Matthias Scholz

Matthias Scholz
Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige | Fondazione Mach · Department of Food Quality and Nutrition (DQAN)

PhD

About

63
Publications
18,550
Reads
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7,363
Citations
Citations since 2017
15 Research Items
5319 Citations
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Introduction
Matthias Scholz is a computer scientist with a Ph.D. in Bioinformatics and several years of experience in analyzing biomedical data. He developed new computational tools in the area of metagenomics with special focus on analyzing the gut microbiome which resulted in two publications in Nature Methods. In 2016 he moved to Edmund Mach Foundation in Italy to study how nutrients and other food components affect the human intestinal microbiota. --> www.matthias-scholz.de
Additional affiliations
July 2016 - present
Edmund Mach Foundation
Position
  • Senior Researcher
July 2013 - July 2016
Università degli Studi di Trento
Position
  • PostDoc Position
July 2010 - June 2013
Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige
Position
  • PostDoc Position

Publications

Publications (63)
Article
Full-text available
Background Previous studies have linked the Mediterranean diet (MED) with improved cardiometabolic health, showing preliminary evidence for a mediating role of the gut microbiome. We recently suggested the Green-Mediterranean (Green-MED) diet as an improved version of the healthy MED diet, with increased consumption of plant-based foods and reduced...
Article
Full-text available
Purpose Aleurone is a cereal bran fraction containing a variety of beneficial nutrients including polyphenols, fibers, minerals and vitamins. Animal and human studies support the beneficial role of aleurone consumption in reducing cardiovascular disease (CVD) risk. Gut microbiota fiber fermentation, polyphenol metabolism and betaine/choline metabol...
Article
Full-text available
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To levera...
Article
Full-text available
PurposeValidated biomarkers of food intake (BFIs) have recently been suggested as a useful tool to assess adherence to dietary guidelines or compliance in human dietary interventions. Although many new candidate biomarkers have emerged in the last decades for different foods from metabolic profiling studies, the number of comprehensively validated...
Article
Full-text available
Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By as...
Article
Background and aims Diet is both a modulator of the gastrointestinal microbiota and an important therapy in irritable bowel syndrome (IBS). We aimed to comprehensively (i) identify diet-microbiota associations in adults with IBS consuming habitual diet; (ii) assess the impact of two nutritional interventions on the microbiota; and (iii) determine w...
Article
Full-text available
Reduced activation of energy metabolism increases adiposity in humans and other mammals. Thus, exploring dietary and molecular mechanisms able to improve energy metabolism is of paramount medical importance, as such mechanisms can be leveraged as a therapy for obesity and related disorders. Here, we show that a designer protein-deprived diet enrich...
Article
This study presents the results of semi-pilot scale anaerobic digestion tests conducted under dry thermophilic conditions with the addition of biochar (6% on fresh mass basis of inoculum), derived from an industrial gasification plant, for determining biogas and biomethane production from organic fraction of municipal solid waste. By using two type...
Article
Full-text available
Background & Aims We evaluated the efficacy and safety of diet-modulated autologous fecal microbiota transplantation (aFMT) for treatment of weight regain after the weight loss phase. Methods In the DIRECT-PLUS weight loss trial (May 2017 through July 2018), abdominally obese or dyslipidemic participants in Israel were randomly assigned to (1)heal...
Presentation
Apples are a rich source of polyphenols and fiber. Proanthocyanidins (PAs), the largest polyphenolic class in apples, can reach the colon almost intact where they interact with the gut microbiota producing simple phenolic acids. These metabolites have the potential to modulate gut microbiota composition and activity and impact on host physiology. A...
Article
Full-text available
Introduction: The gut microbiome has attracted much attention in the last decade due to new studies and technologies revealing how gut microbes play a key role in human health and disease risk. However, we still know little about how diets, foods and nutrients shape the gut microbiome. Materials and Methods: To expand our knowledge about the compl...
Article
White wines from two vintages were bottled in green and flint glass bottles and stored under typical supermarket shelf conditions. Light-strike fault, colour changes, light and temperature exposure were monitored up to 50 days. In general, green glass bottles secured wine quality for the tested period. Only a few flint glass bottled wines developed...
Article
Background & Aims Dietary restriction of fermentable carbohydrates (a low FODMAP diet) has been reported to reduce symptoms in some patients with irritable bowel syndrome (IBS). We performed a randomized, placebo-controlled study to determine its effects on symptoms and the fecal microbiota in patients with IBS. Methods We performed a 2x2 factoria...
Article
Full-text available
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collect...
Preprint
Full-text available
The gut microbiome starts to be shaped in the first days of life and continues to increase its diversity during the first months. Several investigations are assessing the link between the configuration of the infant gut microbiome and infant health, but a comprehensive strain-level assessment of vertically transmitted microbes from mother to infant...
Presentation
Microbial species comprise strains with largely different set of genes and functional potential. Identifying microbial strains and characterizing their genes is thus essential for pathogen discovery, epidemiology and population genomics. Here we present a novel computational strain-level metagenomic profiling tool, called PanPhlAn, for identifying...
Article
Full-text available
Apple (Malus x domestica Borkh.) is a model species for studying the metabolic changes that occur at the onset of ripening in fruit crops and the physiological mechanisms that are governed by the hormone ethylene. In this study, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive an...
Article
Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution....
Article
Full-text available
Necrotizing enterocolitis (NEC) afflicts approximately 10% of extremely preterm infants with high fatality. Inappropriate bacterial colonization with Enterobacteriaceae is implicated, but no specific pathogen has been identified. We identify uropathogenic E. coli (UPEC) colonization as a significant risk factor for the development of NEC and subseq...
Chapter
Microbial communities are complex biological entities that are crucial in virtually all natural and human-associated ecosystems. Whole-metagenome shotgun (WMS) sequencing provides the opportunity to explore the entire genomic content of microbiomes in specific environments, but several computational challenges are encountered in the data analysis....
Article
Full-text available
Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohyd...
Article
Full-text available
Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive na...
Article
The high ethanol level in wine has become an important issue for all the main wine producing countries. Several techniques are available to the wine industry to reduce the ethanol content; among them, the membrane contactors are certainly one of the newest. Very few studies on the effect of this practice on the wine quality and aroma profile and on...
Article
Full-text available
Anthocyanins, which are dietary flavonoids occurring in fruit and beverages, are reported to have a beneficial impact on a wide range of chronic diseases, such as cardiovascular, neurodegenerative and neoplastic dis- eases. To understand the underlying mechanisms, a bio- chemical description of the changes in cell metabolism caused by anthocyanins...
Article
Full-text available
Wine micro-oxygenation is a globally used treatment and its effects were studied here by analysing by untargeted LC-MS the wine metabolomic fingerprint. Eight different procedural variations, marked by the addition of oxygen (four levels) and iron (two levels) were applied to Sangiovese wine, before and after malolactic fermentation. Data analysis...
Data
Average levels of dissolved oxygen (µg/L) measured at four time points using oxo-luminescence with PreSens (Nomacorc) in all wines during the experiment after malolactic fermentation. Also in this case the concentration values never exceeded the concentrations typical for microoxygenation. The vertical bar shows the standard deviations. (TIF)
Data
Average amount of acetaldehyde (mg/L), measured at five time points using GC in all wines during the experiment before malolactic fermentation. The concentration of acetaldehyde was found to increase according to the level of oxygen applied and the duration of the treatments. The vertical bar shows the standard deviations. (TIF)
Data
Average amount of acetaldehyde (mg/L), measured at four time points, using GC, in all wines during the experiment after malolactic fermentation. Also in this experiment the concentration of acetaldehyde was found to increase according to the level of oxygen applied and the duration of the treatments. The vertical bar shows the standard deviations....
Data
Experimental design of the two micro-oxygenation experiments, performed respectively before (pre-MLF) and after malolactic fermentation (post-MLF). (XLS)
Data
Average levels of dissolved oxygen (µg/L) measured at six time points using oxo-luminescence with PreSens (Nomacorc) in all wines during the experiment before malolactic fermentation. Concentration values were always found to fall within the concentrations typical for microoxygenation. The vertical bar shows the standard deviations. (TIF)
Data
Iron level candidate biomarkers. In yellow are marked diagnostic ions of the identified candidates. In red are marked diagnostic fragments of oligosaccharides. (XLS)
Data
Oxygen level candidate biomarkers. In yellow are marked diagnostic ions of the identified candidates. (XLS)
Poster
Full-text available
Background / Purpose: Many biological processes behave in a nonlinear way. Observations over time usually show a curved trajectory in the data space. To understand the dynamics of biological processes we have to identify and analyze the time trajectory. This can be done by using a nonlinear extension of principal component analysis (PCA), which pro...
Article
Heterosis-associated cellular and molecular processes were analyzed in seeds and seedlings of Arabidopsis thaliana accessions Col-0 and C24 and their heterotic hybrids. Microscopic examination revealed no advantages in terms of hybrid mature embryo organ sizes or cell numbers. Increased cotyledon sizes were detectable 4 days after sowing. Growth he...
Article
Full-text available
Linear principal component analysis (PCA) can be extended to a nonlinear PCA by using artificial neural networks. But the benefit of curved components requires a careful control of the model complexity. Moreover, standard techniques for model selection, including cross-validation and more generally the use of an independent test set, fail when appl...
Article
Full-text available
Optimal solvent conditions for grape sample preparation were investigated for the purpose of metabolite profiling studies, with the aim of obtaining as many features as possible with the best analytical repeatability. Mixtures of water, methanol and chloroform in different combinations were studied as solvents for the extraction of ground grapes. T...
Article
Full-text available
How are people linked in a highly connected society? Since in many networks a power-law (scale-free) node-degree distribution can be observed, power-law might be seen as a universal characteristics of networks. But this study of communication in the Flickr social online network reveals that power-law node-degree distributions are restricted to only...
Article
Full-text available
Statistical mining and integration of complex molecular data including metabolites, proteins, and transcripts is one of the critical goals of systems biology (Ideker, T., Galitski, T., and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372). A number of studies have demonstrated the parallel...
Article
Full-text available
The malaria parasite, Plasmodium falciparum, replicates asexually in a well-defined infection cycle within human erythrocytes (red blood cells). The intra-erythrocytic developmental cycle (IDC) proceeds with a 48 hour periodicity. Based on available malaria microarray data, which monitored gene expression over one complete IDC in one-hour time inte...
Chapter
Nonlinear principal component analysis (NLPCA) as a nonlinear generalisation of standard principal component analysis (PCA) means to generalise the principal components from straight lines to curves. This chapter aims to provide an extensive description of the autoassociative neural network approach for NLPCA. Several network architectures will be...
Article
Full-text available
pcaMethods is a Bioconductor compliant library for computing principal component analysis (PCA) on incomplete data sets. The results can be analyzed directly or used to estimate missing values to enable the use of missing value sensitive statistical methods. The package was mainly developed with microarray and metabolite data sets in mind, but can...
Chapter
Full-text available
Integrated data analysis is introduced as the intermediate level of a systems biology approach to analyse different 'omics' datasets, i.e., genome-wide measurements of transcripts, protein levels or protein-protein interactions, and metabolite levels aiming at generating a coherent understanding of biological function. In this chapter we focus on d...
Article
Full-text available
This chapter provides an overview of visualization and analysis techniques applied to large-scale datasets from genomics, metabolomics, and proteomics. The aim is to reduce the number of variables (genes, metabolites, or proteins) by extracting a small set of new relevant variables, usually termed components. The advantages and disadvantages of the...
Conference Paper
Full-text available
Experimental time courses often reveal a nonlinear behaviour. Analysing these nonlinearities is even more challenging when the observed phenomenon is cyclic or oscillatory. This means, in general, that the data describe a circular trajectory which is caused by periodic gene regulation. Nonlinear PCA (NLPCA) is used to approximate this trajectory by...
Article
Advances in biotechnologies rapidly increase the number of molecules of a cell which can be observed simultaneously. This includes expression levels of thousands or ten-thousands of genes as well as concentration levels of metabolites or proteins. Such Profile data, observed at different times or at different experimental conditions (e.g., heat o...
Article
Full-text available
Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while opti...
Article
A novel approach is presented combining quantitative metabolite and protein data and multivariate statistics for the analysis of time-related regulatory effects of plant metabolism at a systems level. For the analysis of metabolites, gas chromatography coupled to a time-of-flight mass analyzer (GC-TOF-MS) was used. Proteins were identified and quan...
Article
Full-text available
Motivation: Metabolite fingerprinting is a technology for providing information from spectra of total compositions of metabolites. Here, spectra acquisitions by microchip-based nanoflow-direct-infusion QTOF mass spectrometry, a simple and high throughput technique, is tested for its informative power. As a simple test case we are using Arabidopsis...
Article
Changes in enzymatic activities in response to carbon starvation were in-vestigated in Arabidopsis thaliana in two distinct experiments. One compares the Columbia ecotype (Col-0) and its starch deficient pgm mutant (plastidial phospho-glucomutase), the other investigates the enzymatic activities of Col-0 under extended night conditions. A classical...
Article
Full-text available
Die Hauptkomponentenanalyse (Principal Component Analysis, PCA) ist eine weit verbreitete und vielfältig anwendbare Methode der Dimensionsreduktion und der Merkmalsextraktion. Sie wird benutzt zur Komprimierung, zum Entrauschen von Daten oder allgemein als Vorverarbeitung bei Klassifikations-, Regressions- oder Quellentrennungsaufgaben. Die PCA ist...
Article
Full-text available
Kernel PCA as a nonlinear feature extractor has proven powerful as a preprocessing step for classification algorithms. But it can also be considered as a natural generalization of linear principal component analysis. This gives rise to the question how to use nonlinear features for data compression, reconstruction, and de-noising, applications comm...
Article
Full-text available
Kernel PCA as a nonlinear feature extractor has proven powerful as a preprocessing step for classification algorithms. But it can also be con- sidered as a natural generalization of linear principal component anal- ysis. This gives rise to the question how to use nonlinear features for data compression, reconstruction, and de-noising, applications...
Article
Circular PCA provides a component which describes the principal curvature of the data by a closed curve. This circular component can then be used as a mathematical model of the developmental cycle of the malaria parasite which gives a continuous and noise-reduced description of the biological process. The model was used to visualize the transcripti...

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