1. Investigación

Las alergias alimentarias son cada vez más prevalentes y de mayor gravedad, y la alergia a las proteínas de la leche de vaca (APLV) es una de las más importantes en lactantes. Varios estudios han sugerido que desequilibrios en la microbiota intestinal, posiblemente influenciados por la microbiota materna, juegan un papel importante en el desarrollo de APLV. La metabolómica ofrece un enfoque prometedor, ya que examina los cambios metabólicos en patologías como las alergias alimentarias. La metabolómica fecal, en concreto, es ideal para estudiar la microbiota intestinal en la APLV. Con este objetivo, se recogieron muestras fecales de lactantes con APLV, sus madres y sus abuelas, y se compararon con los respectivos grupos control. Se recogieron cuestionarios detallados para recabar información sobre variables como la dieta, el modo de nacimiento, el uso de antibióticos y los antecedentes alérgicos. El análisis metabolómico se llevó a cabo en la cohorte final de 200 muestras mediante cromatografía de gases acoplada a espectrometría de masas con analizador de cuadrupolo-tiempo de vuelo (GC-QTOF-MS) y electroforesis capilar con inyección multisegmento acoplada a TOF-MS (MSI-CE-TOF-MS). Con todos estos datos, la tesis se dividió en dos capítulos: el Capítulo 1 presenta la integración de los datos de metabolómica fecal y metagenómica (incluyendo secuenciación del gen 16S rRNA y shotgun) en una prueba de concepto donde se compararon los tres grupos de edad, mientras que en el Capítulo 2 se presentan las diferencias en el metaboloma fecal de los lactantes debidas a la APLV, la dieta y el modo de nacimiento. En conjunto, esta tesis aporta información valiosa sobre el desarrollo del microbioma y los metabolitos asociados a lo largo de la vida. Se necesitan más estudios para arrojar más luz sobre la interacción entre la microbiota y el desarrollo de la APLV, especialmente estudios con fenotipos más graves y el seguimiento de varios puntos temporales de recogida de muestras.

Background: The pathological mechanism of the gastrointestinal forms of food aller-gies is less understood in comparison to other clinical phenotypes, such as asthmaand anaphylaxis Importantly, high-IgE levels are a poor prognostic factor in gastroin-testinal allergies.Methods: This study investigated how high-IgE levels influence the development ofintestinal inflammation and the metabolome in allergic enteritis (AE), using IgE knock-in (IgEki) mice expressing high levels of IgE. In addition, correlation of the altered me-tabolome with gut microbiome was analysed.Results: Ovalbumin-sensitized and egg-white diet-fed (OVA/EW) BALB/c WT micedeveloped moderate AE, whereas OVA/EW IgEki mice induced more aggravated in-testinal inflammation with enhanced eosinophil accumulation. Untargeted metabo-lomics detected the increased levels of N-tau-methylhistamine and 2,3-butanediol,and reduced levels of butyric acid in faeces and/or sera of OVA/EW IgEki mice, whichwas accompanied with reduced Clostridium and increased Lactobacillus at the genus level. Non-sensitized and egg-white diet-fed (NC/EW) WT mice did not exhibit anysigns of AE, whereas NC/EW IgEki mice developed marginal degrees of AE. Comparedto NC/EW WT mice, enhanced levels of lysophospholipids, sphinganine and sphin-gosine were detected in serum and faecal samples of NC/EW IgEki mice. In addi-tion, several associations of altered metabolome with gut microbiome—for exampleAkkermansia with lysophosphatidylserine—were detected.Conclusions: Our results suggest that high-IgE levels alter intestinal and systemic levelsof endogenous and microbiota-associated metabolites in experimental AE. This studycontributes to deepening the knowledge of molecular mechanisms for the developmentof AE and provides clues to advance diagnostic and therapeutic strategies of allergicdiseases

The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.

Leishmania donovani infection of macrophages drives profound changes in the metabolism of both the host macrophage and the parasite, which undergoes different phases of development culminating in replication and propagation. However, the dynamics of this parasite-macrophage cometabolome are poorly understood. In this study, a multiplatform metabolomics pipeline combining untargeted, high-resolution CE-TOF/MS and LC-QTOF/MS with targeted LC-QqQ/MS was followed to characterize the metabolome alterations induced in L. donovani-infected human monocyte-derived macrophages from different donors at 12, 36, and 72 h post-infection. The set of alterations known to occur during Leishmania infection of macrophages, substantially expanded in this investigation, characterized the dynamics of the glycerophospholipid, sphingolipid, purine, pentose phosphate, glycolytic, TCA, and amino acid metabolism. Our results showed that only citrulline, arginine, and glutamine exhibited constant trends across all studied infection time points, while most metabolite alterations underwent a partial recovery during amastigote maturation. We determined a major metabolite response pointing to an early induction of sphingomyelinase and phospholipase activities and correlated with amino acid depletion. These data represent a comprehensive overview of the metabolome alterations occurring during promastigote-to-amastigote differentiation and maturation of L. donovani inside macrophages that contributes to our understanding of the relationship between L. donovani pathogenesis and metabolic dysregulation.

The mechanisms whereby Mycobacterium tuberculosis (Mtb) rewires the host metabolism in vivo are surprisingly unexplored. Here, we used three high-resolution mass spectrometry platforms to track altered lung metabolic changes associated with Mtb infection of mice. The multiplatform data sets were merged using consensus orthogonal partial least squaresdiscriminant analysis (cOPLS-DA), an algorithm that allows for the joint interpretation of the results from a single multivariate analysis. We show that Mtb infection triggers a temporal and progressive catabolic state to satisfy the continuously changing energy demand to control infection. This causes dysregulation of metabolic and oxido-reductive pathways culminating in Mtbassociated wasting. Notably, high abundances of trimethylamine-N-oxide (TMAO), produced by the host from the bacterial metabolite trimethylamine upon infection, suggest that Mtb could exploit TMAO as an electron acceptor under anaerobic conditions. Overall, these new pathway alterations advance our understanding of the link between Mtb pathogenesis and metabolic dysregulation and could serve as a foundation for new therapeutic intervention strategies. Mass spectrometry data has been deposited in the Metabolomics Workbench repository (data-set identifier: ST001328).

Composition of the gut microbiota changes during ageing, but questions remain about whether age is also associated with deficits in microbiome function and whether these changes occur sharply or progressively. The ability to define these deficits in populations of different ages may help determine a chronological age threshold at which deficits occur and subsequently identify innovative dietary strategies for active and healthy ageing. Here, active gut microbiota and associated metabolic functions were evaluated using shotgun proteomics in three well‐defined age groups consisting of 30 healthy volunteers, namely, ten infants, ten adults and ten elderly individuals. Samples from each volunteer at intervals of up to 6 months (n = 83 samples) were used for validation. Ageing gradually increases the diversity of gut bacteria that actively synthesize proteins, that is by 1.4‐fold from infants to elderly individuals. An analysis of functional deficits consistently identifies a relationship between tryptophan and indole metabolism and ageing (p < 2.8e−8). Indeed, the synthesis of proteins involved in tryptophan and indole production and the faecal concentrations of these metabolites are directly correlated (r2 > .987) and progressively decrease with age (r2 > .948). An age threshold for a 50% decrease is observed ca. 11–31 years old, and a greater than 90% reduction is observed from the ages of 34–54 years. Based on recent investigations linking tryptophan with abundance of indole and other “healthy” longevity molecules and on the results from this small cohort study, dietary interventions aimed at manipulating tryptophan deficits since a relatively “young” age of 34 and, particularly, in the elderly are recommended.

The lack of knowledge about the onset and progression of Parkinson’s disease (PD) hampers its early diagnosis and treatment. Metabolomics might shed light on the PD imprint seeking a broader view of the biochemical remodeling induced by this disease in an early and pre-symptomatic stage and unveiling potential biomarkers. To achieve this goal, we took advantage of the great potential of the European Prospective Study on Nutrition and Cancer (EPIC) cohort to apply metabolomics searching for early diagnostic PD markers. This cohort consisted of healthy volunteers that were followed for around 15 years until June 2011 to ascertain incident PD. For this untargeted metabolomics-based study, baseline preclinical plasma samples of 39 randomly selected individuals that developed PD (Pre-PD group) and the corresponding control group were analyzed using a multiplatform approach. Data were statistically analyzed and exposed alterations in 33 metabolites levels, including significantly lower levels of free fatty acids (FFAs) in the preclinical samples from PD subjects. These results were then validated by adopting a targeted HPLC-QqQ-MS approach. After integrating all the metabolites affected, our finding revealed alterations in FFAs metabolism, mitochondrial dysfunction, oxidative stress, and gut–brain axis dysregulation long before the development of PD hallmarks. Although the biological purpose of these events is still unknown, the remodeled metabolic pathways highlighted in this work might be considered worthy prognostic biomarkers of early prodromal PD. The findings revealed by this work are of inestimable value since this is the first study conducted with samples collected many years before the disease development.

The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.

El asma puede presentar múltiples fenotipos, como el asma alérgico o no alérgico. Su tratamiento es complejo, existiendo pacientes graves que no responden a las medicaciones actualmente disponibles, sufren exacerbaciones frecuentes y presentan comorbilidades como la poliposis nasosinusal. La estratificación de pacientes mediante el uso de biomarcadores permitiría mejorar el tratamiento y descubrir nuevas dianas terapéuticas. Para identificar biomarcadores de estratificación por gravedad, se estudiaron pacientes asmáticos alérgicos estratificados por gravedad utilizando metabolómica y proteómica. Los pacientes con asma grave no controlado presentaron una activación característica de las rutas del ácido araquidónico, la fosfolipasa A2, y la respuesta Th2. Además, para evaluar la contribución del fenotipo alérgico al asma, se realizó un análisis metabolómico de pacientes graves no controlados con y sin alergia. Los pacientes asmáticos alérgicos mostraron una activación de la ruta de la fosfolipasa A2 y una alteración en el perfil de ácidos biliares. Por último, para conocer el papel sistémico y local de la alergia en la poliposis nasal, se estudiaron pacientes con poliposis con y sin alergia utilizando metabolómica de suero y tejido y análisis histológicos. Los pacientes alérgicos presentaron niveles reducidos de lisofosfolípidos, bilirrubina y cortisol; y un mayor número de eosinófilos en sus pólipos.

Se ha diseñado, implementado y validado una herramienta computacional de anotación de metabolitos que: (1) integró metabolitos de diferentes bases de datos basadas en su estructura única; (2) desarrolló un modelo relacional para la explotación de los datos; (3) desarrolló un sistema experto de conocimiento para puntuar las anotaciones en experimentos de matabolómica no dirigida oteniendo evidencia que soporte o refute las mismas en base a las posibilidades de ionización, reglas de intensidad entre diferentes aductos y orden de elución de compuestos en cromatografía de fase reversa. De esta forma, se puede obtener un nivel mayor de confianza sobre las anotaciones y se complementa la técnica de espectrometría en tándem para la identificación de matabolitos. La correcta identificación de metabolitos va a resultar en una mejor interpretación del análisis biológico subsecuente. Esta herramienta es la primera en utilizar información analítica y no analítica para soportar la anotación de metabolitos, aumentando de esta forma el nivel de confianza sobre los metabolitos.