Imperial College London

DrIsabelGarcia Perez

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Lecturer in Precision & Systems Medicine
 
 
 
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i.garcia-perez

 
 
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101Sir Alexander Fleming BuildingSouth Kensington Campus

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Publications

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46 results found

Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Gulyás B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson Set al., 2019, The gut microbiota influences skeletal muscle mass and function in mice, Science Translational Medicine, Vol: 11, ISSN: 1946-6234

The functional interactions between the gut microbiota and the host are important for host physiology, homeostasis, and sustained health. We compared the skeletal muscle of germ-free mice that lacked a gut microbiota to the skeletal muscle of pathogen-free mice that had a gut microbiota. Compared to pathogen-free mouse skeletal muscle, germ-free mouse skeletal muscle showed atrophy, decreased expression of insulin-like growth factor 1, and reduced transcription of genes associated with skeletal muscle growth and mitochondrial function. Nuclear magnetic resonance spectrometry analysis of skeletal muscle, liver, and serum from germ-free mice revealed multiple changes in the amounts of amino acids, including glycine and alanine, compared to pathogen-free mice. Germ-free mice also showed reduced serum choline, the precursor of acetylcholine, the key neurotransmitter that signals between muscle and nerve at neuromuscular junctions. Reduced expression of genes encoding Rapsyn and Lrp4, two proteins important for neuromuscular junction assembly and function, was also observed in skeletal muscle from germ-free mice compared to pathogen-free mice. Transplanting the gut microbiota from pathogen-free mice into germ-free mice resulted in an increase in skeletal muscle mass, a reduction in muscle atrophy markers, improved oxidative metabolic capacity of the muscle, and elevated expression of the neuromuscular junction assembly genes <jats:italic>Rapsyn</jats:italic> and <jats:italic>Lrp4</jats:italic>. Treating germ-free mice with short-chain fatty acids (microbial metabolites) partly reversed skeletal muscle impairments. Our results suggest a role for the gut microbiota in regulating skeletal muscle mass and function in mice.</jats:p>

Journal article

Allegretti JR, Kassam Z, Mullish BH, Chiang A, Carrellas M, Hurtado J, Marchesi JR, McDonald JAK, Pechlivanis A, Barker GF, Miguens Blanco J, Garcia Perez I, Wong WF, Gerardin Y, Silverstein M, Kennedy K, Thompson Cet al., 2019, Effects of fecal microbiota transplantation with oral capsules in obese patients, Clinical Gastroenterology and Hepatology, ISSN: 1542-3565

Background & AimsStudies in mice have shown that the intestinal microbiota can contribute to obesity via the anorexigenic gut hormone glucagon-like peptide 1 (GLP1) and bile acids, which affect lipid metabolism. We performed a randomized, placebo-controlled pilot study of the effects of fecal microbiota transplantation (FMT) in obese, metabolically uncompromised patients.MethodsWe performed a double-blind study of 22 obese patients (body mass index [BMI] ≥ 35kg/m2) without a diagnosis of diabetes, non-alcoholic steatohepatitis, or metabolic syndrome. Participants were randomly assigned (1:1) to groups that received FMT by capsules (induction dose of 30 capsules at week 4 and maintenance dose of 12 capsules at week 8) or placebo capsules. FMT capsules were derived from a single, lean donor (BMI, 17.5 kg/m2). Patients were followed through week 26; the primary outcome was safety. Stool and serum samples were collected from patients at baseline and at weeks 1, 4, 6, 8 and 12 after administration of the first dose of FMT or placebo and analyzed by 16S RNA gene sequencing. Stool and serum samples were analyzed for metabolomics by liquid chromatography-mass spectrometry. Additional outcomes were change in area under the curve for GLP1 at week 12.ResultsWe observed no significant differences in adverse events between patients who received FMT vs placebo. There was no increase in the area under the curve of GLP1 in either group. Patients who received FMT had sustained shifts in microbiomes associated with obesity toward those of the donor (P<.001). Patients who received FMT had a sustained decrease in stool levels of taurocholic acid (P<.05), compared with baseline; bile acid profiles began to more closely resemble those of the donor. We did not observe significant changes in mean BMI at week 12 in either group.ConclusionsIn a placebo-controlled pilot study, we found that FMT capsules (derived from a lean donor) were safe but did not reduce BMI in obese metabol

Journal article

Wilson T, Garcia-Perez I, Posma JM, Lloyd AJ, Chambers ES, Tailliart K, Zubair H, Beckmann M, Mathers JC, Holmes E, Frost G, Draper Jet al., 2019, Spot and cumulative urine samples are suitable replacements for 24-hour urine collections for objective measures of dietary exposure in adults using metabolite biomarkers, Journal of Nutrition, ISSN: 0022-3166

BACKGROUND: Measurement of multiple food intake exposure biomarkers in urine may offer an objective method for monitoring diet. The potential of spot and cumulative urine samples that have reduced burden on participants as replacements for 24-h urine collections has not been evaluated. OBJECTIVE: The aim of this study was to determine the utility of spot and cumulative urine samples for classifying the metabolic profiles of people according to dietary intake when compared with 24-h urine collections in a controlled dietary intervention study. METHODS: Nineteen healthy individuals (10 male, 9 female, aged 21-65 y, BMI 20-35 kg/m2) each consumed 4 distinctly different diets, each for 1 wk. Spot urine samples were collected ∼2 h post meals on 3 intervention days/wk. Cumulative urine samples were collected daily over 3 separate temporal periods. A 24-h urine collection was created by combining the 3 cumulative urine samples. Urine samples were analyzed with metabolite fingerprinting by both high-resolution flow infusion electrospray mass spectrometry (FIE-HRMS) and proton nuclear magnetic resonance spectroscopy (1H-NMR). Concentrations of dietary intake biomarkers were measured with liquid chromatography triple quadrupole mass spectrometry and by integration of 1H-NMR data. RESULTS: Cross-validation modeling with 1H-NMR and FIE-HRMS data demonstrated the power of spot and cumulative urine samples in predicting dietary patterns in 24-h urine collections. Particularly, there was no significant loss of information when post-dinner (PD) spot or overnight cumulative samples were substituted for 24-h urine collections (classification accuracies of 0.891 and 0.938, respectively). Quantitative analysis of urine samples also demonstrated the relation between PD spot samples and 24-h urines for dietary exposure biomarkers. CONCLUSIONS: We conclude that PD spot urine samples are suitable replacements for 24-h urine collections. Alternatively, cumulative samples collected overn

Journal article

Lloyd AJ, Willis ND, Wilson T, Zubair H, Xie L, Chambers E, Garcia-Perez I, Tailliart K, Beckmann M, Mathers JC, Draper Jet al., 2019, Developing a food exposure and urine sampling strategy for dietary exposure biomarker validation in free-living individuals, Molecular Nutrition and Food Research, ISSN: 1613-4125

SCOPE: Dietary choices modulate the risk of chronic diseases and improving diet is a central component of public health strategies. Food-derived metabolites present in urine could provide objective biomarkers of dietary exposure. To assist biomarker validation we aimed to develop a food intervention strategy mimicking a typical annual diet over a short period of time and assessed urine sampling protocols potentially suitable for future deployment of biomarker technology in free-living populations. METHODS AND RESULTS: Six different menu plans representing comprehensively a typical UK annual diet that were split into two dietary experimental periods. Free-living adult participants (n = 15 and n = 36, respectively) were provided with all their food, as a series of menu plans, over a period of 3 consecutive days. Multiple spot urine samples were collected and stored at home. CONCLUSION: We established a successful food exposure strategy following a conventional UK eating pattern, which was suitable for biomarker validation in free-living individuals. The urine sampling procedure was acceptable for volunteers and delivered samples suitable for biomarker quantification. Our study design provides scope for validation of existing biomarker candidates and potentially for discovery of new biomarker-leads and should help inform the future deployment of biomarker technology for habitual dietary exposure measurement.

Journal article

Lloyd AJ, Willis ND, Wilson T, Zubair H, Chambers E, Garcia-Perez I, Xie L, Tailliart K, Beckmann M, Mathers JC, Draper Jet al., 2019, Addressing the pitfalls when designing intervention studies to discover and validate biomarkers of habitual dietary intake, Metabolomics, Vol: 15, ISSN: 1573-3882

IntroductionDietary exposure monitoring within populations is reliant on self-reported measures such as Food Frequency Questionnaires and diet diaries. These methods often contain inaccurate information due to participant misreporting, non-compliance and bias. Urinary metabolites derived from individual foods could provide additional objective indicators of dietary exposure. For biomarker approaches to have utility it is essential that they cover a wide-range of commonly consumed foods and the methodology works in a real-world environment.ObjectivesTo test that the methodology works in a real-world environment and to consider the impact of the major sources of likely variance; particularly complex meals, different food formulations, processing and cooking methods, as well as the dynamics of biomarker duration in the body.MethodsWe designed and tested a dietary exposure biomarker discovery and validation strategy based on a food intervention study involving free-living individuals preparing meals and collecting urine samples at home. Two experimental periods were built around three consecutive day menu plans where all foods and drinks were provided (n = 15 and n = 36).ResultsThe experimental design was validated by confirming known consumption biomarkers in urinary samples after the first menu plan. We tested biomarker performance with different food formulations and processing methods involving meat, wholegrain, fruits and vegetables.ConclusionIt was demonstrated that spot urine samples, together with robust dietary biomarkers, despite major sources of variance, could be used successfully for dietary exposure monitoring in large epidemiological studies.

Journal article

Churchward MA, Michaud ER, Blanco JM, Garcia-Perez I, Mullish BH, Marchesi J, Xu H, Kao DH, Todd Ket al., 2019, Sa1924 – Effect of short chain fatty acids on gut-brain axis using a microglial cell model, Gastroenterology, Vol: 156, Pages: S-455-S-455, ISSN: 0016-5085

Journal article

Byrne C, Chambers E, Brignardello J, Garcia-Perez I, Holmes E, Gareth W, Tom P, Catriona T, Douglas M, Gary S Fet al., 2019, Effects of inulin propionate ester incorporated into palatable food products on appetite and resting energy expenditure: a randomised crossover study, Nutrients, Vol: 11, ISSN: 2072-6643

Supplementation with inulin-propionate ester (IPE), which delivers propionate to the colon, suppresses ad libitum energy intake and stimulates the release of satiety hormones acutely in humans, and prevents weight gain. In order to determine whether IPE remains effective when incorporated into food products (FP), IPE needs to be added to a widely accepted food system. A bread roll and fruit smoothie were produced. Twenty-one healthy overweight and obese humans participated. Participants attended an acclimatisation visit and a control visit where they consumed un-supplemented food products (FP). Participants then consumed supplemented-FP, containing 10 g/d inulin or IPE for six days followed by a post-supplementation visit in a randomised crossover design. On study visits, supplemented-FP were consumed for the seventh time and ad libitum energy intake was assessed 420 min later. Blood samples were collected to assess hormones and metabolites. Resting energy expenditure (REE) was measured using indirect calorimetry. Taste and appearance ratings were similar between FP. Ad libitum energy intake was significantly different between treatments, due to a decreased intake following IPE-FP. These observations were not related to changes in blood hormones and metabolites. There was an increase in REE following IPE-FP. However, this effect was lost after correcting for changes in fat free mass. Our results suggest that IPE suppresses appetite and may alter REE following its incorporation into palatable food products.

Journal article

Chambers E, Byrne C, Morrison D, Murphy K, Preston T, Tedford MC, Garcia Perez I, Fountana S, Serrano Contreras J, Holmes E, Roberts J, Reynolds C, Boyton R, Altmann D, McDonald J, Marchesi J, Akbar A, Riddell N, Wallis G, Frost Get al., 2019, Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised crossover trial, Gut, ISSN: 0017-5749

Objective: To investigate the underlying mechanisms behind changes in glucose homeostasis with delivery of propionate to the human colon by comprehensive and coordinated analysis of gut bacterial composition, plasma metabolome and immune responses.Design: Twelve non-diabetic adults with overweight and obesity received 20g/day of inulin-propionate ester (IPE), designed to selectively deliver propionate to the colon, a high-fermentable fibre control (inulin) and a low-fermentable fibre control (cellulose) in a randomised, double-blind, placebo controlled, crossover design. Outcome measurements of metabolic responses, inflammatory markers and gut bacterial composition were analysed at the end of each 42-day supplementation period.Results: Both IPE and inulin supplementation improved insulin resistance compared to cellulose supplementation, measured by homeostatic model assessment (HOMA) 2 (Mean±SEM 1.23±0.17 IPE vs. 1.59±0.17 cellulose, P=0.001; 1.17±0.15 inulin vs. 1.59±0.17 cellulose, P=0.009), with no differences between IPE and inulin (P=0.272). Fasting insulin was only associated positively with plasma tyrosine and negatively with plasma glycine following inulin supplementation. IPE supplementation decreased pro-inflammatory IL-8 levels compared to cellulose, whilst inulin had no impact on the systemic inflammatory markers studied. Inulin promoted changes in gut bacterial populations at the class level (increased Actinobacteria and decreased Clostridia) and order level (decreased Clostridales) compared to cellulose, with small differences at the species level observed between IPE and cellulose. Conclusion: These data demonstrate a distinctive physiological impact of raising colonic propionate delivery in humans, as improvements in insulin sensitivity promoted by IPE and inulin were accompanied with different effects on the plasma metabolome, gut bacterial populations and markers of systemic inflammation.

Journal article

Byrne C, Preston T, Brignardello J, Garcia-Perez I, Holmes E, Frost G, Morrison Det al., 2018, The effect of L-rhamnose on intestinal transit time, short chain fatty acids and appetite regulation: a pilot human study using combined 13CO2 / H2 breath tests, Journal of Breath Research, Vol: 12, ISSN: 1752-7155

Background: The appetite-regulating effects of non-digestible carbohydrates (NDC) have in part previously been attributed to their effects on intestinal transit rates as well as microbial production of short chain fatty acids (SCFA). Increased colonic production of the SCFA propionate has been shown to reduce energy intake and stimulate gut hormone secretion acutely in humans. Objective: We investigated the effect of the propiogenic NDC, L-rhamnose, on gastrointestinal transit times using a combined 13CO2/H2 breath test. We hypothesised that L-rhamnose would increase plasma propionate leading to a reduction in appetite, independent of changes in gastrointestinal transit times.Design: We used a dual 13C-octanoic acid/lactose 13C-ureide breath test combined with breath H2 to measure intestinal transit times following the consumption of 25g/d L-rhamnose, compared with inulin and cellulose, in 10 healthy humans in a randomised cross-over design pilot study. Gastric emptying (GE) and oro-caecal transit times (OCTT) were derived from the breath 13C data and compared with breath H2. Plasma SCFA and peptide YY (PYY) were also measured alongside subjective measures of appetite. Results: L-rhamnose significantly slowed GE rates (by 19.5min) but there was no difference in OCTT between treatments. However, breath H2 indicated fermentation of L-rhamnose before it reached the caecum. OCTT was highly correlated with breath H2 for inulin but not for L-rhamnose or cellulose. L-rhamnose consumption significantly increased plasma propionate and PYY but did not significantly reduce subjective appetite measures. Conclusions: The NDCs tested had a minimal effect on intestinal transit time. Our data suggest that L-rhamnose is partially fermented in the small intestine and that breath H2 reflects the site of gastrointestinal fermentation and is only a reliable marker of OCTT for certain NDCs (e.g. inulin). Future studies should focus on investigating the appetite-suppressing potential of L

Journal article

Cronin O, Barton W, Skuse P, Penney NC, Garcia-Perez I, Murphy EF, Woods T, Nugent H, Fanning A, Melgar S, Falvey EC, Holmes E, Cotter PD, O'Sullivan O, Molloy MG, Shanahan Fet al., 2018, A prospective metagenomic and metabolomic analysis of the impact of exercise and/or whey protein supplementation on the gut microbiome of sedentary adults, mSystems, Vol: 3, ISSN: 2379-5077

Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomics- and metabolomics-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in the diversity of microbial populations in the gut. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement. IMPORTANCE The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to mo

Journal article

Posma JM, Garcia Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson Jet al., 2018, Optimized phenotypic biomarker discovery and confounder elimination via covariate-adjusted projection to latent structures from metabolic spectroscopy data, Journal of Proteome Research, Vol: 17, Pages: 1586-1595, ISSN: 1535-3893

Metabolism is altered by genetics, diet, disease status, environment and many other factors. Modelling either one of these is often done without considering the effects of the other covariates. Attributing differences in metabolic profile to one of these factors needs to be done while controlling for the metabolic influence of the rest. We describe here a data analysis framework and novel confounder-adjustment algorithm for multivariate analysis of metabolic profiling data. Using simulated data we show that similar numbers of true associations and significantly less false positives are found compared to other commonly used methods. Covariate-Adjusted Projections to Latent Structures (CA-PLS) is exemplified here using a large-scale metabolic phenotyping study of two Chinese populations at different risks for cardiovascular disease. Using CA-PLS we find that some previously reported differences are actually associated with external factors and discover a number of previously unreported biomarkers linked to different metabolic pathways. CA-PLS can be applied to any multivariate data where confounding may be an issue and the confounder-adjustment procedure is translatable to other multivariate regression techniques.

Journal article

Byrne CS, Preston T, Brignardello J, Garcia-Perez I, Holmes E, Frost GS, Morrison DJet al., 2018, The effect of L-rhamnose on gastrointestinal transit rates, short chain fatty acids and appetite regulation, Publisher: CAMBRIDGE UNIV PRESS, Pages: E155-E155, ISSN: 0029-6651

Conference paper

Garcia Perez I, Posma JM, Gibson R, Chambers ES, Nicholson JK, Holmes E, Frost Get al., 2017, Modernizing dietary assessment, IUNS 21st ICN International Congress of Nutrition, Publisher: Karger Publishers, Pages: 286-287, ISSN: 1421-9697

Conference paper

Swann JR, Garcia-Perez I, Braniste V, Wilson I, Sidaway JE, Nicholson JK, Pettersson S, Holmes Eet al., 2017, Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: a metabonomic study of gut microbial influence on host brain metabolism, Journal of Pharmaceutical and Biomedical Analysis, Vol: 143, Pages: 141-146, ISSN: 1873-264X

H NMR Spectroscopy has been applied to determine the neurochemical profiles of brain extracts from the frontal cortex and hippocampal regions of germ free and normal mice and rats. The results revealed a number of differences between germ free (GF) and conventional (CV) rats or specific pathogen-free (SPF) mice with microbiome-associated metabolic variation found to be both species- and region-dependent. In the mouse, the GF frontal cortex contained lower amounts of creatine, N-acetyl-aspartate (NAA), glycerophosphocholine and lactate, but greater amounts of choline compared to that of specific pathogen free (SPF) mice. In the hippocampus, the GF mice had greater creatine, NAA, lactate and taurine content compared to those of the SPF animals, but lower relative quantities of succinate and an unidentified lipid-related component. The GF rat frontal cortex contained higher relative quantities of lactate, creatine and NAA compared to the CV animals whilst the GF hippocampus was characterized by higher taurine and phosphocholine concentrations and lower quantities of NAA, N-acetylaspartylglutamate and choline compared to the CV animals. Of note is that, in both rat and mouse brain extracts, concentrations of hippocampal taurine were found to be greater in the absence of an established microbiome. The results provide further evidence that brain biochemistry can be influenced by gut microbial status, specifically metabolites involved in energy metabolism demonstrating biochemical dialogue between the microbiome and brain.

Journal article

Barton W, Penney NC, Cronin O, Garcia-Perez I, Molloy MG, Holmes E, Shanahan F, Cotter PD, O'Sullivan Oet al., 2017, The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level, Gut, Vol: 67, Pages: 625-633, ISSN: 0017-5749

OBJECTIVE: It is evident that the gut microbiota and factors that influence its composition and activity effect human metabolic, immunological and developmental processes. We previously reported that extreme physical activity with associated dietary adaptations, such as that pursued by professional athletes, is associated with changes in faecal microbial diversity and composition relative to that of individuals with a more sedentary lifestyle. Here we address the impact of these factors on the functionality/metabolic activity of the microbiota which reveals even greater separation between exercise and a more sedentary state. DESIGN: Metabolic phenotyping and functional metagenomic analysis of the gut microbiome of professional international rugby union players (n=40) and controls (n=46) was carried out and results were correlated with lifestyle parameters and clinical measurements (eg, dietary habit and serum creatine kinase, respectively). RESULTS: Athletes had relative increases in pathways (eg, amino acid and antibiotic biosynthesis and carbohydrate metabolism) and faecal metabolites (eg, microbial produced short-chain fatty acids (SCFAs) acetate, propionate and butyrate) associated with enhanced muscle turnover (fitness) and overall health when compared with control groups. CONCLUSIONS: Differences in faecal microbiota between athletes and sedentary controls show even greater separation at the metagenomic and metabolomic than at compositional levels and provide added insight into the diet-exercise-gut microbiota paradigm.

Journal article

Posma JM, Garcia Perez I, Heaton JC, Burdisso P, Mathers JC, Draper J, Lewis M, Lindon JC, Frost G, Holmes E, Nicholson JKet al., 2017, An integrated analytical and statistical two-dimensional spectroscopy strategy for metabolite identification: application to dietary biomarkers, Analytical Chemistry, Vol: 89, Pages: 3300-3309, ISSN: 1086-4377

A major purpose of exploratory metabolic profiling is for the identification of molecular species that are statistically associated with specific biological or medical outcomes; unfortunately the structure elucidation process of unknowns is often a major bottleneck in this process. We present here new holistic strategies that combine different statistical spectroscopic and analytical techniques to improve and simplify the process of metabolite identification. We exemplify these strategies using study data collected as part of a dietary intervention to improve health and which elicits a relatively subtle suite of changes from complex molecular profiles. We identify three new dietary biomarkers related to the consumption of peas (N-methyl nicotinic acid), apples (rhamnitol) and onions (N-acetyl-S-(1Z)-propenyl-cysteine-sulfoxide) that can be used to enhance dietary assessment and assess adherence to diet. As part of the strategy, we introduce a new probabilistic statistical spectroscopy tool, RED-STORM (Resolution EnhanceD SubseT Optimization by Reference Matching), that uses 2D J-resolved ¹H-NMR spectra for enhanced information recovery using the Bayesian paradigm to extract a subset of spectra with similar spectral signatures to a reference. RED-STORM provided new information for subsequent experiments (e.g. 2D-NMR spectroscopy, Solid-Phase Extraction, Liquid Chromatography prefaced Mass Spectrometry) used to ultimately identify an unknown compound. In summary, we illustrate the benefit of acquiring J-resolved experiments alongside conventional 1D ¹H-NMR as part of routine metabolic profiling in large datasets and show that application of complementary statistical and analytical techniques for the identification of unknown metabolites can be used to save valuable time and resource.

Journal article

Brignardello J, Holmes E, Garcia-Perez I, 2017, Metabolic phenotyping of diet and dietary Intake, Advances in Food and Nutrition Research, Pages: 231-270, ISBN: 978-0-12-811916-7

Nutrition provides the building blocks for growth, repair, and maintenance of the body and is key to maintaining health. Exposure to fast foods, mass production of dietary components, and wider importation of goods have challenged the balance between diet and health in recent decades, and both scientists and clinicians struggle to characterize the relationship between this changing dietary landscape and human metabolism with its consequent impact on health. Metabolic phenotyping of foods, using high-density data-generating technologies to profile the biochemical composition of foods, meals, and human samples (pre- and postfood intake), can be used to map the complex interaction between the diet and human metabolism and also to assess food quality and safety. Here, we outline some of the techniques currently used for metabolic phenotyping and describe key applications in the food sciences, ending with a broad outlook at some of the newer technologies in the field with a view to exploring their potential to address some of the critical challenges in nutritional science.

Book chapter

Garcia Perez I, Posma JM, Gibson R, Chambers ES, Hansen TH, Vestergaard H, Hansen T, Beckmann M, Pedersen O, Elliott P, Stamler J, Nicholson JK, Draper J, Mathers JC, Holmes E, Frost Get al., 2017, Objective assessment of dietary patterns using metabolic phenotyping: a randomized, controlled, crossover trial, The Lancet Diabetes & Endocrinology, Vol: 5, Pages: 184-195, ISSN: 2213-8587

Background: The burden of non-communicable diseases, such as obesity, diabetes, coronary heart disease and cancer, can be reduced by the consumption of healthy diets. Accurate monitoring of changes in dietary patterns in response to food policy implementation is challenging. Metabolic profiling allows simultaneous measurement of hundreds of metabolites in urine, many of them influenced by food intake. We aim to classify people according to dietary behaviour and enhance dietary reporting using metabolic profiling of urine.Methods: To develop metabolite models from 19 healthy volunteers who attended a clinical research unit for four day periods on four occasions. We used the World Health Organisation’s healthy eating guidelines (increase fruits, vegetables, wholegrains, dietary fibre and decrease fats, sugars, and salt) to develop four dietary interventions lasting for four days each that ranged from a diet associated with a low to high risk of developing non-communicable disease. Urine samples were measured by 1H-NMR spectroscopy. This study is registered as an International Standard Randomized Controlled Trial, number ISRCTN 43087333. INTERMAP U.K. (n=225) and a healthy-eating Danish cohort (n=66) were used as free-living validation datasets.Findings: There was clear separation between the urinary metabolite profiles of the four diets. We also demonstrated significant stepwise differences in metabolite levels between the lowest and highest metabolic risk diets and developed metabolite models for each diet. Application of the derived metabolite models to independent cohorts confirmed the association between urinary metabolic and dietary profiles in INTERMAP (P<0•001) and the Danish cohort (P<0•001).Interpretation: Urinary metabolite models, developed in a highly controlled environment, can classify groups of free-living people into consumers of dietary profiles associated with lower or higher non-communicable disease risk based on multivariate m

Journal article

Lloyd AJ, Zubair H, Willis ND, Wilson T, Xie L, Tailliart K, Chambers ES, Garcia-Perez I, Holmes E, Frost G, Mathers JC, Beckmann M, Draper Jet al., 2016, Quantification of dietary biomarkers in spot urine samples reflects the intake of foods of UK high public health importance, Publisher: Cambridge University Press (CUP), Pages: E248-E248, ISSN: 0029-6651

An understanding of causal relations between diet and health is hindered by the lack of robust biological markers of food exposure (1).The rapid development of metabolomics technology offers opportunity for the identification of urine biomarkers for the intake of arange of foods of high public health importance (2), (3). Using high mass resolution mass spectrometry and machine learning data analysis,we have discovered potential urinary biomarkers in controlled clinical studies with a range of analytical techniques (2). To haveutility for population monitoring, we aim to validate biomarker performance in free-living individuals using urine samples collected inthe home with a minimal impact on normal daily activities.Two complementary multiple reaction monitoring (MRM) routines using triple quadrupole mass spectrometry (QQQ-MS) havebeen developed to quantify concurrently dietary exposure biomarkers of more than 20 foods of high public health importance inthe UK. MRM quantification of metabolite levels in spot urines collected either before bed time or a first morning void identifieda sub-set of potential biomarkers that demonstrated robust linkage with reported dietary intake (examples in Table 1). Figure 1demonstrates the ability of selected biomarkers to report exposure in relation to muscle meat intake from lunch time to bedtime(Beefburger; 106gm, Chicken breast; 130gm; Processed Ham; 40·5 gm) in 6 free-living individuals. Anserine was strongly, and specifically,associated with poultry intake, whilst the urinary outputs of 3-methyl histidine and carnosine reflect striated muscle intake,with levels substantially reduced when meals contain lower quality, and processed, meats with reduced levels of striated musclecontent.

Conference paper

Kaluarachchi MR, Boulangé CL, Garcia-Perez I, Lindon JC, Minet EFet al., 2016, Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers, Bioanalysis, Vol: 8, Pages: 2023-2043, ISSN: 1757-6199

Aim: Determining perturbed biochemical functions associated with tobacco smoking should be helpful for establishing causal relationships between exposure and adverse events. Results: A multiplatform comparison of serum of smokers (n = 55) and never-smokers (n = 57) using nuclear magnetic resonance spectroscopy, UPLC–MS and statistical modeling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modeling adverse biological events using available databases. Perturbation of metabolites involved in chronic obstructive pulmonary disease, cardiovascular diseases and cancer were identified and discussed. Conclusion: Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development, which can be applied to next-generation tobacco and nicotine products for comparative risk assessment.

Journal article

Serrano-Contreras JI, Garcia-Perez I, Melendez-Camargo ME, Gerardo Zepeda Let al., 2016, NMR-Based Metabonomic Analysis of Physiological Responses to Starvation and Refeeding in the Rat, Journal of Proteome Research, Vol: 15, Pages: 3241-3254, ISSN: 1535-3893

Starvation is a postabsorptive condition derived from a limitation on food resources by external factors. Energy homeostasis is maintained under this condition by using sources other than glucose via adaptive mechanisms. After refeeding, when food is available, other adaptive processes are linked to energy balance. However, less has been reported about the physiological mechanisms present as a result of these conditions, considering the rat as a supraorganism. Metabolic profiling using 1H nuclear magnetic resonance spectroscopy was used to characterize the physiological metabolic differences in urine specimens collected under starved, refed, and recovered conditions. In addition, because starvation induced lack of faecal production and not all animals produced faeces during refeeding, 24 h pooled faecal water samples were also analyzed. Urinary metabolites upregulated by starvation included 2-butanamidoacetate, 3-hydroxyisovalerate, ketoleucine, methylmalonate, p-cresyl glucuronide, p-cresyl sulfate, phenylacetylglycine, pseudouridine, creatinine, taurine, and N-acetyl glycoprotein, which were related to renal and skeletal muscle function, β-oxidation, turnover of proteins and RNA, and host–microbial interactions. Food-derived metabolites, including gut microbial cometabolites, and tricarboxylic acid cycle intermediates were upregulated under refed and recovered conditions, which characterized anabolic urinary metabotypes. The upregulation of creatine and pantothenate indicated an absorptive state after refeeding. Fecal short chain fatty acids, 3-(3-hydroxyphenyl)propionate, lactate, and acetoin provided additional information about the combinatorial metabolism between the host and gut microbiota. This investigation contributes to allow a deeper understanding of physiological responses associated with starvation and refeeding.

Journal article

Byrne CS, Chambers ES, Alhabeeb H, Chhina N, Morrison DJ, Preston T, Tedford C, Fizpatrick J, Irani C, Busza A, Garcia-Perez I, Fountana S, Holmes E, Goldstone AP, Frost GSet al., 2016, Increased colonic propionate reduces anticipatory reward responses in the human striatum to high-energy foods, American Journal of Clinical Nutrition, Vol: 104, ISSN: 1938-3207

BACKGROUND: Short-chain fatty acids (SCFAs), metabolites produced through the microbial fermentation of nondigestible dietary components, have key roles in energy homeostasis. Animal research suggests that colon-derived SCFAs modulate feeding behavior via central mechanisms. In humans, increased colonic production of the SCFA propionate acutely reduces energy intake. However, evidence of an effect of colonic propionate on the human brain or reward-based eating behavior is currently unavailable. OBJECTIVES: We investigated the effect of increased colonic propionate production on brain anticipatory reward responses during food picture evaluation. We hypothesized that elevated colonic propionate would reduce both reward responses and ad libitum energy intake via stimulation of anorexigenic gut hormone secretion. DESIGN: In a randomized crossover design, 20 healthy nonobese men completed a functional magnetic resonance imaging (fMRI) food picture evaluation task after consumption of control inulin or inulin-propionate ester, a unique dietary compound that selectively augments colonic propionate production. The blood oxygen level-dependent (BOLD) signal was measured in a priori brain regions involved in reward processing, including the caudate, nucleus accumbens, amygdala, anterior insula, and orbitofrontal cortex (n = 18 had analyzable fMRI data). RESULTS: Increasing colonic propionate production reduced BOLD signal during food picture evaluation in the caudate and nucleus accumbens. In the caudate, the reduction in BOLD signal was driven specifically by a lowering of the response to high-energy food. These central effects were partnered with a decrease in subjective appeal of high-energy food pictures and reduced energy intake during an ad libitum meal. These observations were not related to changes in blood peptide YY (PYY), glucagon-like peptide 1 (GLP-1), glucose, or insulin concentrations. CONCLUSION: Our results suggest that colonic propionate production may play

Journal article

Garcia-Perez I, Posma JM, Chambers ES, Nicholson JK, C Mathers J, Beckmann M, Draper J, Holmes E, Frost Get al., 2016, An analytical pipeline for quantitative characterization of dietary intake: application to assess grape intake., Journal of Agricultural and Food Chemistry, Vol: 64, Pages: 2423-2431, ISSN: 1520-5118

Lack of accurate dietary assessment in free-living populations requires discovery of new biomarkers reflecting food intake qualitatively and quantitatively to objectively evaluate effects of diet on health. We provide a proof-of-principle for an analytical pipeline to identify quantitative dietary biomarkers. Tartaric acid was identified as dose-responsive urinary biomarker of grape intake and subsequently quantified in volunteers who followed a series of 4-day dietary interventions incorporating 0g/day, 50g/day, 100g/day and 150g/day of grapes in standardized diets from a randomized controlled clinical trial. The most accurate quantitative prediction of grape intake was obtained in 24h urine samples which have the strongest linear relationship between grape intake and tartaric acid excretion (r2=0.90). This new methodological pipeline for estimating nutritional intake based on coupling dietary intake information and quantified nutritional biomarkers was developed and validated in a controlled dietary intervention study, showing that this approach can improve the accuracy of estimating nutritional intakes.

Journal article

Stradling C, Thomas GN, Hemming K, Frost G, Garcia-Perez I, Redwood S, Taheri Set al., 2016, Randomised controlled pilot study to assess the feasibility of a Mediterranean Portfolio dietary intervention for cardiovascular risk reduction in HIV dyslipidaemia: a study protocol., BMJ Open, Vol: 6, ISSN: 2044-6055

INTRODUCTION: HIV drug treatment has greatly improved life expectancy, but increased risk of cardiovascular disease remains, potentially due to the additional burdens of infection, inflammation and antiretroviral treatment. The Mediterranean Diet has been shown to reduce cardiovascular risk and mortality in the general population, but no evidence exists for this effect in the HIV population. This study will explore the feasibility of a randomised controlled trial (RCT) to examine whether a Mediterranean-style diet that incorporates a portfolio of cholesterol-lowering foods, reduces cardiovascular risk in people with HIV dyslipidaemia. METHODS AND ANALYSIS: 60 adults with stable HIV infection on antiretroviral treatment and low-density lipoprotein cholesterol >3 mmol/L will be recruited from 3 West Midlands HIV services. Participants will be randomised 1:1 to 1 of 2 dietary interventions, with stratification by gender and smoking status. Participants allocated to Diet1 will receive advice to reduce saturated fat intake, and those to Diet2 on how to adopt the Mediterranean Portfolio Diet with additional cholesterol-lowering foods (nuts, stanols, soya, oats, pulses). Measurements of fasting blood lipids, body composition and arterial stiffness will be conducted at baseline, and month 6 and 12 of the intervention. Food intake will be assessed using the Mediterranean Diet Score, 3-day food diaries and metabolomic biomarkers. Questionnaires will be used to assess quality of life and process evaluation. Qualitative interviews will explore barriers and facilitators to making dietary changes, and participant views on the intervention. Qualitative data will be analysed using the Framework Method. Feasibility will be assessed in terms of trial recruitment, retention, compliance to study visits and the intervention. SD of outcomes will inform the power calculation of the definitive RCT. ETHICS: The West Midlands Ethics Committee has approved this study and informed consent f

Journal article

Serrano-Contreras JI, Garcia-Perez I, Melendez-Camargo ME, Zepeda-Vallejo LGet al., 2016, NMR-based metabonomic analysis of normal rat urine and faeces in response to (+/-)-venlafaxine treatment, Journal of Pharmaceutical and Biomedical Analysis, Vol: 123, Pages: 82-92, ISSN: 0731-7085

(±)-Venlafaxine, a bicyclic antidepressant of the serotonin-norepinephrine reuptake inhibitor (SNRI) class, is prescribed for the treatment of depression and anxiety disorders. As is the case with other antidepressants, its precise mechanisms of action are still unknown. Pharmacometabonomic approaches allow for the detection of diverse metabolites, unlike classic methods for analysing drug interaction based on single metabolites and linear pathways. This provides a global view of the state of homeostasis during treatment and an insight into the mechanisms of action of a drug. Accordingly, the final outcome of treatment is characterised by the network of reactome pathways derived from the on-target and off-target effects of the drug. Regarding antidepressants, the drug network may be located in the gut–microbiome–brain–liver–kidney–immune–cardiovascular system axis (GMBLKICA), implying that neurotransmitters participate as signalling molecules in bidirectional communication. If their bioavailability is increased, this communication and the state of homeostasis may be disrupted. With a pharmacometabonomic approach using NMR in combination with different chemometric methods, a determination was made of subtle changes in the metabolic profile (metabotype) of urine and faeces in normal Wistar rats following a single administration of pharmacological doses of (±)-venlafaxine hydrochloride. Based on the drug-response metabotypes observed, (±)-venlafaxine had effects on gut microbial co-metabolites and osmolytes. Hence, it can be hypothesized that bidirectional communication in the multiorgan axis was perturbed by this drug, and very likely by its active metabolite, (±)-desvenlafaxine. This disrupted signalling could be related not only to therapeutic and adverse effects, but also to the lag period in treatment response.

Journal article

Andreas NJ, Hyde MJ, Gomez-Romero M, Lopez-Gonzalvez MA, Villaseñor A, Wijeyesekera A, Barbas C, Modi N, Holmes E, Garcia-Perez Iet al., 2015, Multiplatform characterization of dynamic changes in breast milk during lactation., Electrophoresis, Vol: 36, Pages: 2269-2285, ISSN: 1522-2683

The multicomponent analysis of human breast milk (BM) by metabolic profiling is a new area of study applied to determining milk composition, and is capable of associating BM composition with maternal characteristics, and subsequent infant health outcomes. A multi-platform approach combining high-performance as well as ultra-performance liquid-chromatography (HPLC-MS and UPLC-MS), gas chromatography (GC-MS), capillary electrophoresis (CE-MS) coupled to mass spectrometry and (1) H NMR spectroscopy was used to comprehensively characterize metabolic profiles from seventy BM samples. A total of 710 metabolites spanning multiple molecular classes were defined. The utility of the individual and combined analytical platforms was explored in relation to numbers of metabolites identified, as well as the reproducibility of the methods. The greatest number of metabolites were identified by the single phase HPLC-MS method, whilst CE-MS uniquely profiled amino acids in detail and NMR was the most reproducible, whereas GC-MS targeted volatile compounds and short chain fatty acids. Dynamic changes in BM composition were characterized over the first 3 months of lactation. Metabolites identified as altering in abundance over lactation included fucose, di- and triacylglycerols and short chain fatty acids, known to be important for infant immunological, neurological and gastrointestinal development, as well as being an important source of energy. This extensive metabolic coverage of the dynamic BM metabolome provides a baseline for investigating the impact of maternal characteristics, as well as establishing the impact of environmental and dietary factors on the composition of BM, with a focus on the downstream health consequences this may have for infants. This article is protected by copyright. All rights reserved.

Journal article

Elliott P, Posma JM, Chan Q, Garcia-Perez I, Wijeyesekera A, Bictash M, Ebbels TMD, Ueshima H, Zhao L, van Horn L, Daviglus M, Stamler J, Holmes E, Nicholson JKet al., 2015, Urinary metabolic signatures of human adiposity, SCIENCE TRANSLATIONAL MEDICINE, Vol: 7, ISSN: 1946-6234

Journal article

Willis ND, Dodds SE, Lloyd AJ, Xie L, Chambers ES, Garcia-Perez I, Frost G, Beckmann M, Draper J, Mathers JCet al., 2015, Dietary compliance in a human intervention study investigating the impact of specific foods on urinary metabolites, PROCEEDINGS OF THE NUTRITION SOCIETY, Vol: 74, Pages: E127-E127, ISSN: 0029-6651

Journal article

Garcia-Perez I, Lindon JC, Minet E, 2014, Application of CE-MS to a metabonomics study of human urine from cigarette smokers and non-smokers, BIOANALYSIS, Vol: 6, Pages: 2733-2749, ISSN: 1757-6180

Journal article

Hall AM, Vilasi A, Garcia-Perez I, Lapsley M, Alston CL, Pitceathly RDS, McFarland R, Schaefer AM, Turnbull DM, Beaumont NJ, Hsuan JJ, Cutillas PR, Lindon JC, Holmes E, Unwin RJ, Taylor RW, Gorman GS, Rahman S, Hanna MGet al., 2014, The urinary proteome and metabonome differ from normal in adults with mitochondrial disease, Kidney International, Vol: 87, Pages: 610-622, ISSN: 1523-1755

We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin; established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.

Journal article

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