Gempipe: A tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models Gioele Lazzari, Giovanna E. Felis, Elisa Salvetti, Matteo Calgaro, Francesca Di Cesare, et al. Msystems, 2026 Genome-scale metabolic models (GSMMs) can mechanistically explain phenotypic differences among closely related bacterial strains. However, high-throughput multi-strain reconstructions of GSMMs are still challenging: reference-based methods inherit curated information while missing new contents; alternatively (universe-based), reference-free methods could cover strain-specific reactions, but they disregard curated information. Ideally, references should be curated pan-GSMMs for species (or genus), but their reconstruction is extremely demanding, making them still rare in the literature. Here, Gempipe is presented, a computational tool streamlining the multi-strain reconstruction and analysis of GSMMs, going through the production of a pan-GSMM. Its reconstruction method is hybrid; as an optional reference, GSMM is automatically expanded with extra reactions taken from a reference-free reconstruction. Gempipe also downloads, filters, and annotates genomes; performs in-depth gene recovery; annotates models’ contents; and predicts strain-specific capabilities. The companion programming interface includes functions ranging from the (pan-)GSMMs’ curation to the multi-strain analysis. Gempipe was validated using multi-strain data sets, showing improved accuracy when compared with state-of-the-art tools. Moreover, metabolic diversities within Limosilactobacillus reuteri were explored, grouping strains into metabolically coherent clusters and systematically predicting health-related metabolites’ biosynthesis. IMPORTANCE Available genome-scale metabolic model (GSMM) reconstruction tools present major limitations in the context of multi-strain modeling. Gempipe surpasses these limitations by implementing a novel, hybrid reconstruction strategy. Not only does it produce more accurate strain-specific GSMMs, but it also produces pan-GSMMs when the only available reference is a manually curated model for a single strain, which is currently the most common case. With the vast availability of genome sequences, the high-throughput, multi-strain GSMM reconstruction and analysis approach provided by Gempipe will facilitate large-scale studies of exploration and bioprospecting of strain-level bacterial metabolic diversity, moving a step forward in strains’ screening and rational selection.
NMR-based-Metabolomics Evaluation in Dogs Infected with Canine Parvovirus: A New Approach for Biomarker/s A. Basoglu, R. Bicici, F. Di Cesare, N. Başpınar, L. Tenori, et al. Veterinaria Italiana, 2025 Despite aggressive treatment, canine parvovirus (CPV) enteritis remains a major cause of morbidity and mortality in puppies. Identifying reliable biomarkers of CPV enteritis is important for determining severity, length of hospital stay, and predicting clinical outcomes. This the first study that aims to emphasize the relevance of the manuscript. Forty-three (43) CPV-infected dogs were diagnosed by a rapid antigen test kit and subsequent PCR, and 10 healthy dogs were enrolled. In this prospective study, metabolomics and cardiac troponin were measured by NMR and ELISA, respectively. The diseased dogs showed statistically significant lower levels of fructose, glucose, citrate, glycerate, glutamate, carnitine, glycine, formate, and higher levels of isoleucine, isovalerate, glycolate, and creatine compared with healthy dogs. The same analysis performed on lipid parameters showed statistically significant higher levels of cholesterol variants, fatty acyl variants, free cholesterol, glycerol backbone, and sphingomyelin and lower levels of phosphoglycerates and esterified cholesterol in the diseased groups. The changes in metabolomics could be attributed to energy deficit, fat mobilization, gluconeogenesis, tricarboxylic acid cycle deficiency, and multiple organ failure. Decreased citrate, and increased fatty acyl chain-CH2CO and sphingomyelin levels will serve as the most useful biomarkers in the prognosis of dogs suffering from CPV infection.
Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals Francesca Di Cesare, Matteo Calgaro, Veronica Ghini, Diletta Francesca Squarzanti, Annachiara De Prisco, et al. Journal of Proteome Research, 2023 Probiotics are live microorganisms that confer health benefits when administered in adequate amounts. They are used to promote gut health and alleviate various disorders. Recently, there has been an increasing interest in the potential effects of probiotics on human physiology. In the presented study, the effects of probiotic treatment on the metabolic profiles of human urine and serum using a nuclear magnetic resonance (NMR)-based metabonomic approach were investigated. Twenty-one healthy volunteers were enrolled in the study, and they received two different dosages of probiotics for 8 weeks. During the study, urine and serum samples were collected from volunteers before and during probiotic supplementation. The results showed that probiotics had a significant impact on the urinary and serum metabolic profiles without altering their phenotypes. This study demonstrated the effects of probiotics in terms of variations of metabolite levels resulting also from the different probiotic posology. Overall, the results suggest that probiotic administration may affect both urine and serum metabolomes, although more research is needed to understand the mechanisms and clinical implications of these effects. NMR-based metabonomic analysis of biofluids is a powerful tool for monitoring host-gut microflora dynamic interaction as well as for assessing the individual response to probiotic treatment.
Exploration of Blood Metabolite Signatures of Colorectal Cancer and Polyposis through Integrated Statistical and Network Analysis Francesca Di Cesare, Alessia Vignoli, Claudio Luchinat, Leonardo Tenori, Edoardo Saccenti Metabolites, 2023 Colorectal cancer (CRC), one of the most prevalent and deadly cancers worldwide, generally evolves from adenomatous polyps. The understanding of the molecular mechanisms underlying this pathological evolution is crucial for diagnostic and prognostic purposes. Integrative systems biology approaches offer an optimal point of view to analyze CRC and patients with polyposis. The present study analyzed the association networks constructed from a publicly available array of 113 serum metabolites measured on a cohort of 234 subjects from three groups (66 CRC patients, 76 patients with polyposis, and 92 healthy controls), which concentrations were obtained via targeted liquid chromatography-tandem mass spectrometry. In terms of architecture, topology, and connectivity, the metabolite-metabolite association network of CRC patients appears to be completely different with respect to patients with polyposis and healthy controls. The most relevant nodes in the CRC network are those related to energy metabolism. Interestingly, phenylalanine, tyrosine, and tryptophan metabolism are found to be involved in both CRC and polyposis. Our results demonstrate that the characterization of metabolite–metabolite association networks is a promising and powerful tool to investigate molecular aspects of CRC.
Nuclear Magnetic Resonance-Based Metabolomics to Predict Early and Late Adverse Outcomes in Ischemic Stroke Treated with Intravenous Thrombolysis Cristina Licari, Leonardo Tenori, Francesca Di Cesare, Claudio Luchinat, Betti Giusti, et al. Journal of Proteome Research, 2023 Metabolic perturbations and inflammatory mediators play a fundamental role in both early and late adverse post-acute ischemic stroke outcomes. Using data from the observational MAGIC (MArker bioloGici nell’Ictus Cerebrale) study, we evaluated the effect of 130 serum metabolic features, using a nuclear magnetic spectroscopy approach, on the following outcomes: hemorrhagic transformation at 24 h after stroke, non-response to intravenous thrombolytic treatment with the recombinant tissue plasminogen activator (rt-PA), and the 3 month functional outcome. Blood circulating metabolites, lipoproteins, and inflammatory markers were assessed at the baseline and 24 h after rt-PA treatment. Adjusting for the major determinants for unfavorable outcomes (i.e., age, sex, time onset-to-treatment, etc.), we found that acetone and 3-hydroxybutyrate were associated with symptomatic hemorrhagic transformation and with non-response to rt-PA; while 24 h after rt-PA, levels of triglycerides high-density lipoprotein (HDL) and triglycerides low-density lipoprotein (LDL) were associated with 3 month mortality. Cholesterol and phospholipids levels, mainly related to smaller and denser very low-density lipoprotein (VLDL) and LDL subfractions were associated with 3 month poor functional outcomes. We also reported associations between baseline 24 h relative variation (Δ) in VLDL subfractions and ΔC-reactive protein, Δinterleukin-10 levels with hemorrhagic transformation. All observed metabolic changes reflect a general condition of energy failure, oxidative stress, and systemic inflammation that characterize the development of adverse outcomes.
Association of Plasma Metabolites and Lipoproteins with Rh and ABO Blood Systems in Healthy Subjects Francesca Di Cesare, Leonardo Tenori, Claudio Luchinat, Edoardo Saccenti Journal of Proteome Research, 2022 This study investigated the associations between the levels of 27 plasma metabolites, 114 lipoprotein parameters, determined using nuclear magnetic resonance spectroscopy, and the ABO blood groups and the Rhesus (Rh) blood system in a cohort of n = 840 Italian healthy blood donors of both sexes. We observed good multivariate discrimination between the metabolomic and lipoproteomic profiles of subjects with positive and negative Rh. In contrast, we did not observe significant discrimination for the ABO blood group pairwise comparisons, suggesting only slight metabolic differences between these group-specific metabolic profiles. We report univariate associations (P-value < 0.05) between the subfraction HDL1 related to Apo A1, the subfraction HDL2 related to cholesterol and phospholipids, and the particle number of LDL2 related to free cholesterol, cholesterol, phospholipids, and Apo B and the ABO blood groups; we observed association of the lipid main fraction LDL4 related to free cholesterol, triglycerides, and Apo B; creatine; the particle number of LDL5; the subfraction LDL5 related to Apo B; the particle number of LDL4; and the subfraction LDL4 related to Apo B with Rh blood factors. These results suggest blood group-dependent (re)shaping of lipoprotein metabolism in healthy subjects, which may provide relevant information to explain the differential susceptibility to certain diseases observed in different blood groups.
Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models G Lazzari, GE Felis, E Salvetti, M Calgaro, F Di Cesare, B Teusink, ... Msystems 11 (1), e01007-25 , 2026 2026.0
Inoculation with Pseudomonas Thivervalensis and Variovorax Paradoxus Enhances Yield and Grain Quality and Alters Rhizosphere Microbiota in Cereal–Legume Intercropping System N Ferchichi, W Toukabri, M Barbouchi, F Di Cesare, H Bahri, ... Journal of Soil Science and Plant Nutrition 25 (2), 5157-5172 , 2025 2025.0 Citations: 2
NMR-based metabolomic approach to estimate chemical and sensorial profiles of olive oil G Meoni, L Tenori, F Di Cesare, S Brizzolara, P Tonutti, C Cherubini, ... Computational and Structural Biotechnology Journal 27, 1359-1369 , 2025 2025.0 Citations: 9
NMR-based-Metabolomics Evaluation in Dogs Infected with Canine Parvovirus: A New Approach for Biomarker/s A Basoglu, RO Bicici, F Di Cesare, N Baspinar, L Tenori, M Ider, ... Veterinaria Italiana 61, 0-0 , 2025 2025.0 Citations: 2
Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals F Di Cesare, M Calgaro, V Ghini, DF Squarzanti, A De Prisco, A Visciglia, ... Journal of Proteome Research 22 (12), 3866-3878 , 2023 2023.0 Citations: 3
Fingerprinting and profiling in metabolomics of biosamples V Ghini, G Meoni, A Vignoli, F Di Cesare, L Tenori, P Turano, C Luchinat Progress in Nuclear Magnetic Resonance Spectroscopy 138, 105-135 , 2023 2023.0 Citations: 48
Exploration of blood metabolite signatures of colorectal cancer and polyposis through integrated statistical and network analysis F Di Cesare, A Vignoli, C Luchinat, L Tenori, E Saccenti Metabolites 13 (2), 296 , 2023 2023.0 Citations: 5
Nuclear magnetic resonance-based metabolomics to predict early and late adverse outcomes in ischemic stroke treated with intravenous thrombolysis C Licari, L Tenori, F Di Cesare, C Luchinat, B Giusti, A Kura, R De Cario, ... Journal of proteome research 22 (1), 16-25 , 2022 2022.0 Citations: 10
NMR-based metabolomics to evaluate individual response to treatments A Vignoli, G Meoni, V Ghini, F Di Cesare, L Tenori, C Luchinat, P Turano Metabolomics and Its Impact on Health and Diseases, 209-245 , 2022 2022.0 Citations: 10
Association of plasma metabolites and lipoproteins with Rh and ABO blood systems in healthy subjects F Di Cesare, L Tenori, C Luchinat, E Saccenti Journal of proteome research 21 (11), 2655-2663 , 2022 2022.0 Citations: 9
Age-and sex-dependent changes of free circulating blood metabolite and lipid abundances, correlations, and ratios F Di Cesare, C Luchinat, L Tenori, E Saccenti The Journals of Gerontology: Series A 77 (5), 918-926 , 2022 2022.0 Citations: 19
Lipid and metabolite correlation networks specific to clinical and biochemical covariate show differences associated with sexual dimorphism in a cohort of nonagenarians F Di Cesare, L Tenori, G Meoni, AM Gori, R Marcucci, B Giusti, ... GeroScience 44 (2), 1109-1128 , 2022 2022.0 Citations: 6
Application of NMR-based metabolomics on biomedical research F Di Cesare 2022.0
Functional metagenomics for identification of antibiotic resistance genes (ARGs) F Di Cesare Bacterial Pangenomics: Methods and Protocols, 173-183 , 2021 2021.0 Citations: 7
Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... Microorganisms 8 (7), 1003 , 2020 2020.0 Citations: 37
WS19-4 The personalised temporal dynamics of microbiome in the airways of cystic fibrosis patients A Bevivino, G Bacci, G Taccetti, V Lucidi, D Dolce, E Fiscarelli, ... Journal of Cystic Fibrosis 18, S36 , 2019 2019.0 Citations: 1
Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... bioRxiv, 609057 , 2019 2019.0 Citations: 2
The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients 2 G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... bioRxiv, 609057 , 2019 2019.0 Citations: 1
Taxonomic and functional dynamics of lung microbiome in cystic fibrosis patients chronically infected with Pseudomonas aeruginosa G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, FD Cesare, V Lucidi, ... bioRxiv , 2019 2019.0 Citations: 2
OPEN ACCESS EDITED BY A Vignoli, V Biasin, F Di Cesare, L Moreno, D Morales-Cano, ...
MOST CITED SCHOLAR PUBLICATIONS
Fingerprinting and profiling in metabolomics of biosamples V Ghini, G Meoni, A Vignoli, F Di Cesare, L Tenori, P Turano, C Luchinat Progress in Nuclear Magnetic Resonance Spectroscopy 138, 105-135 , 2023 2023.0 Citations: 48
Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... Microorganisms 8 (7), 1003 , 2020 2020.0 Citations: 37
Age-and sex-dependent changes of free circulating blood metabolite and lipid abundances, correlations, and ratios F Di Cesare, C Luchinat, L Tenori, E Saccenti The Journals of Gerontology: Series A 77 (5), 918-926 , 2022 2022.0 Citations: 19
Nuclear magnetic resonance-based metabolomics to predict early and late adverse outcomes in ischemic stroke treated with intravenous thrombolysis C Licari, L Tenori, F Di Cesare, C Luchinat, B Giusti, A Kura, R De Cario, ... Journal of proteome research 22 (1), 16-25 , 2022 2022.0 Citations: 10
NMR-based metabolomics to evaluate individual response to treatments A Vignoli, G Meoni, V Ghini, F Di Cesare, L Tenori, C Luchinat, P Turano Metabolomics and Its Impact on Health and Diseases, 209-245 , 2022 2022.0 Citations: 10
NMR-based metabolomic approach to estimate chemical and sensorial profiles of olive oil G Meoni, L Tenori, F Di Cesare, S Brizzolara, P Tonutti, C Cherubini, ... Computational and Structural Biotechnology Journal 27, 1359-1369 , 2025 2025.0 Citations: 9
Association of plasma metabolites and lipoproteins with Rh and ABO blood systems in healthy subjects F Di Cesare, L Tenori, C Luchinat, E Saccenti Journal of proteome research 21 (11), 2655-2663 , 2022 2022.0 Citations: 9
Functional metagenomics for identification of antibiotic resistance genes (ARGs) F Di Cesare Bacterial Pangenomics: Methods and Protocols, 173-183 , 2021 2021.0 Citations: 7
Lipid and metabolite correlation networks specific to clinical and biochemical covariate show differences associated with sexual dimorphism in a cohort of nonagenarians F Di Cesare, L Tenori, G Meoni, AM Gori, R Marcucci, B Giusti, ... GeroScience 44 (2), 1109-1128 , 2022 2022.0 Citations: 6
Exploration of blood metabolite signatures of colorectal cancer and polyposis through integrated statistical and network analysis F Di Cesare, A Vignoli, C Luchinat, L Tenori, E Saccenti Metabolites 13 (2), 296 , 2023 2023.0 Citations: 5
Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease. Microorganisms 2020; 8: 8 G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare Citations: 5
Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals F Di Cesare, M Calgaro, V Ghini, DF Squarzanti, A De Prisco, A Visciglia, ... Journal of Proteome Research 22 (12), 3866-3878 , 2023 2023.0 Citations: 3
Inoculation with Pseudomonas Thivervalensis and Variovorax Paradoxus Enhances Yield and Grain Quality and Alters Rhizosphere Microbiota in Cereal–Legume Intercropping System N Ferchichi, W Toukabri, M Barbouchi, F Di Cesare, H Bahri, ... Journal of Soil Science and Plant Nutrition 25 (2), 5157-5172 , 2025 2025.0 Citations: 2
NMR-based-Metabolomics Evaluation in Dogs Infected with Canine Parvovirus: A New Approach for Biomarker/s A Basoglu, RO Bicici, F Di Cesare, N Baspinar, L Tenori, M Ider, ... Veterinaria Italiana 61, 0-0 , 2025 2025.0 Citations: 2
Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... bioRxiv, 609057 , 2019 2019.0 Citations: 2
Taxonomic and functional dynamics of lung microbiome in cystic fibrosis patients chronically infected with Pseudomonas aeruginosa G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, FD Cesare, V Lucidi, ... bioRxiv , 2019 2019.0 Citations: 2
WS19-4 The personalised temporal dynamics of microbiome in the airways of cystic fibrosis patients A Bevivino, G Bacci, G Taccetti, V Lucidi, D Dolce, E Fiscarelli, ... Journal of Cystic Fibrosis 18, S36 , 2019 2019.0 Citations: 1
The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients 2 G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ... bioRxiv, 609057 , 2019 2019.0 Citations: 1
Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models G Lazzari, GE Felis, E Salvetti, M Calgaro, F Di Cesare, B Teusink, ... Msystems 11 (1), e01007-25 , 2026 2026.0
Application of NMR-based metabolomics on biomedical research F Di Cesare 2022.0
