Available online at www.sciencedirect.com ScienceDirectNutritional metabolomics: Recent developments and future needs Maaria Kortesniemi1, Stefania Noerman2, Anna Kårlund1, Jasmin Raita1, Topi Meuronen1, Ville Koistinen1,3, Rikard Landberg2 and Kati Hanhineva1,3Abstract Metabolomics has rapidly been adopted as one of the key methods in nutrition research. This review focuses on the recent developments and updates in the field, including the analytical methodologies that encompass improved instrument sensitivity, sampling techniques and data integration (multiomics). Metab- olomics has advanced the discovery and validation of dietary biomarkers and their implementation in health research. Metabolomics has come to play an important role in the un- derstanding of the role of small molecules resulting from the diet–microbiota interactions when gut microbiota research has shifted towards improving the understanding of the activity and functionality of gut microbiota rather than composition alone. Currently, metabolomics plays an emerging role in precision nutrition and the recent developments therein are discussed. Addresses 1 Food Sciences Unit, Department of Life Technologies, University of Turku, FI-20014 Turun yliopisto, Finland 2 Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden 3 Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland Corresponding author: Kortesniemi, Maaria (mkkort@utu.fi)Current Opinion in Chemical Biology 2023, 77:102400 This review comes from a themed issue on Omics - Metabolomics (2023) Edited by James McCullagh and Hector Keun For a complete overview see the Issue and the Editorial Available online xxx https://doi.org/10.1016/j.cbpa.2023.102400 1367-5931/© 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/). Keywords: Metabolomics, Nutrition, Biomarker, Dietary pattern, Endogenous metabolite, Gut microbiota, Precision prevention. Introduction Metabolomics has become a keymethodological approach in nutrition research. It allows the characterization of the molecular phenotypes of individuals, their metabolicwww.sciencedirect.comresponsiveness to various foods and diets, and compre- hensive assessment of their mechanistic and predictive role in health. Ultimately, this may pave the way for the development of novel precision prevention approaches [1]. The use of metabolomics in nutritional research also helps to gain a mechanistic understanding of the role of dietary compounds in nutritional status and metabolism, provides a read-out from gut microbiota composition and function, and may reflect other external exposures and their interactions with the host with implications for human health. Metabolomics may also provide novel, objective biomarkers that reflect specific dietary and lifestyle exposures. Single metabolites or metabolite profiles reflecting specific exposures could be used to assess individual responses to dietary interventions eventually enabling improved disease risk prediction. In precision nutrition, metabolomics is emerging as an important technique to assess the impact of foods and diets on an individual level [1] and to determine metab- otypes, i.e., subgroups of individuals with a similar meta- bolic response to diet [2]. Self-sampling and the use of non-invasive sample materials are emerging and could further enhance practical applications for precision nutrition and precision medicine, where frequent sam- pling is warranted, but comprehensive metabolomics techniques integrated and validated with the self- sampling techniques are yet lacking [3]. Advances in instrumentation, spectral databases, and computational tools have promoted the understanding of the complexity related to nutrition due to the wealth of biochemicals derived from foods, especially those produced fromwhole plants, although this “darkmatter” of food remainsmostly unresolved and poorly acknowledged [4*,5]. In this review, we highlight the most recent developments and challenges in nutritional metabolomics including meth- odological aspects and their application in nutrition research to reflect dietary and life-style exposures, mo- lecular responses, dietemicrobiota interactions, eventu- ally offering possibilities for tailored precision nutrition.Methodological advancements and challenges The primary analytical techniques used in nutritional metabolomics are MS- and NMR-based methods.Current Opinion in Chemical Biology 2023, 77:102400 2 Omics - Metabolomics (2023)Coupled with UHPLC, and more recently with ion mobility, the MS techniques provide broad metabolite coverage and high sensitivity [6,7]. Although ion mobility greatly enhances the separation and identifi- cation of metabolite and lipid isomers by providing an additional dimension to the measurements, its utiliza- tion in nutritional research has thus far been limited [8]. In NMR-based metabolomics, increased sensitivity of probes, optimized NMR excitation pulse schemes, hybrid NMR approaches and faster spectra preprocess- ing are important recent developments [9]. The main methodological advantages during the past few years have come from merging the metabolomics data with other omics, clinical, and dietary data along- side with developments of tools and pipelines for the purpose [10e13*,14**,15e21]. Since the plasma metabolome represents a snap-shot read-out modified by the host genetics, gut microbiota, diet and the exposome, recent research is increasingly focused on elucidating their interactions [11,22]. The most widely used multiomics approaches in current nutritional studies include combining metabolomics data and metagenomics data on gut microbial composition with a variety of available computational methods, such as metabolic networks, Spearman’s correlation networks, and Sparse Generalized Canonical Correlation Analysis (SGCCA) [10e12,16,18e20]. Eventually, multiomics and data integration will help to unravel interactions between diet, gut microbiota and health [14**]. To promote this, novel multiomics databases are being introduced [14**,23]. Furthermore, the use of new sampling techniques, such as dried blood spot by finger- prick lancet [24], allowing for the first time quantitative measurement of metabolites in small volume samples [25], as well as alternative biofluids, including saliva [26], sweat [27], and breast milk [12], broaden the possibilities of metabolomics in human nutritional studies because of their non-invasive and less labor- intensive nature, allowing the samples to be collected at home. So far, these applications have been only used to a limited extent in nutritional studies. The variation of the reported metabolites in different biological matrices and the question of their representativeness of the food intake are challenging the field. One of the biggest challenges in metabolomics is also to comprehensively characterize and annotate the vast number of compounds measured. This is particularly challenging in the case of nutritional metabolomics, as the immense pool of compounds gained from foods adds a level of complexity that needs to be addressed [4*,28]. In the case of lipidomics, essential improve- ments within the analytical methods as well as identi- fication of lipids have been accomplished recently [29,30]. Besides the advancements in analytical tech- nology, both open-access and commercial spectralCurrent Opinion in Chemical Biology 2023, 77:102400databases are continuously expanding, and software utilizing machine learning and molecular networking have emerged to assist with the laborious process of metabolite identification [14**,15,17,31]. To fully un- derstand the nutritional and eventually health proper- ties of foods and diets, remarkable advancements are still required in our capacity to identify the individual metabolites to track down their metabolism and effects in the body. Randomized controlled trials represent the gold standard for establishing a causal relationship be- tween food/diets and the metabolome of the collected sample material. Considering the inter- and intra- individual variability is vital and identifying responders and non-responders and their underlying determinants (i.e., metabotypes) will provide new possibilities to tailored diets to improve the efficacy of in- terventions [1,32*]. Biomarkers of food intake and dietary patterns Dietary biomarkers are metabolites objectively depict- ing the intake of certain foods or dietary patterns. Biomarkers can be classified based on the level of evi- dence [33**]. Recently, biomarker development and validation frameworks have been advanced [34] and the most promising biomarkers across important foods cat- egories have been recently comprehensively reviewed [35**]. There are currently few validated food intake biomarkers, such as alkylresorcinols for whole grain wheat and rye intake, proline betaine for citrus fruits, and 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) for fish [33**,34,36*]. The search of novel biomarkers brings constantly emerging candidates for various food categories as summarized for the past 2e3 years in Table 1. For example, a study conducted by following the protocols of the Food Biomarker Alliance (FoodBAll) project aiming for the systematic coverage and validation of food biomarkers, shows promise for novel volatile biomarkers for dairy, cheese and soy-based drink intake [37]. Sex-specific differences in metabolic outcomes portray as one important aspect of biomarker discovery. Langenau et al. [38], for example, have re- ported differential biomarkers between men and women for coffee and fish. In addition to individual foods, various studies have suggested biomarker candidates also for dietary pat- terns, as summarized for the past 2e3 years in Table 2. Mediterranean and Nordic diets are frequently referred as healthy dietary patterns with e.g. fish and whole-grain consumption as common elements. For example, Gu¨rdeniz et al. [36*] reported urinary DHBA-glycine, CMPF and CMPF-glucuronide being significant me- tabolites associated with Healthy Nordic Diet. To accommodate both human and planetary health, plant- rich diets are increasingly important, which also shows in the recent research (Table 2).www.sciencedirect.com Table 1 Most recently suggested biomarkers of food intake (reported in 2020–2023). Food Biomarker HMDB ID Sample; method Reference Almond alpha-Tocopherol HMDB0001893 Feces; GC–MS [39] 5-Hydroxyindoleacetic acid (5-HIAA) HMDB0000763 Beer L-Cysteine HMDB0000574 Plasma; GC–MS Urine; GC–MS [40] D-Lactose HMDB0041627 D-Psicose HMDB0250793 Bell pepper Six capsanthin- and capsorubin-derived glucuronides (see ref. for exact structures) n/a Urine; LC-MS, structural elucidation with NMR [41] Butter Undecylenic acid (11:1n−1) HMDB0033724 Serum; LC-MS/MS [38] Cheese 2-Heptanone HMDB0003671 Plasma; GC–MS [37] 2-Undecanone HMDB0033713 Coffee Glutamic acid HMDB0000148 Plasma; GC–MS Serum; LC-MS/MS Urine; GC–MS [38,40] Quinic acid HMDB0003072 Paraxanthine (in men) HMDB0001860 Catechol HMDB0000957 Dimethyluric acid HMDB0001857 Methyluric acid HMDB0003099 Niacin HMDB0001488 D-Psicose HMDB0250793 Dairy 3,5-Dimethyloctan-2-one n/a Plasma; GC–MS [37] Fish EPA (20:5n−3) (in men) HMDB0001999 Serum; LC-MS/MS [38] Milk 3-Ethylphenol HMDB0059873 Urine; GC–MS [37] Poultry 3-Methylhistidine HMDB0000479 Serum; LC-MS/MS [38] Spinach Des-aminoarginine pentenol ester* n/a Urine; LC-MS [42] D/L-Malic acid-p-coumarate HMDB0303755 Walnut 5-HIAA HMDB0000763 Feces; GC–MS [39] Uric acid HMDB0000289 White bread Dodecanoic acid HMDB0000638 Plasma; GC–MS [40] Whole-grain (wheat/rye) 5-Aminovaleric acid betaine (5-AVAB) HMDB0240732 Serum; LC-MS [43,44**] Pipecolic acid betaine HMDB0304559 Tetradecanedioic acid HMDB0000872 Wine Erythritol HMDB0002994 Plasma; GC–MS Urine; GC–MS [40] Xylitol HMDB0242149 Cinnamoylglycine HMDB0011621 Citramalate HMDB0000426 Erythritol HMDB0002994 D-Gluconic acid HMDB0000625 Tartaric acid HMDB0000956 * Tentative identification, novel structure not verified N u tritio n al M etab o lo m ics – R ecen t D evelo p m en ts K ortesniem iet al. 3 w w w .sciencedirect.com C u rren t O p in io n in C h em ical B io lo g y 2023, 77:102400 Table 2 Examples of biomarker candidates of dietary patterns (reported in 2021–2022). Most of the biomarkers remain to be validated. Food intake pattern Associated foods Associated metabolites HMDB ID Reference Dietary approaches to stop hypertension (DASH) Rich in fruits, vegetables, low-fat dairy products; moderate in meat, fish, poultry, nuts, and beans; low in sugar and red meat 2-Methylserine n/a [45–47] 4-Allylphenol sulfate HMDB0170765 beta-Cryptoxanthine HMDB0033844 CAR 3:0 HMDB0000824 DG 18:2/18:3 HMDB0007249 DG 18:2/22:6 HMDB0007266 N-Methylproline HMDB0094696 Ornithine HMDB0000214 Panthotenate HMDB0000210 Proline betaine HMDB0004827 S-Allylcysteine HMDB0034323 Threonate HMDB0245425 Healthy Nordic diet Berries, fish, fruits, low/non-fat dairy, vegetables, whole- grain 3,5-Dihydroxybenzoic acid (3,5-DHBA) HMDB0013677 [36*,48] 3,5-DHBA-glycine n/a CEHC n/a 3-Carboxy-4-methyl-5-propyl-2-furanpropionic acid (CMPF) HMDB0061112 CMPF-glucuronide n/a CAR 8:1 n/a CAR 10:3 n/a (Glycine) betaine HMDB0000043 Hippuric acid HMDB0000714 Indole-3-propionic acid HMDB0002302 Linoleamide HMDB0062656 Loliolide HMDB0302428 Methylimidazoleacetic acid HMDB0002820 Phenylalanine HMDB0000159 Proline betaine HMDB0004827 Healthy plant-based diet (hPDI) Coffee, fruits, legumes, nuts, plant protein, tea, vegetables, whole- grain 1-Methylnicotinamide HMDB0000699 [49,50] 1-Methyluric acid HMDB0003099 3-Hydroxypyridine sulfate HMDB0240652 4-Pyridoxic acid HMDB0000017 4-Vinylphenol sulfate HMDB0062775 Glyceric acid HMDB0000139 Hippuric acid HMDB0000714 Hydrocinnamic acid (3-phenylpropionic acid) HMDB0000764 Indole-3-propionic acid HMDB0002302 Lenticin (tryptophan betaine) HMDB0061115 myo-Inositol HMDB0000211 N1-methyl-2-pyridone-5-carboxamide HMDB0004193 N-Acetylornithine n/a O-methoxycatechol-O-sulfate HMDB0060013 Pantothenic acid HMDB0000210 Pipecolic acid HMDB0000070 Pyrocatechol sulfate HMDB0059724 Quinic acid HMDB0003072 Threitol HMDB0004136 4 O m ics - M etab o lo m ics (2023) C u rren t O p in io n in C h em ical B io lo g y 2023, 77:102400 w w w .sciencedirect.com Threonic acid HMDB0000943 Trigonelline HMDB0000875 Mediterranean diet Fruits, legumes, olive oil, red wine, seafood, vegetables, whole-grain 5-Hydroxyindole HMDB0059805 [10,51,52] Deoxycholic acid glucuronide HMDB0002596 Hydroxyperoxyeicosapentaenoic acid n/a L-Aspartylphenylalanine HMDB0000706 PC 35:1 n/a PC 40:6 n/a Succinic acid HMDB0000254 TMA HMDB0000906 Plant-based diet (overall PDI) Plant foods in general 4-Vinylphenol sulfate HMDB0062775 [49,50] gamma-CEHC HMDB0001931 gamma-Glutamyl peptides n/a (Glycine) betaine HMDB0000043 Cinnamoylglycine HMDB0011621 Glutamine HMDB0000641 Glycerate HMDB0000139 Glycine HMDB0000123 Hippuric acid HMDB0000714 Indole-3-propionic acid HMDB0002302 Lenticin HMDB0061115 myo-Inositol HMDB0000211 N-Acetylornithine n/a N-Methylproline HMDB0094696 O-methoxycatechol-O-sulfate HMDB0060013 Paraxanthine HMDB0001860 Pipecolic acid HMDB0000070 Proline betaine HMDB0004827 Pyrocatechol sulfate HMDB0059724 scyllo-Inositol HMDB0006088 Threonic acid HMDB0000943 Trigonelline HMDB0000875 Sugar-rich diet E.g. sugar- sweetened beverages Chenodeoxycholic acid HMDB0000518 [53] Glycocholic acid HMDB0000138 Glutamic acid HMDB0000148 Lithocholic acid HMDB0000761 Phenylglycine HMDB0002210 Tyrosine HMDB0000158 Unhealthy plant- based diet (uPDI) Desserts, fruit juices, potatoes, refined grains, sugar- sweetened and artificially sweetened beverages, sweets 1,5-Anhydrosorbitol (1,5-anhydroglucitol) HMDB0002712 [49] 3-Methyl-2-oxovaleric acid HMDB0000491 gamma-CEHC HMDB0001931 Bilirubin (Z,Z) HMDB0000054 Bradykinin HMDB0004246 Hydroxyphenyllactic acid HMDB0000755 N2,N2-Dimethylguanosine HMDB0004824 Proline HMDB0000162 S–N-Methylcysteine HMDB0302211 Ultra-processed foods Industrially processed meat- containing products, instant noodles, 3-Methyl-2-oxovaleric acid HMDB0000491 [54,55] 4-Methylsyringol sulfate n/a Bradykinin HMDB0004246 Elaidic acid HMDB0000573 (continued on next page) N u tritio n al M etab o lo m ics – R ecen t D evelo p m en ts K ortesniem iet al. 5 w w w .sciencedirect.com C u rren t O p in io n in C h em ical B io lo g y 2023, 77:102400 T ab le 2. (c o n ti n u ed ) F o o d in ta ke p a tte rn A ss o ci a te d fo o d s A ss o ci a te d m e ta b o lit e s H M D B ID R e fe re n ce co n fe ct io n e ry , m a rg a rin e N 2 ,N 2 -D im e th yl g u a n o si n e H M D B 0 0 0 4 8 2 4 S a cc h a rin H M D B 0 0 2 9 7 2 3 V e g a n d ie t F ru its , le g u m e s, ve g e ta b le s, w h o le - g ra in 4 -A ce ty lp h e n yl su lfa te n /a [5 6 ,5 7] 4 -A lly lp yr o ca te ch o ls u lfa te H M D B 0 3 0 4 9 3 4 4 -E th yl p h e n yl su lfa te H M D B 0 0 6 2 5 5 1 b e ta -C ry p to xa n th in H M D B 0 0 3 3 8 4 4 a lp h a -L in o le n ic a ci d H M D B 0 0 0 1 3 8 8 B u ty ric a ci d H M D B 0 0 0 0 0 3 9 F o lic a ci d H M D B 0 0 0 0 1 2 1 G ly co h yo ch o lic a ci d H M D B 0 2 4 0 6 0 7 In d o le -3 -p ro p io n ic a ci d H M D B 0 0 0 2 3 0 2 N -M e th yl p ro lin e H M D B 0 0 9 4 6 9 6 P ro lin e b e ta in e H M D B 0 0 0 4 8 2 7 S -M e th yl m e th io n in e H M D B 0 0 3 8 6 7 0 A b b re vi a tio n s: C A R , a cy lc a rn iti n e ; C E H C , ca rb o xy e th yl h yd ro xy ch ro m a n ; T M A , tr im e th yl a m in e ; P C , p h o sp h a tid yl ch o lin e . 6 Omics - Metabolomics (2023) Current Opinion in Chemical Biology 2023, 77:102400Host and gut metabolites reflecting diet Gut microbiota is an essential modulator of the meta- bolic response to diet and resulting health effects [10,53,58**,59,60]. Indeed, gut microbiota has been shown to contribute to approx. 13% of the total variation in plasma metabolites [58**]. The importance of microbiota is evidenced by the recent cataloguing of the metabolites related to dietemicrobiota interactions [14**,59]. Indolepropionic acid is a microbial conver- sion product from dietary tryptophan linked with better insulin as well as lower risk of type 2 diabetes (T2D) and metabolic syndrome [61*], while indolelactic acid is associated with obesity, insulin resistance, and higher T2D risk [62]. Indolepropionic acid levels in blood were associated with a lower intake of animal-based food and a higher intake of fiber-rich plant-based foods [62], and partially explained by indolepropionic acid-associated gut bacteria, such as Firmicutes and Bifidobacterium. The interaction between diet, gut microbiota, and metabo- lite profiles was particularly shown by the association between higher milk intake, higher levels of bifidobac- teria and serum indolepropionic acid (detected only among lactase non-persistent individuals) [62]. Among the most recently emerged compounds related to diet, gut microbiota and health is 5-aminovaleric acid betaine (5-AVAB) [44**,63,64]. It can be directly absorbed from its dietary sources, such as whole-grain cereals (Table 1), or conversion of other compounds with trimethyl groups potentially mediated by gut microbiota. Despite its anti-inflammatory, anticancer, and antioxidant properties, associations with fatty liver disease and cognitive decline have been reported, call- ing for further studies to disentangle if the association between 5-AVAB and health outcomes is depending on certain constraints or individual factors [44**]. Another controversial metabolite in terms of health relevance is trimethylamine N-oxide (TMAO), that has been linked with a higher risk of cardiovascular disease [65e67]. TMAO can enter circulation either directly from dietary sources such as fish, or via the activity of gut bacteria and liver metabolism from dietary pre- cursors such as carnitine and choline rich in for example red meat [66,68,69]. Interestingly, females seem to have a higher abundance of bacteria producing trimethyl- amine, despite generally higher consumption of meat in males [68]. Even when TMAO levels can be associated with foods such as fish, whole-grains, poultry and eggs, these dietary items per se are not linked with adverse health outcomes, but merely the opposite, which high- lights the fact that we have not yet fully understood the metabolic role of TMAO [66,67,70]. Short-chain fatty acids (SCFAs; formate, acetate, pro- pionate, and butyrate) have been shown to benefit gut health e.g. by protecting epithelial integrity andwww.sciencedirect.com Nutritional Metabolomics – Recent Developments Kortesniemi et al. 7suppressing pro-inflammatory pathways [71]. SCFAs have also been shown to play roles in the regulation of intestinal hormones, appetite, and blood pressure, as well as glucose and lipid homeostasis [52]. Consumption of fiber-rich foods has been shown to increase SCFA levels, e.g. in vegan and Mediterranean diets [10,16]. Other determinants of SCFAs are intestinal gases, iron abundance, and colonic pH, all connected to both diet and gut microbial composition and activity [72]. Recent studies have suggested that plasma SCFA concentra- tions are of greater importance than fecal SCFA concerning metabolic risk factors and diseases [73e75]. Glycerophospholipids have been suggested to provide a pool of early biomarker candidates for metabolic syn- drome, cardiometabolic diseases [13*,76,77*,78] and adherence to healthy eating patterns [36*]. Lysophos- phatidylcholine (LPC) species may be the most inter- esting group of glycerophospholipids regarding the discovery of dietary biomarkers for metabolic health. For example, decreased LPC 18:2 levels have been sug- gested to indicate metabolic syndrome risk [13*,76] whereas a positive association has been found between LPC 18:1 and LPC 18:2 and adherence to dietary rec- ommendations of The World Cancer Research Fund and American Institute for Cancer Research (WCRF/AICR) [79]. As LPC 18:2 may play a role as a robust biomarker for healthy dietary patterns and metabolic health, acyl- carnitine (CAR) with an 18:2 fatty acid tail has been found to correlate positively with the intake of linoleic acid (18:2), as well as with circulating ornithine and male sex [80]. In general, circulating acylcarnitines are often suggested as markers of impaired lipid and/or glucose metabolism [80]. Besides phospholipids, two other interesting categories to mention are bile acids and ceramides. Sex-based differences in fecal levels of bile acids have been observed [81]. Adherence to certain dietary patterns, such as vegan, Mediterranean or sugar-rich diet, has been shown to modulate such bile acids profiles and metabolic risk markers [10,16,52,53]. Fecal chenodeox- ycholic acid, glycocholic acid, cholic acid, and hyodeox- ycholic acid have been shown to be associated with higher circulating glucose, insulin, triglycerides, and LDL, especially in individuals with metabolic syndrome [13*]. Ceramides (Cer) seem to associate with either a higher or lower risk of T2D depending on the acyl chain length. For example, Cer 16:0, Cer 18:0 and dihy- droceramide dhCer 20:0 were associated with higher risk, whereas Cer 20:0, dhCer 22:2 and dhCer 26:1 were associated with lower T2D risk [82]. These ceramides were also suggested to partly mediate the previously reported adverse effect of high red meat consumption on T2D risk. Similarly, Cer 22:2 was suggested to mediate the positive effect of coffee consumption on T2D risk. Ceramides may exemplify how metaboliteswww.sciencedirect.commay mediate the interaction between diet and cardio- metabolic health [82].Towards precision nutrition and prevention with metabolomics It is well established that people vary in response to diet [83], which makes it important to find metabolites indicating or responsible for such variations in metabolic phenotypes (metabotypes) [84]. Thus, profiling such metabolites is promising in predicting dietary responses and stratifying the individuals based on their predicted responses. Once the metabolites are well characterized, further attempts can be made to trace the dietary sources or other factors responsible for such metabolites. This knowledge will aid in precision prevention, either using specific dietary components or lifestyle intervention to target the alteration of such metabolites to achieve the desired metabolite profiles. On the other hand, a preci- sion intervention strategy specifically targeted to re- sponders [47] will help improve the efficacy rate of the intervention [85]. For example, giving dietary interven- tion according to tissue-specific metabotypes has been shown to enhance improvement in cardiometabolic health markers in targeted participants [86]. The PERSonalized Glucose Optimization Through Nutri- tional Intervention (PERSON) study was one of the first randomized clinical trials to test effects of a personalized dietary intervention based on metabolism related phe- notypes [87*]. Also in the PREVENTOMICS platform individuals are classified into clusters for personalized dietary plans [32*]. Although a personalized diet plan did not show significant improvement in the endpoint markers compared to a generic healthy diet, the PREVENTOMICS study may work as a pioneer study to further investigate the use of metabolomics together with other omics in biomarker-guided dietary in- terventions [32*].Concluding remarks Metabolomics holds the potential for wider utilization in all aspects related to nutrition as discussed in this review, as long as the computational methods to process, mine, and visualize the complex metabolomics data, including the identification of the metabolites, continue to be developed to provide reliable results and informative interpretations of the data. This is also the prerequisite in order to fully exploit the latest technological ad- vancements and to have them more widely adopted. Metabolomics-based frameworks keep accelerating the discovery and validation of dietary biomarkers. Examples mentioned here raise the importance of the examination of metabolome profiles in investigating the links between diet, gut microbiota and metabolic health outcomes. Metabolomics has a key role in defining more detailed and personalized nutritional recommendations and dividing foods into more health-relevant categories.Current Opinion in Chemical Biology 2023, 77:102400 8 Omics - Metabolomics (2023)Author contributions Conceptualization: KH, RL; Writing e Original Draft: MK, SN, AK, JR, TM, VK; Writing e Review & Editing: RL, KH, MK, SN, VK, AK, TM, JR.Declaration of competing interest The authors declare the following financial interests/ personal relationships that may be considered as poten- tial competing interests: Kati Hanhineva reports a rela- tionship with Afekta Technologies that includes: board membership, employment, and equity or stocks. Ville Koistinen reports a relationship with Afekta Technologies that includes: board membership, employment, and equity or stocks. Topi Meuronen reports a relationship with Afekta Technologies that includes: consulting or advisory and paid expert testimony.Data availability No data was used for the research described in the article. Acknowledgments Funding from the Swedish Research Council (2019-01264; RL), Formas (2019e02201) under the umbrella of the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (RL, SN), ERA-NET Cofund HDHL INTIMIC (GA N 727565 of the EU Horizon 2020 Research and Innovation Programme; RL, SN), Jane and Aatos Erkko Foundation (KH, AK, JR, TM, VK), Academy of Finland (no. 321716 and 334814; KH), EU Horizon 2020 (no. 874739; KH), EU Horizon Europe (no. 101060247; KH, AK), and Lantma¨nnen Research Foundation (KH, VK) are acknowledged. 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