The DOI matches its Crossref record; 193 of the 198 references it cites were found in a registry or an index; 5 of the 159 sources its claims cite were checked for support.
The food metabolome: a window over dietary exposure
Open accessAbstract
The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food compositions by using hypothesis-driven approaches. However, the rapid development of metabolomics resulting from the development of highly sensitive modern analytic instruments, the availability of metabolite databases, and progress in (bio)informatics has made agnostic approaches more attractive as shown by the recent identification of novel biomarkers of intakes for fruit, vegetables, beverages, meats, or complex diets. Moreover, examples also show how the scrutiny of the food metabolome can lead to the discovery of bioactive molecules and dietary factors associated with diseases. However, researchers still face hurdles, which slow progress and need to be resolved to bring this emerging field of research to maturity. These limits were discussed during the First International Workshop on the Food Metabolome held in Glasgow. Key recommendations made during the workshop included more coordination of efforts; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health.
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Claims the paper makes
96 Not checked yet · 43 Own interpretation · 20 No basis given · 3 Partly supported · 1 Supported so far · accuracy not yet measured
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In the paper
“Consequently, weaker correlations with intakes of foods or of their constituents were observed for microbial metabolites when compared with untransformed food compounds and host-transformed metabolites (41).”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
What the sources say
- Partly supportedcites [41] Pérez-Jiménez, 2010, Urinary metabolites as biomarkers of polyphenol intake in humans—a systematic review, Am J Clin Nutr sourceExperimental — accuracy not yet measured
The discussion (section 15; page not provided) reports weaker intake correlations for three microbial metabolites of daidzein than for daidzein itself. It does not establish the broader comparison for microbial metabolites generally versus both untransformed compounds and host-transformed metabolites; the same section identifies enterolactone, a microbial metabolite, as a good biomarker. (LLM, conf=0.87)
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In the paper
“As an example, the recent description of benzoxazinoids in rye facilitated the identification of some of their metabolites (2,4-dihydroxy-1,4-benzoxazin-3-one, 2-aminophenol sulfate, and hydroxylated phenylacetamides) in urinary metabolic profiles observed after rye bread consumption (86,114).”
§ The food metabolome: a window over dietary exposure 1-3 > Identification of new potentially bioactive food-derived metabolites
What the sources say
- Not checked yetcites [86] Bondia-Pons, 2013, UPLC-QTOF/MS metabolic profiling unveils urinary changes in humans after a whole grain rye versus refined wheat bread intervention, Mol Nutr Food Res source
- Partly supportedcites [114] Beckmann, 2013, Hydroxylated phenylacetamides derived from bioactive benzoxazinoids are bioavailable in humans after habitual consumption of whole grain sourdough rye bread, Mol Nutr Food Res sourceExperimental — accuracy not yet measured
Section 3.3 and the Figure 5 legend identify hydroxylated phenylacetamide conjugates in urine after wholegrain sourdough rye bread consumption. The Figure 6 legend places DIBOA conjugates in rye flour and bread, not the reported urine profiles; section 3.3 identifies a 2-aminophenol fragment of HPAA sulfate, not urinary 2-aminophenol sulfate. The paper therefore supports the phenylacetamide part of the list, but not the other two compounds as identified urinary metabolites. (LLM, conf=0.89)
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In the paper
“Information on these biomarkers has been systematically collected in the novel Exposome-Explorer database (V Neveu, DS Wishart, and A Scalbert, unpublished data, 2014); w100 biomarkers could be identified”
§ The food metabolome: a window over dietary exposure 1-3 > Dietary biomarkers measured in population studies
What the sources say
- Not checked yetcites V Neveu, DS Wishart, and A Scalbert, unpublished data, 2014
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“With the exception of 2 studies on dietary fiber and milk protein diet, all discovery studies were conducted on urine samples as opposed to blood samples (Table 3).”
§ The food metabolome: a window over dietary exposure 1-3 > Novel dietary biomarkers identified through a metabolomic approach
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In the paper
“alkylresorcinols for whole-grain cereals (19,20)”
§ The food metabolome: a window over dietary exposure 1-3 > Dietary biomarkers measured in population studies
What the sources say
- Not checked yetcites [19] Ross, 2012, Plasma alkylresorcinols as a biomarker of whole-grain food consumption in a large population: results from the WHOLEheart Intervention Study, Am J Clin Nutr source
- Not checked yetcites [20] Andersson, 2011, Plasma alkylresorcinol concentrations correlate with whole grain wheat and rye intake and show moderate reproducibility over a 2-to 3-month period in free-living Swedish adults, J Nutr source
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In the paper
“Dietary exposure has traditionally been measured with self-reported methods, namely dietary recalls or food-frequency questionnaires (10).”
§ The food metabolome: a window over dietary exposure 1-3 > DIETARY BIOMARKERS IN THE PRE-OMICS ERA
What the sources say
- Not checked yetcites [10] Rutishauser, 2005, Dietary intake measurements, Public Health Nutr source
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In the paper
“Biomarkers are also useful when little or no data exist on food composition, as is often the case for bioactive molecules such as glucosinolates or food contaminants such as aflatoxins (15,16).”
§ The food metabolome: a window over dietary exposure 1-3 > DIETARY BIOMARKERS IN THE PRE-OMICS ERA
What the sources say
- Not checked yetcites [15] London, 2000, Isothiocyanates, glutathione S-transferase M1 and T1 polymorphisms, and lung-cancer risk: a prospective study of men in Shanghai, China, Lancet source
- Not checked yetcites [16] Kensler, 2011, Aflatoxin: a 50-year odyssey of mechanistic and translational toxicology, Toxicol Sci source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The application of dietary biomarkers as more objective measures of dietary exposure in nutritional epidemiology has been particularly significant (13).”
§ The food metabolome: a window over dietary exposure 1-3 > DIETARY BIOMARKERS IN THE PRE-OMICS ERA
What the sources say
- Not checked yetcites [13] Jenab, 2009, Biomarkers in nutritional epidemiology: applications, needs and new horizons, Hum Genet source
plain- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“polyphenols, carotenoids, and vitamin C for fruit and vegetables (17,18)”
§ The food metabolome: a window over dietary exposure 1-3 > Dietary biomarkers measured in population studies
What the sources say
- Not checked yetcites [17] Baldrick, 2011, Biomarkers of fruit and vegetable intake in human intervention studies: a systematic review, Crit Rev Food Sci Nutr source
- Not checked yetcites [18] Mennen, 2006, Urinary flavonoids and phenolic acids as biomarkers of intake for polyphenol-rich foods, Br J Nutr source
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These biomarkers may thus be useful only in populations who regularly and frequently consume these dietary sources.”
§ The food metabolome: a window over dietary exposure 1-3 > Pharmacokinetics and reliability of dietary biomarkers
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- It may state two separate claims as one. 48
- Probably not a substantial claim. 32
- The quote only partly states this claim. 1
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In the paper
“Biomarkers such as vitamin C or selenium in erythrocyte glutathione peroxidase show saturable effects and may not be suitable for use at high levels of exposure (29,42).”
§ The food metabolome: a window over dietary exposure 1-3 > Biomarker sensitivity and specificity
What the sources say
- Partly supportedcites [29] Crews, 2001, A critical assessment of some biomarker approaches linked with dietary intake, Br J Nutr sourceExperimental — accuracy not yet measured
The Selenium section (3.2; page unavailable) says erythrocyte glutathione peroxidase activity plateaus above certain selenium concentrations, limiting its sensitivity at higher exposure. The passages found on vitamin C do not establish a comparable saturable effect, so that part of the claim is unsupported by this source. (LLM, conf=0.84)
- Supportedcites [42] Levine, 1996, Vitamin C pharmacokinetics in healthy volunteers: evidence for a recommended dietary allowance, Proc Natl Acad Sci USA source
The study summary (page not provided) reports that vitamin C plasma concentrations plateaued, reaching complete saturation at 1000 mg daily. That supports the citing sentence’s qualified point that vitamin C may be unsuitable as a biomarker at high exposure levels. This citation supports the vitamin C example; the sentence also cites a separate source for selenium. (LLM, conf=0.86)
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It may state two separate claims as one.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“These include the mode of sample preparation, method of chromatography, mode of detection, and the choice of data reduction methods (116, 117).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
What the sources say
- Not checked yetcites [116] Barri, 2012, Metabolic fingerprinting of high-fat plasma samples processed by centrifugation- and filtration-based protein precipitation delineates significant differences in metabolite information coverage, Anal Chim Acta source
- Supportedcites [117] Gika, 2010, Does the mass spectrometer define the marker? A comparison of global metabolite profiling data generated simultaneously via UPLC-MS on two different mass spectrometers, Anal Chem source
The Introduction identifies sample preparation, instrumentation, and data processing as factors that complicate comparisons between metabolomic datasets. The Conclusions likewise discuss results obtained with the same sample processing and chromatography, and state that the mass spectrometer and data-processing software can influence the outcome. Together, these passages support the cited sentence as a broad statement about methodological choices affecting the final dataset. (LLM, conf=0.85)
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In the paper
“It is important to point out that the identities of many of the proposed biomarkers in Table 3 (marked with an asterisk) have not been fully validated with proper chemical standards because these standards are often not commercially available.”
§ The food metabolome: a window over dietary exposure 1-3 > Novel dietary biomarkers identified through a metabolomic approach
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In the paper
“The resulting misclassification of subjects, especially when sorting them according to dietary intake, can influence observed associations between dietary exposures and disease outcomes and underlies inconsistencies in published findings in the field of nutritional epidemiology (12).”
§ The food metabolome: a window over dietary exposure 1-3 > DIETARY BIOMARKERS IN THE PRE-OMICS ERA
What the sources say
- Not checked yetcites [12] Marshall, 1999, Diet and health risk: risk patterns and disease-specific associations, Am J Clin Nutr source
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The food metabolome is therefore highly complex and also highly variable.”
§ The food metabolome: a window over dietary exposure 1-3 > INTRODUCTION
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In the paper
“The various foods consumed by humans contain .25,000compounds, most of them being further metabolized in the human body (9).”
§ The food metabolome: a window over dietary exposure 1-3 > INTRODUCTION
What the sources say
- Not checked yetcites [9] Wishart, 2013, HMDB 3.0—the Human Metabolome Database in 2013, Nucleic Acids Res
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“However, a number of random and systematic errors are inherent in such methods, including recall bias and difficulty in assessing portion sizes (11).”
§ The food metabolome: a window over dietary exposure 1-3 > DIETARY BIOMARKERS IN THE PRE-OMICS ERA
What the sources say
- Not checked yetcites [11] Bingham, 2007, Epidemiologic assessment of sugars consumption using biomarkers: comparisons of obese and nonobese individuals in the European Prospective Investigation of Cancer Norfolk, Cancer Epidemiol Biomarkers Prev source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Some dietary compounds such as isothiocyanates and acrylamide also form adducts with blood albumin and hemoglobin (37,38), with half-lives varying between 3 and 8 wk, and may be used as longer-term biomarkers.”
§ The food metabolome: a window over dietary exposure 1-3 > Pharmacokinetics and reliability of dietary biomarkers
What the sources say
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Up to 200,000 different metabolites are estimated to occur in the plant kingdom, and combinations of several hundreds of secondary metabolites generally characterize each edible plant (6,64,65).”
§ The food metabolome: a window over dietary exposure 1-3 > The food metabolome as part of the human metabolome
What the sources say
- Not checked yetcites [6] Manach, 2009, The complex links between dietary phytochemicals and human health deciphered by metabolomics, Mol Nutr Food Res source
- Not checked yetcites [64] Fiehn, 2002, Metabolomics—the link between genotypes and phenotypes, Plant Mol Biol source
- Not checked yetcites [65] Iijima, 2008, Metabolite annotations based on the integration of mass spectral information, Plant J source
hedged- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
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In the paper
“Proline betaine and lycopene are well-established biomarkers for citrus fruit and tomato products, respectively (44,45).”
§ The food metabolome: a window over dietary exposure 1-3 > Biomarker sensitivity and specificity
What the sources say
- Not checked yetcites [44] Lloyd, 2011, Proline betaine and its biotransformation products in fasting urine samples are potential biomarkers of habitual citrus fruit consumption, Br J Nutr source
- Not checked yetcites [45] Al-Delaimy, 2005, Plasma carotenoids as biomarkers of intake of fruits and vegetables: individual-level correlations in the European Prospective Investigation into Cancer and Nutrition (EPIC), Eur J Clin Nutr source
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In the paper
“The possible exceptions are the essential amino acids, essential fatty acids along with most vitamins, and minerals, which cannot be produced by humans and must originate from external dietary sources.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Most of these compounds are common to all living organisms and identical to human endogenous metabolites.They cannot generally be used as dietary biomarkers because of their common identity and the impossibility to trace their dietary origin.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
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In the paper
“The Folin assay, commonly used to estimate total polyphenols in foods (46), has also been applied to urine samples to compare polyphenol intake (47), but such use may be inappropriate because of the presence of interfering reducing metabolites in such complex biological matrices (46).”
§ The food metabolome: a window over dietary exposure 1-3 > Single biomarker or combinations of biomarkers
What the sources say
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“In fact, there are .300different empirical rules that allow one to predict the fate of metabolites on the basis of their chemical structure (69).”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
What the sources say
- Not checked yetcites [69] Langowski, 2002, Computer systems for the prediction of xenobiotic metabolism, Adv Drug Deliv Rev source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Lipophilic markers (carotenoids, lipids) (36) or biomarkers associated with erythrocytes (folate, fatty acids) (29) have longer half-lives (week to month) because of the equilibrium of biomarkers between blood and fatty tissues, or because of their integration into erythrocytes.”
§ The food metabolome: a window over dietary exposure 1-3 > Pharmacokinetics and reliability of dietary biomarkers
What the sources say
- Not checked yetcites [36] Burri, 2001, Serum carotenoid depletion follows first-order kinetics in healthy adult women fed naturally low carotenoid diets, J Nutr source
- Not checked yetcites [29] Crews, 2001, A critical assessment of some biomarker approaches linked with dietary intake, Br J Nutr source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Dietary biomarkers not only include natural food constituents but also certain food additives such as iodine in milk (26) or food contaminants such as polychlorinated biphenyls in fatty fish (27).”
§ The food metabolome: a window over dietary exposure 1-3 > Dietary biomarkers measured in population studies
What the sources say
- Not checked yetcites [26] Brantsaeter, 2009, Evaluation of urinary iodine excretion as a biomarker for intake of milk and dairy products in pregnant women in the Norwegian Mother and Child Cohort Study (MoBa), Eur J Clin Nutr source
- Not checked yetcites [27] Turunen, 2010, Dioxins, polychlorinated biphenyls, methyl mercury and omega-3 polyunsaturated fatty acids as biomarkers of fish consumption, Eur J Clin Nutr source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“These microbial metabolites include short-chain fatty acids, secondary bile acids, protein and amino acid metabolites, as well as plant polyphenol metabolites (67).”
§ The food metabolome: a window over dietary exposure 1-3 > The food metabolome as part of the human metabolome
What the sources say
- Not checked yetcites [67] Nicholson, 2012, Host-gut microbiota metabolic interactions, Science source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Some of the biomarkers listed in Table 1 have half-lives that do not exceed 24 h [polyphenols, alkylresorcinols, and amino acids (34,35)].”
§ The food metabolome: a window over dietary exposure 1-3 > Pharmacokinetics and reliability of dietary biomarkers
What the sources say
- Not checked yetcites [34] Manach, 2005, Bioavailability and bioefficacy of polyphenols in humans. I. Review of 97 bioavailability studies, Am J Clin Nutr source
- Not checked yetcites [35] Söderholm, 2009, Plasma pharmacokinetics of alkylresorcinol metabolites: new candidate biomarkers for whole-grain rye and wheat intake, Am J Clin Nutr source
hedged- Asserted: passes — The authors put it forward as true.
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In the paper
“noticeable differences in human metabolomes could be detected that appeared to depend strongly on diet, sex, health status, genetics, kinetics, physiology, and age-with diet being most important (59)(60)(61)(62).”
§ The food metabolome: a window over dietary exposure 1-3 > The food metabolome as part of the human metabolome
What the sources say
- Not checked yetcites (59)(60)(61)(62)
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The yield of phase I/II reactions are often very high (68,71), and host-transformed metabolites retain many of the features of their parent compounds.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
What the sources say
- Not checked yetcites [68] Testa, 2012, Foundation review: reactions and enzymes in the metabolism of drugs and other xenobiotics, Drug Discov Today source
- Not checked yetcites [71] Silberberg, 2006, The bioavailability of polyphenols is highly governed by the capacity of the intestine and of the liver to secrete conjugated metabolites, Eur J Nutr source
plain- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The human body maintains a complex defense system consisting of dozens of enzymes and membrane transporters to recognize these foreign and potentially toxic chemicals and to neutralize them by rapid biotransformation and/or elimination.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Food compounds that are not useful for basic metabolism or that do not correspond to familiar endogenous metabolites are treated as”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Food constituents can be metabolized in 3 different ways: 1) they can be digested in the mouth, stomach, and small intestine into simple nutrients that can be absorbed through the gut barrier; 2) they can be further transformed by host tissues, especially the liver and kidney; or 3) they can be processed by the gut microbiota in the large intestine.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
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In the paper
“Classically, the biotransformation process consists of 2 types of chemical reactions, phase I and phase II transformations, both of which occur primarily in the liver, kidney, and intestine.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Microbes have a very different set of enzymes from mammals, and given that there are .1000different species of microbes in the human gut (72) there is an enormous diversity of enzymatic processes that act on foodderived compounds.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
What the sources say
- Not checked yetcites [72] Peris-Bondia, 2011, The active human gut microbiota differs from the total microbiota, PLoS ONE source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Minimally, the human metabolome contains 50,000 different detectable compounds (9,63), but as instrument sensitivity and separation technologies improve, this number is expected to increase.”
§ The food metabolome: a window over dietary exposure 1-3 > The food metabolome as part of the human metabolome
What the sources say
- Not checked yetcites [9] Wishart, 2013, HMDB 3.0—the Human Metabolome Database in 2013, Nucleic Acids Res
- Not checked yetcites [63] Smith, 2005, METLIN—a metabolite mass spectral database, Ther Drug Monit source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“They may be altered because of possible interactions with genetic factors, physiologic or health status (ie, age or obesity) (30), dietary factors such as fats for lipophilic biomarkers (31), and lifestyle factors such as alcohol intake or smoking (32).”
§ The food metabolome: a window over dietary exposure 1-3 > Pharmacokinetics and reliability of dietary biomarkers
What the sources say
- Not checked yetcites [30] Vioque, 2007, Plasma concentrations of carotenoids and vitamin C are better correlated with dietary intake in normal weight than overweight and obese elderly subjects, Br J Nutr source
- Not checked yetcites [31] Brown, 2004, Carotenoid bioavailability is higher from salads ingested with full-fat than with fat-reduced salad dressings as measured with electrochemical detection, Am J Clin Nutr source
- Not checked yetcites [32] Albanes, 1997, Effects of supplemental beta-carotene, cigarette smoking, and alcohol consumption on serum carotenoids in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study, Am J Clin Nutr source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In explorative science there is no fixed rule for the acceptability level of the FDR, and any level from 5% to 50% may be useful, depending on further data analysis steps.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Metabolite identification in metabolomic studies relies on the comparison of generated spectra with those in curated metabolite databases.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolite identification
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The gut microbiota also processes indigestible carbohydrates through a variety of fermentative pathways yielding short-chain fatty acids such as butyric acid and propionic acid.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As with any experimentally based analytic method, multiple variables can substantially affect the final data set.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In principle, untargeted metabolomics provides a wider coverage and is likely to show the presence of new metabolites in biofluids and tissues.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“These phenolic acids can be further conjugated to glycine as in hippurate.”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Briefly, NMR is robust, nondestructive, 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 micromolar concentrations.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
What the sources say
- Not checked yetcites [111] Theodoridis, 2008, LC-MS-based methodology for global metabolite profiling in metabonomics/metabolomics, Trends Analyt Chem source
- Not checked yetcites [112] Scalbert, 2009, Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research, Metabolomics source
- Not checked yetcites [113] Issaq, 2009, Analytical and statistical approaches to metabolomics research, J Sep Sci source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Supervised multivariate analysis is commonly the next step in many data analysis methods but has a strong tendency to overfit the data.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“There are a large number of supervised methods (120, 127), with the most commonly used analysis for comparing 2 groups being partial least-squares discriminant analysis (PLS-DA) (132) or one of its several variants.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
What the sources say
- Not checked yetcites [120] Sugimoto, 2012, bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis, Current Bioinformatics source
- Not checked yetcites [127] Worley, 2013, Utilities for quantifying separation in PCA/PLS-DA scores plots, Anal Biochem source
- Not checked yetcites [132] Wold, 1983, The multivariate calibration problem in chemistry solved by the PLS methods source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It is crucial to align the different sample profiles, which do not match exactly because of small variations in retention times, masses, or chemical shifts.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“These include data preprocessing, data alignment, data normalization, and signal correction followed by the analysis through various statistical methods.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
What the sources say
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The features associated with any pattern can be shown by the loadings in a PCA plot; however, PCA is generally not well suited to identify the most prominent part of the pattern.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Certain microbial metabolites can be useful as food biomarkers, although there is a complex relation between the food source, the predominant gut microbial species, and the resulting food metabolites (73).”
§ The food metabolome: a window over dietary exposure 1-3 > Metabolism of food constituents
What the sources say
- Not checked yetcites [73] Moco, 2012, A metabolomics view on gut microbiome modulation by polyphenol-rich foods, J Proteome Res source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“First, it comprises a much greater chemical diversity than any other part of the metabolome (see Food metabolome and metabolite databases section).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The main current limitation of MS is the very challenging and burdensome task of the structural elucidation of the detected ions (see below).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Direct flow injection-MS has also been used (82,114), which offers the advantage of high-throughput analysis, as would be required for large-scale epidemiologic studies.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
What the sources say
- Not checked yetcites [82] Lloyd, 2011, Use of mass spectrometry fingerprinting to identify urinary metabolites after consumption of specific foods, Am J Clin Nutr source
- Not checked yetcites [114] Beckmann, 2013, Hydroxylated phenylacetamides derived from bioactive benzoxazinoids are bioavailable in humans after habitual consumption of whole grain sourdough rye bread, Mol Nutr Food Res source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MS is by far the most sensitive technique and the only method able to cover the nonnutrient metabolites of the food metabolome occurring at low concentrations in biological samples.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Overall, the field of metabolomics is rich with data analysis options, and the challenge in the future will be to optimally apply these to food metabolomic studies.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“The use of food-frequency questionnaires may directly lead to the identification of biomarkers of habitual dietary exposure, but the lower accuracy and lower number of foods documented may limit their value for such discovery studies (105).”
§ The food metabolome: a window over dietary exposure 1-3 > Novel dietary biomarkers identified through a metabolomic approach
What the sources say
- Not checked yetcites [105] May, 2013, Metabolomic profiling of urine: response to a randomised, controlled feeding study of select fruits and vegetables, and application to an observational study, Br J Nutr source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The reason for this is partly technical because of the higher concentrations of food-derived metabolites in urine as compared with blood and because of the lack of interfering proteins.”
§ The food metabolome: a window over dietary exposure 1-3 > Novel dietary biomarkers identified through a metabolomic approach
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This provides an objective assessment of the principal patterns in the data set (eg, intake or no intake of a specific food component or diet).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Statistical analysis of untargeted metabolomic data is often an initial step in the biomarker discovery process that should not be confused with hypothesis testing, because there is no a priori hypothesis.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The metabolic profile of raw data generated by the spectrometric analysis of biological samples can be analyzed in several steps (119, 120).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
What the sources say
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, ion suppression effects, due to inefficient ionization of certain ions in complex matrices and the inability to discriminate between isomers, limit the use of this approach.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of the food metabolome
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Multivariate analysis is most commonly used for explorative analysis of metabolic profiling data (127).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
What the sources say
- Not checked yetcites [127] Worley, 2013, Utilities for quantifying separation in PCA/PLS-DA scores plots, Anal Biochem source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In cross-sectional studies this large contrast seldom applies, but approximate dose-response relations from food-frequency questionnaires may help in the identification of food intake biomarkers.”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In dietary intervention studies with single foods, the contrast observed for a good biomarker can be large, sometimes even infinite, making it possible to work robustly with small sample sets and discriminate potential intake biomarkers from more subtle changes in endogenous metabolites (126).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
What the sources say
- Not checked yetcites [126] Kristensen, 2012, LC-MS metabolomics top-down approach reveals new exposure and effect biomarkers of apple and apple-pectin intake, Metabolomics source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“As opposed to univariate analysis, multivariate analysis can be performed in an unsupervised manner (ie, without including information on group assignment for the analysis).”
§ The food metabolome: a window over dietary exposure 1-3 > Analysis of metabolomic data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“All of these discriminatory biomarkers point to dietary sources, sometimes in combination with cometabolism by gut microbiota.”
§ The food metabolome: a window over dietary exposure 1-3 > Discovering disease-related dietary factors
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: Alanine is associated with diets that emphasize animal products rather than vegetables.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although they are not specific to the food metabolome, these resources are useful for metabolite identification because fragmentation data or NMR signals of known metabolites can be compared with the unknown query to gain structural information.”
§ The food metabolome: a window over dietary exposure 1-3 > Spectral databases for the food metabolome
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“In fact, MWASs can be regarded as a special case of the exposome-wide association study, which investigates disease associations with all exposures to low-and high-molecular-weight compounds (167).”
§ The food metabolome: a window over dietary exposure 1-3 > Discovering disease-related dietary factors
What the sources say
- Not checked yetcites [167] Rappaport, 2012, Biomarkers intersect with the exposome, Biomarkers source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Recently, a large number of 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 useful for food metabolite identification.”
§ The food metabolome: a window over dietary exposure 1-3 > Spectral databases for the food metabolome
What the sources say
- Not checked yetcites [9] Wishart, 2013, HMDB 3.0—the Human Metabolome Database in 2013, Nucleic Acids Res
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The alternative untargeted approach makes no a priori assumptions regarding sources of exposure that are causal for a particular disease but instead relies on comparisons of comprehensive profiles of metabolomic features between cases and controls to find discriminating exposure biomarkers.”
§ The food metabolome: a window over dietary exposure 1-3 > Discovering disease-related dietary factors
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“biomarkers were identified, namely alanine, which was directly correlated with blood pressure, and formate and hippurate, both of which were inversely correlated with blood pressure.”
§ The food metabolome: a window over dietary exposure 1-3 > Discovering disease-related dietary factors
What the sources say
- Not checked yetcites [59] Holmes, 2008, Human metabolic phenotype diversity and its association with diet and blood pressure, Nature source
- Not checked yetcites [166] Bictash, 2010, Opening up the “black box”: metabolic phenotyping and metabolome-wide association studies in epidemiology, J Clin Epidemiol source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one. The quote only partly states this claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These associations were tentatively explained by either different amounts of dietary intake or differential fatty acid metabolism in cases and controls.”
§ The food metabolome: a window over dietary exposure 1-3 > Discovering disease-related dietary factors
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“The most comprehensive and best-curated chemical (commercial) database is currently SciFinder, which includes many food metabolome compounds collected from the literature (151).”
§ The food metabolome: a window over dietary exposure 1-3 > Spectral databases for the food metabolome
What the sources say
- Not checked yetcites [151] American Chemical Society. SciFinder. Available from: https://scifinder.cas.org (cited 3 September 2013).
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The human metabolome database has recently expanded to include compounds found in common foods because these are, at least initially before metabolism, also present within the human body (9).”
§ The food metabolome: a window over dietary exposure 1-3 > Databases
What the sources say
- Not checked yetcites [9] Wishart, 2013, HMDB 3.0—the Human Metabolome Database in 2013, Nucleic Acids Res
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“A number of loci associated with variations in the concentration of endogenous metabolites could be identified in genome-wide analysis studies, and many of these genes were coding for metabolic enzymes (180-182).”
§ The food metabolome: a window over dietary exposure 1-3 > Identification of new potentially bioactive food-derived metabolites
What the sources say
- Not checked yetcites [180] Suhre, 2011, Human metabolic individuality in biomedical and pharmaceutical research, Nature source
- Not checked yetcites [181] Illig, 2010, A genome-wide perspective of genetic variation in human metabolism, Nat Genet source
- Not checked yetcites [182] Kettunen, 2012, Genome-wide association study identifies multiple loci influencing human serum metabolite levels, Nat Genet source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The Metabolomics Standards Initiative (MSI) launched by the Metabolomics Society is an example of such an initiative, and the MSI has already had significant impact on reporting formats in metabolomics (110, 188).”
§ The food metabolome: a window over dietary exposure 1-3 > NETWORKING AND RECOMMENDATIONS TO MOVE THE FIELD FORWARD
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For example, many studies have been conducted with oranges (Table 3), but a broad coverage of all citrus and many other fruit as well as kinetic studies have been necessary to interpret proline betaine as a short-term marker of citrus that is dominated by orange and orange juice intake (80).”
§ The food metabolome: a window over dietary exposure 1-3 > Coordination of dietary studies
What the sources say
- Not checked yetcites [80] Heinzmann, 2010, Metabolic profiling strategy for discovery of nutritional biomarkers: proline betaine as a marker of citrus consumption, Am J Clin Nutr source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Some commercial software exists for the pharmaceutical area (192,193) and covers many phase I and II reactions.”
§ The food metabolome: a window over dietary exposure 1-3 > Software tools
What the sources say
- Not checked yetcites [192] T’Jollyn, 2011, Evaluation of three state-of-the-art metabolite prediction software packages (Meteor, MetaSite, and StarDrop) through independent and synergistic use, Drug Metab Dispos source
- Not checked yetcites [193] Piechota, 2013, pragmatic approaches to using computational methods to predict xenobiotic metabolism, J Chem Inf Model source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“They should also significantly contribute to a better understanding of the complex interactions between diet and human health.”
§ The food metabolome: a window over dietary exposure 1-3 > CONCLUSIONS
boostedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
In the paper
“The MSI, initiated by the Metabolomics Society, has already issued several reference articles on good practice for metabolomic research.”
§ The food metabolome: a window over dietary exposure 1-3 > Standardization initiatives
What the sources say
- Not checked yetcites [189] Metabolomics Standards Initiative. Homepage. Available from: http://msi-workgroups.sourceforge.net/ (cited 3 September 2013).
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Some proof-of-principle studies have established the feasibility of metabolomic approaches to identify novel dietary biomarkers and suggest that these approaches could greatly expand the field of molecular nutritional epidemiology and contribute to future progress in nutrition research.”
§ The food metabolome: a window over dietary exposure 1-3 > CONCLUSIONS
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: unclear — It is unclear whether it could be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Several training workshops on metabolomics and nutrition were supported by the Nutrigenomics Organization (112).”
§ The food metabolome: a window over dietary exposure 1-3 > Training
What the sources say
- Not checked yetcites [112] Scalbert, 2009, Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research, Metabolomics source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper relies on this without support.
The food metabolome spans a huge range of concentrations, from picomolar or nanomolar for some contaminants or phytochemical metabolites to millimolar for nutrients such as sugars.
“A second feature of the food metabolome is the huge range of concentrations, from picomolar or nanomolar concentrations for some contaminants or phytochemical metabolites to millimolar concentrations for nutrients such as sugars.”
The paper relies on this without support.
Many components of the food metabolome are unknown.
“Third, many components of the food metabolome are unknown.”
The paper relies on this without support.
The metabolism of a large proportion of nonnutrients in humans has never been studied, and the chemical structures of their circulating metabolites have not been identified.
“Indeed, the metabolism for a large proportion of nonnutrients in humans has never been studied and the chemical structures of their circulating metabolites have not been identified.”
The paper relies on this without support.
Plasma or serum samples are more commonly available in biobanks than other biospecimens.
“More metabolomic studies using blood samples should be carried out because of the more common availability of plasma or serum samples in biobanks.”
The paper relies on this without support.
Alanine is associated with diets that emphasize animal products rather than vegetables.
“alanine is associated with diets that emphasize animal products rather than vegetables”
The paper relies on this without support.
Many compounds in foods have structures that are uncommon in pharmaceuticals.
“many compounds in foods have structures that are uncommon in pharmaceuticals.”
The paper relies on this without support.
Food constituents may be degraded by specialized enzymes and may also be extensively metabolized by gut microbiota.
“Food constituents may be degraded by specialized enzymes and may also be extensively metabolized by the gut microbiota”
The paper relies on this without support.
The large majority of components of the food metabolome are not commercially available.
“The large majority of the components of the food metabolome are not commercially available.”
The paper relies on this without support.
Definitive identification of biomarkers is often hampered by the lack of available chemical standards.
“The definitive identification of biomarkers is often hampered by the lack of available chemical standards.”
The paper relies on this without support.
The food metabolome is exceedingly complex because it encompasses metabolites derived from as many metabolomes as there are edible species.
“The food metabolome is exceedingly complex because it encompasses metabolites derived from as many metabolomes as there are edible species.”
The paper relies on this without support.
Within one group, it is difficult to cover all the techniques and methods required to perform a comprehensive metabolomic study.
“Within one group, it is difficult to cover all the techniques and methods required to perform a comprehensive metabolomic study.”
The paper relies on this without support.
For many funding agencies, data sharing is becoming a key condition of funding.
“for many funding agencies, this is becoming a key condition of funding.”
The paper relies on this without support.
There is no current standardization initiative for the food metabolome.
“there is no current standardization initiative for the food metabolome”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Fourth, the gut microbiota are affected by environmental factors37, 38 such as dietary intakes,39, 40, 41 which may, in turn, influence blood levels of TMAO and its precursors.4”
From Gut Microbiota Metabolites and Risk of Major Adverse Cardiovascular Disease Events and Death: A Systematic Review and Meta‐Analysis of Prospective Studies (2017) · cites this paper as [37]
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“Other biomarkers, particularly those identified in controlled intervention studies, may prove to be less robust in populations because of the possible existence of a variety of precursors as seen for TMAO, or the occurrence of the same precursor in various foods.”
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Biomarkers intersect with the exposome
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A critical assessment of some biomarker approaches linked with dietary intake
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Urinary N‐methylpyridinium and trigonelline as candidate dietary biomarkers of coffee consumption
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Total polyphenol excretion and blood pressure in subjects at high cardiovascular risk
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“The Folin assay, commonly used to estimate total polyphenols in foods (46), has also been applied to urine samples to compare polyphenol intake (47), but such use may be inappropriate because of the presence of interfering reducing metabolites in such complex biological matrices (46).”
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“Some have been used as surrogate biomarkers of food intake, as follows: polyphenols, carotenoids, and vitamin C for fruit and vegetables (17, 18); alkylresorcinols for whole-grain cereals (19, 20); isoflavones for soy (21); amino acids and fatty acids for meat (22, 23); fatty acids for dairy products and fish (22, 24)…”
MethodMetabolomics Provide New Insight on the Metabolism of Dietary Phytochemicals in Rats
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Urinary excretion of methylamines in men with varying intake of fish from the baltic sea
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Cys34 Adducts of Reactive Oxygen Species in Human Serum Albumin
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Self-citationLC-QTOF/MS metabolomic profiles in human plasma after a 5-week high dietary fiber intake
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Self-citationHuman Metabolome Database: Completing the ‘Human Parts List’
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Metabolomic fingerprint in patients at high risk of cardiovascular disease by cocoa intervention
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Metabolomics: beyond biomarkers and towards mechanisms
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Metadata
- Authors
- Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S.
- Affiliations
- University College Dublin (IE)
- ORCID
- Venue
- The American Journal of Clinical Nutrition
- Publisher
- Elsevier BV
- Published
- 2014-06
- Volume
- 99
- Issue
- 6
- Pages
- 1286-1308
- ISSN
- 0002-9165 (ISSN-L)
- OpenAlex
- W2169779482
- Cited by
- 519
- References
- 198
- Citations by year
- 2026: 19 · 2025: 32 · 2024: 38 · 2023: 27 · 2022: 39 · 2021: 50 · 2020: 49 · 2019: 40 · 2018: 61 · 2017: 60 · 2016: 61 · 2015: 25 · 2014: 16
- FWCI
- 5.08
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- American Journal of Clinical Nutrition (publishedVersion, other-oa)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- World Health Organization
- European Commission (KBBE-2011-5, FP7-KBBE-2011–5, 289511, 260791)
- Agence Nationale de la Recherche (ANR-10-ALIA-0007, ANR-10)
- Medical Research Council (MR/J010308/1)
- FP7 Food, Agriculture and Fisheries, Biotechnology
- CHIST-ERA
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
- Keywords
- dietary biomarkers, dietary exposure assessment, metabolomics, metabolomics databases, dietary bioactive compounds
- MeSH terms
- Animals, Diet, Digestion, Food, Humans, Models, Biological, Biomarkers, Nutritional Sciences, Metabolomics, Metabolome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
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