Engelsen SB, Astrup global metabolite profiling data generated simultaneously via UPLC-
A, Larsen TM, Dragsted LO. Assessment of dietary exposure related MS on two different mass spectrometers. Anal Chem 2010;82:8226–
to dietary GI and fibre intake in a nutritional metabolomic study of 34.
human urine. Genes Nutr 2012;7:281–93. 118. Guo B, Chen B, Liu AM, Zhu WT, Yao SZ. Liquid chromatography-
100. Johansson-Persson A, Barri T, Ulmius M, Onning G, Dragsted LO. mass spectrometric multiple reaction monitoring-based strategies for
LC-QTOF/MS metabolomic profiles in human plasma after a 5-week expanding targeted profiling towards quantitative metabolomics. Curr
high dietary fiber intake. Anal Bioanal Chem 2013;405:4799–809. Drug Metab 2012;13:1226–43.
101. Stanstrup J, Rasmussen J, Ritz C, Holmer-Jensen J, Hermansen K, 119. Katajamaa M, Oresic M. Data processing for mass spectrometry-
Dragsted L. Intakes of whey protein hydrolysate and whole whey based metabolomics. J Chromatogr A 2007;1158:318–28.
proteins are discriminated by LC-MS metabolomics. Metabolomics 120. Sugimoto M, Kawakami M, Robert M, Soga T, Tomita M. bio-
2013;Nov 17 (Epub ahead of print; DOI 10.1007/s11306-013-0607-9). informatics tools for mass spectroscopy-based metabolomic data
102. Stella C, Beckwith-Hall B, Cloarec O, Holmes E, Lindon JC, Powell processing and analysis. Current Bioinformatics 2012;7:96–108.
J, van der Ouderaa F, Bingham S, Cross AJ, Nicholson JK. Suscep- 121. Savorani F, Kristensen M, Larsen FH, Astrup A, Engelsen SB. High
tibility of human metabolic phenotypes to dietary modulation. throughput prediction of chylomicron triglycerides in human plasma
J Proteome Res 2006;5:2780–8. by nuclear magnetic resonance and chemometrics. Nutr Metab (Lond)
103. Bertram HC, Hoppe C, Petersen BO, Duus JO, Molgaard C, 2010;7:43.
Michaelsen KF. An NMR-based metabonomic investigation on effects 122. Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G. XCMS:
of milk and meat protein diets given to 8-year-old boys. Br J Nutr processing mass spectrometry data for metabolite profiling using
2007;97:758–63. nonlinear peak alignment, matching, and identification. Anal Chem
104. Xu J, Yang S, Cai S, Dong J, Li X, Chen Z. Identification of bio- 2006;78:779–87.
chemical changes in lactovegetarian urine using 1H NMR spectros- 123. Pluskal T, Castillo S, Villar-Briones A, Oresic M. MZmine 2: Mod-
copy and pattern recognition. Anal Bioanal Chem 2010;396:1451–63. ular framework for processing, visualizing, and analyzing mass
105. May DH, Navarro SL, Ruczinski I, Hogan J, Ogata Y, Schwarz Y, spectrometry-based molecular profile data. BMC Bioinformatics
Levy L, Holzman T, McIntosh MW, Lampe JW. Metabolomic pro- 2010;11:395.
filing of urine: response to a randomised, controlled feeding study of 124. Lommen A, Kools HJ. MetAlign 3.0: performance enhancement by
efficient use of advances in computer hardware. Metabolomics 2012;
select fruits and vegetables, and application to an observational study.
8:719–26.
Br J Nutr 2013;110:1760–70.
125. Gürdeniz G, Kristensen M, Skov T, Dragsted LO. The effect of LC-
106. Andersen MB, Rinnan A, Manach C, Poulsen SK, Pujos-Guillot E,
MS data preprocessing methods on the selection of plasma bio-
Larsen TM, Astrup A, Dragsted LO. Untargeted metabolomics as
markers in fed vs. fasted rats. Metabolites 2012;2:77–99.
a screening tool for estimating compliance to a dietary pattern. 126. Kristensen M, Engelsen SB, Dragsted LO. LC-MS metabolomics top-
J Proteome Res 2014;13:1405–18. down approach reveals new exposure and effect biomarkers of apple
107. Svensson BG, Akesson B, Nilsson A, Paulsson K. Urinary excretion and apple-pectin intake. Metabolomics 2012;8:64–73.
of methylamines in men with varying intake of fish from the Baltic 127. Worley B, Halouska S, Powers R. Utilities for quantifying separation
Sea. J Toxicol Environ Health 1994;41:411–20. in PCA/PLS-DA scores plots. Anal Biochem 2013;433:102–4.
108. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt 128. Acar E, Gurdeniz G, Rasmussen MA, Rago D, Dragsted LO, Bro R.
EB, Fu X, Wu Y, Li L, et al. Intestinal microbiota metabolism of Coupled matrix factorization with sparse factors to identify potential
l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med biomarkers in metabolomics. Int J Knowledge Discov Bioinformatics
2013;19:576–85. 2012;3:1–22.
109. Altmaier E, Kastenmuller G, Romisch-Margl W, Thorand B, Weinberger 129. Gürdeniz G, Hansen L, Rasmussen M, Acar E, Olsen A, Christensen
KM, Illig T, Adamski J, Doring A, Suhre K. Questionnaire-based self- J, Barri T, Tjønneland A, Dragsted L. Patterns of time since last meal
reported nutrition habits associate with serum metabolism as revealed by revealed by sparse PCA in an observational LC-MS based metab-
quantitative targeted metabolomics. Eur J Epidemiol 2011;26:145–56. olomics study. Metabolomics 2013;9:1073–81.
110. Sumner LW, Amberg A, Barrett D, Beale M, Beger R, Daykin C, Fan 130. Hanhineva K, Barri T, Kolehmainen M, Pekkinen J, Pihlajamaki J,
T, Fiehn O, Goodacre R, Griffin J, et al. Proposed minimum reporting Vesterbacka A, Solano-Aguilar G, Mykkanen H, Dragsted LO, Urban
standards for chemical analysis. Metabolomics 2007;3:211–21. JF Jr, et al. Comparative nontargeted profiling of metabolic changes in

on 16 July 2018
tissues and biofluids in high-fat diet-fed Ossabaw pig. J Proteome Res 153. Wolf S, Schmidt S, Muller-Hannemann M, Neumann S. In silico
2013;12:3980–92. fragmentation for computer assisted identification of metabolite mass
131. Kjeldahl K, Bro R. Some common misunderstandings in chemo- spectra. BMC Bioinformatics 2010;11:148.
metrics. J Chemometr 2010;24:558–64. 154. Rojas-Cherto M, Peironcely JE, Kasper PT, van der Hooft JJJ, De Vos
132. Wold S, Martens H, Wold H, Ruhe A, Kågstrøm B, eds. The multi- RCH, Vreeken RJ, Hankemeier T, Reijmers T. Metabolite identifi-
variate calibration problem in chemistry solved by the PLS methods. cation using automated comparison of high resolution MSn spectral
In: Ruhe A, Kågstrøm B, eds. Proceedings of the Conference on trees. Anal Chem 2012;84:5524–34.
Matrix Pencils, Lecture Notes in Mathematics. Heidelberg, Germany: 155. HighChem. Mass Frontier. Available from: http://www.highchem.
Springer Verlag, 1983:286–93. com/index.php/massfrontier (cited 3 September 2013).
133. Smilde AK, Jansen JJ, Hoefsloot HCJ, Lamers R, van der Greef J, 156. Gerlich M, Neumann S. MetFusion: integration of compound iden-
Timmerman ME. ANOVA-simultaneous component analysis (AS- tification strategies. J Mass Spectrom 2013;48:291–8.
CA): a new tool for analyzing designed metabolomics data. Bio- 157. Stanstrup J, Gerlich M, Dragsted LO, Neumann S. Metabolite pro-
informatics 2005;21:3043–8. filing and beyond: approaches for the rapid processing and annotation
134. Rago D, Mette K, Gürdeniz G, Marini F, Poulsen M, Dragsted L. A of human blood serum mass spectrometry data. Anal Bioanal Chem
LC-MS metabolomics approach to investigate the effect of raw apple 2013;405:5037–48.
intake in the rat plasma metabolome. Metabolomics 2013;9:1202–15. 158. Kuhl C, Tautenhahn R, Bottcher C, Larson TR, Neumann S. CAM-
135. van Velzen EJJ, Westerhuis JA, van Duynhoven JPM, van Dorsten FA, ERA: an integrated strategy for compound spectra extraction and
Hoefsloot HCJ, Jacobs DM, Smit S, Draijer R, Kroner CI, Smilde annotation of liquid chromatography/mass spectrometry data sets.
AK. Multilevel data analysis of a crossover designed human nutri- Anal Chem 2012;84:283–9.
tional intervention study. J Proteome Res 2008;7:4483–91. 159. Leibniz Institute of Plant Biochemistry. CAMERA annotation of LC/
136. Hochberg Y, Benjamini Y. More powerful procedures for multiple MS data. Available from: http://msbi.ipb-halle.de/msbi/CAMERA
significance testing. Stat Med 1990;9:811–8. (cited 3 September 2013).
137. Benjamini Y, Heller R, Yekutieli D. Selective inference in complex 160. Matsuda F, Nakabayashi R, Sawada Y, Suzuki M, Hirai MY, Kanaya
research. Philos Trans A Math Phys Eng Sci 2009;367:4255–71. S, Saito K. Mass spectra-based framework for automated structural
138. Xia J, Broadhurst D, Wilson M, Wishart D. Translational biomarker elucidation of metabolome data to explore phytochemical diversity.
discovery in clinical metabolomics: an introductory tutorial. Metab- Front Plant Sci 2011;2:40.
olomics 2013;9:280–99. 161. Stalmach A, Mullen W, Barron D, Uchida K, Yokota T, Cavin C,
139. Del Rio D, Rodriguez-Mateos A, Spencer JPE, Tognolini M, Borges Steiling H, Williamson G, Crozier A. Metabolite profiling of hy-
G, Crozier A. Dietary (poly)phenolics in human health: structures, droxycinnamate derivatives in plasma and urine after the ingestion of
bioavailability, and evidence of protective effects against chronic coffee by humans: identification of biomarkers of coffee consump-
diseases. Antioxid Redox Signal 2013;18:1818–92. tion. Drug Metab Dispos 2009;37:1749–58.
140. van der Hooft JJJ, Vos RCH, Ridder L, Vervoort J, Bino RJ. Structural 162. Ridder L, van der Hooft JJJ, Verhoeven S, De Vos RCH, Bino RJ,
elucidation of low abundant metabolites in complex sample matrices. Vervoort J. Automatic chemical structure annotation of an LC-MSn
Metabolomics 2013;9:1009–18. based metabolic profile from green tea. Anal Chem 2013;85:6033–40.
141. Wishart DS. Advances in metabolite identification. Bioanalysis 2011; 163. van der Hooft JJJ, de Vos RCH, Mihaleva V, Bino RJ, Ridder L, de
3:1769–82. Roo N, Jacobs DM, van Duynhoven JPM, Vervoort J. structural
142. Draper J, Enot DP, Parker D, Beckmann M, Snowdon S, Lin W, elucidation and quantification of phenolic conjugates present in hu-
Zubair H. Metabolite signal identification in accurate mass metab- man urine after tea intake. Anal Chem 2012;84:7263–71.
olomics data with MZedDB, an interactive m/z annotation tool uti- 164. Kirchmair J, Howlett A, Peironcely JE, Murrell DS, Williamson MJ,
lising predicted ionisation behaviour ’rules’. BMC Bioinformatics Adams SE, Hankemeier T, van Buren L, Duchateau G, Klaffke W,
2009;10:227. et al. How do metabolites differ from their parent molecules and how
143. Draper J, Lloyd A, Goodacre R, Beckmann M. Flow infusion electro- are they excreted? J Chem Inf Model 2013;53:354–67.
spray ionisation mass spectrometry for high throughput, non-targeted 165. Nicholson JK, Holmes E, Elliott P. The Metabolome-Wide Associa-
metabolite fingerprinting: a review. Metabolomics 2013;9:4–29. tion Study: a new look at human disease risk factors. J Proteome Res
144. van der Hooft JJJ, Vervoort J, Bino RJ, Beekwilder J, de Vos RCH. 2008;7:3637–8.
Polyphenol identification based on systematic and robust high-resolution 166. Bictash M, Ebbels TM, Chan Q, Loo RL, Yap IKS, Brown IJ, de Iorio
accurate mass spectrometry fragmentation. Anal Chem 2011;83: M, Daviglus ML, Holmes E, Stamler J, et al. Opening up the “black
409–16. box”: metabolic phenotyping and metabolome-wide association
145. Tikunov YM, Laptenok S, Hall RD, Bovy A, de Vos RCH. MSClust: studies in epidemiology. J Clin Epidemiol 2010;63:970–9.
a tool for unsupervised mass spectra extraction of chromatography-mass 167. Rappaport SM. Biomarkers intersect with the exposome. Biomarkers
spectrometry ion-wise aligned data. Metabolomics 2012;8:714–8. 2012;17:483–9.
146. Li L, Li R, Zhou J, Zuniga A, Stanislaus AE, Wu Y, Huan T, Zheng J, 168. Saadatian-Elahi M, Slimani N, Chajes V, Jenab M, Goudable J, Biessy
Shi Y, Wishart DS, et al. MyCompoundID: using an evidence-based C, Ferrari P, Byrnes G, Autier P, Peeters PHM, et al. Plasma phospho-
metabolome library for metabolite identification. Anal Chem 2013; lipid fatty acid profiles and their association with food intakes: results
85:3401–8. from a cross-sectional study within the European Prospective In-
147. Gong P, Cui N, Wu L, Liang Y, Hao K, Xu X, Tang W, Wang G, Hao vestigation into Cancer and Nutrition. Am J Clin Nutr 2009;89:331–46.
H. Chemicalome and metabolome matching approach to elucidating 169. Chajès V, Jenab M, Romieu I, Ferrari P, Dahm CC, Overvad K,
biological metabolic networks of complex mixtures. Anal Chem Egeberg R, Tjonneland A, Clavel-Chapelon F, Boutron-Ruault M-C,
2012;84:2995–3002. et al. Plasma phospholipid fatty acid concentrations and risk of gastric
148. Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF. In adenocarcinomas in the European Prospective Investigation into
silico enzymatic synthesis of a 400,000 compound biochemical database Cancer and Nutrition (EPIC-EURGAST). Am J Clin Nutr 2011;94:
for non-targeted metabolomics. J Chem Inf Model 2013;53:2483–92. 1304–13.
149. Tohge T, Fernie AR. Web-based resources for mass-spectrometry- 170. Nicholson JK, Holmes E, Wilson ID. Gut microorganisms, mamma-
based metabolomics: a user’s guide. Phytochemistry 2009;70:450–6. lian metabolism and personalized health care. Nat Rev Microbiol
150. Scalbert A, Andres-Lacueva C, Arita M, Kroon P, Manach C, Urpi-Sarda 2005;3:431–8.
M, Wishart D. Databases on food phytochemicals and their health 171. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, DuGar B,
promoting effects. J Agric Food Chem 2011;59:4331–48. Feldstein AE, Britt EB, Xiaoming F, Yoon-Mi C, et al. Gut flora
151. American Chemical Society. SciFinder. Available from: https:// metabolism of phosphatidylcholine promotes cardiovascular disease.
scifinder.cas.org (cited 3 September 2013). Nature 2011;472:57–63.
152. National Institutes of Standards and Technology. NIST 11 EPA/NIH 172. Tang WHW, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y,
Mass Spectral Database and Search Program (NIST11/NIST08). Hazen SL. Intestinal microbial metabolism of phosphatidylcholine
Available from: http://www.chemsw.com/Software-and-Solutions/ and cardiovascular risk. N Engl J Med 2013;368:1575–84.
Laboratory-Software/NIST-Mass-Spectral-Database/NIST-EPA-NIH- 173. Lee SM, Kwon GY, Kim K-O, Kim Y-S. Metabolomic approach for
Mass-Spectral-Database.aspx (cited 3 September 2013). determination of key volatile compounds related to beef flavor in

on 16 July 2018
1308 SCALBERT ET AL
glutathione-Maillard reaction products. Anal Chim Acta 2011;703: 185. Willett WC. Balancing life-style and genomics research for disease
204–11. prevention. Science 2002;296:695–8.
174. Mena P, Calani L, Dall’Asta C, Galaverna G, Garcia-Viguera C, Bruni 186. Smith GD, Ebrahim S. ’Mendelian randomization’: can genetic epi-
R, Crozier A, Del Rio D. Rapid and comprehensive evaluation of demiology contribute to understanding environmental determinants of
(poly)phenolic compounds in pomegranate (Punica granatum L.) disease? Int J Epidemiol 2003;32:1–22.
juice by UHPLC-MSn. Molecules 2012;17:14821–40. 187. Schroeter H, Heiss C, Balzer J, Kleinbongard P, Keen CL, Hollenberg
175. Moco S, Forshed J, De Vos RCH, Bino RJ, Vervoort J. Intra- and NK, Sies H, Kwik-Uribe C, Schmitz HH, Kelm M. (-)-Epicatechin
inter-metabolite correlation spectroscopy of tomato metabolomics mediates beneficial effects of flavanol-rich cocoa on vascular function
data obtained by liquid chromatography-mass spectrometry and nu- in humans. Proc Natl Acad Sci USA 2006;103:1024–9.
clear magnetic resonance. Metabolomics 2008;4:202–15. 188. Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison
176. Adhikari KB, Laursen BB, Laerke HN, Fomsgaard IS. bioactive N, Sumner L, Goodacre R, Hardy N, Taylor C, et al. The Metabolomics
benzoxazinoids in rye bread are absorbed and metabolized in pigs. Standards Initiative (MSI). Metabolomics 2007;3:175–8.
J Agric Food Chem 2012;60:2497–506. 189. Metabolomics Standards Initiative. Homepage. Available from: http://
177. Morand C, Dubray C, Milenkovic D, Lioger D, Martin JF, Scalbert A, msi-workgroups.sourceforge.net/ (cited 3 September 2013).
Mazur A. Hesperidin contributes to the vascular protective effects of 190. Metabolomics Forum. Homepage. Available from: http://metabolomics-
orange juice: a randomized crossover study in healthy volunteers. Am forum.com (cited 3 September 2013).
J Clin Nutr 2011;93:73–80. 191. NIH. ClinicalTrials.gov. Available from: www.ClinicalTrials.gov (cited
178. Lan K, Xie G, Jia W. Towards polypharmacokinetics: pharmacoki- 3 September 2013).
netics of multicomponent drugs and herbal medicines using a metab- 192. T’Jollyn H, Boussery K, Mortishire-Smith RJ, Coe K, De Boeck B, Van
Bocxlaer JF, Mannens G. Evaluation of three state-of-the-art metabolite
olomics approach. Evid Based Complement Alternat Med 2013;2013:
prediction software packages (Meteor, MetaSite, and StarDrop) through
819147.
independent and synergistic use. Drug Metab Dispos 2011;39:2066–75.
179. Johnson CH, Slanar O, Krausz KW, Kang DW, Patterson AD,
193. Piechota P, Cronin MTD, Hewitt M, Madden JC. pragmatic ap-
Kim J-H, Luecke H, Gonzalez FJ, Idle JR. Novel metabolites and
proaches to using computational methods to predict xenobiotic me-
roles for alpha-tocopherol in humans and mice discovered by mass tabolism. J Chem Inf Model 2013;53:1282–93.
spectrometry-based metabolomics. Am J Clin Nutr 2012;96:818–30. 194. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ,
180. Suhre K, Shin S-Y, Petersen A-K, Mohney RP, Meredith D, Waegele Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2013;41:D36–42.
B, Altmaier E, Deloukas P, Erdmann J, Grundberg E, et al. Human 195. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky
metabolic individuality in biomedical and pharmaceutical research. M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al. NCBI
Nature 2011;477:54–60. GEO: archive for functional genomics data sets—update. Nucleic
181. Illig T, Gieger C, Zhai GJ, Romisch-Margl W, Wang-Sattler R, Prehn C, Acids Res 2013;41:D991–5.
Altmaier E, Kastenmuller G, Kato BS, Mewes HW, et al. A genome- 196. Riffle M, Eng JK. Proteomics data repositories. Proteomics 2009;9:
wide perspective of genetic variation in human metabolism. Nat Genet 4653–63.
2010;42:137–41. 197. Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M,
182. Kettunen J, Tukiainen T, Sarin A-P, Ortega-Alonso A, Tikkanen E, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, et al.
Lyytikainen L-P, Kangas AJ, Soininen P, Wuertz P, Silander K, et al. MetaboLights—an open-access general-purpose repository for me-
Genome-wide association study identifies multiple loci influencing tabolomics studies and associated meta-data. Nucleic Acids Res 2013;
human serum metabolite levels. Nat Genet 2012;44:269–76. 41:D781–6.
183. Lampe JW. Interindividual differences in response to plant-based 198. van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R, de
diets: implications for cancer risk. Am J Clin Nutr 2009;89:1553S–7S. Groot P, Kaput J, Mathers JC, Muller M, Pepping F, et al. Challenges
184. Reszka E, Wasowicz W, Gromadzinska J. Genetic polymorphism of of molecular nutrition research 6: the nutritional phenotype database
xenobiotic metabolising enzymes, diet and cancer susceptibility. Br J to store, share and evaluate nutritional systems biology studies. Genes
Nutr 2006;96:609–19. Nutr 2010;5:189–203.

on 16 July 2018

Food Metabolome Review

Uploaded by

Copyright:

Available Formats

Food Metabolome Review

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Food Metabolome Review

Uploaded by

Copyright:

Available Formats

Narrative Review

The food metabolome: a window over dietary exposure1–3

ABSTRACT Although classical hypothesis-driven approaches have been

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

FIGURE 1. The human metabolomes. sp., species.

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

HMDB Endogenous, microbial, biotransformed, and exogenous/ .40,000 www.hmdb.ca (9)

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Fruit, fruit juices

by Universidade de São Paulo - IO user

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

control sulforaphane N-cysteine,* N-acetyl-S-(N-3-methylthiopropyl)cysteine,*

Dietary factor and No. of Dietary assessment Analytic

by Universidade de São Paulo - IO user

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Dietary factor and No. of Dietary assessment Analytic

Mixed red wine/grape

by Universidade de São Paulo - IO user

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Dietary factor and No. of Dietary assessment Analytic

by Universidade de São Paulo - IO user

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

equol,* glycitein,* O-desmethylangolensin,* enterolactone,* trigonelline*

Sulforaphane,* proline betaine,* hippuric acid,* genistein,* daidzein,*

(2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid, 3,4,5,6-tetrahydrohippurate*

Trimethylamine-N-oxide, hydroquinone-glucuronide, hippuric acid,

and quantitative but has a relatively low sensitivity, which narrows

metabolites of the food metabolome occurring at low concen-

derivatization has been used to analyze constituents of the food

been performed by using high-resolution liquid chromatography-

compounds such as terpene metabolites, diketopiperazine me-

tabolites, phenylvalerolactones, and benzoxazinoid metabolites,

which are interesting candidate biomarkers of food intake that

would not be easily detected in biofluids by NMR or GC-MS

compounds. Highly polar compounds may have to be analyzed

by using hydrophilic interaction chromatography, whereas spe-

fers the advantage of high-throughput analysis, as would be

suppression effects, due to inefficient ionization of certain ions

in complex matrices and the inability to discriminate between

The main current limitation of MS is the very challenging and

(see below). However, because of its sensitivity and breadth of

coverage, LC-MS has certainly become the method of choice for

untargeted analysis of the food metabolome. Rapid advances in

time-of-flight and single-stage Orbitrap (Exactive; Thermo Sci-

mass accuracy, which will be critically important for the analysis

of the food metabolome (115). As with any experimentally based

final data set. These include the mode of sample preparation,

method of chromatography, mode of detection, and the choice of

data reduction methods (116, 117). No standardized method

exists yet, and the need for improved harmonization is certainly

desirable for further progress on the food metabolome.

Achieving absolute quantification rather than relative quantifi-

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352

Downloaded from https://academic.oup.com/ajcn/article-abstract/99/6/1286/4577352