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1. A patient-centric modeling framework captures recovery from SARS-CoV-2 infection

Author

Ruffieux, Hélène, Hanson, Aimee L., Lodge, Samantha, Lawler, Nathan G., Whiley, Luke, Gray, Nicola, Nolan, Tui H., Bergamaschi, Laura, Mescia, Federica, Turner, Lorinda, de Sa, Aloka, Pelly, Victoria S., Kotagiri, Prasanti, Kingston, Nathalie, Bradley, John R., Holmes, Elaine, Wist, Julien, Nicholson, Jeremy K., Lyons, Paul A., Smith, Kenneth G. C., Richardson, Sylvia, Bantug, Glenn R., and Hess, Christoph

Published
2023
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5. Cross-Validation of Metabolic Phenotypes in SARS-CoV-2 Infected Subpopulations Using Targeted Liquid Chromatography–Mass Spectrometry (LC-MS)

Author

Whiley, Luke, primary, Lawler, Nathan G., additional, Zeng, Annie Xu, additional, Lee, Alex, additional, Chin, Sung-Tong, additional, Bizkarguenaga, Maider, additional, Bruzzone, Chiara, additional, Embade, Nieves, additional, Wist, Julien, additional, Holmes, Elaine, additional, Millet, Oscar, additional, Nicholson, Jeremy K., additional, and Gray, Nicola, additional

Published
2024
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7. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Author

McAlpine, James B, Chen, Shao-Nong, Kutateladze, Andrei, MacMillan, John B, Appendino, Giovanni, Barison, Andersson, Beniddir, Mehdi A, Biavatti, Maique W, Bluml, Stefan, Boufridi, Asmaa, Butler, Mark S, Capon, Robert J, Choi, Young H, Coppage, David, Crews, Phillip, Crimmins, Michael T, Csete, Marie, Dewapriya, Pradeep, Egan, Joseph M, Garson, Mary J, Genta-Jouve, Grégory, Gerwick, William H, Gross, Harald, Harper, Mary Kay, Hermanto, Precilia, Hook, James M, Hunter, Luke, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, Rivera-Chávez, José, Robien, Wolfgang, Saunders, Carla M, Schmidt, Thomas J, Seger, Christoph, Shen, Ben, Steinbeck, Christoph, Stuppner, Hermann, Sturm, Sonja, Taglialatela-Scafati, Orazio, Tantillo, Dean J, Verpoorte, Robert, Wang, Bin-Gui, Williams, Craig M, Williams, Philip G, Wist, Julien, Yue, Jian-Min, Zhang, Chen, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Biological Products, Magnetic Resonance Spectroscopy, Reproducibility of Results, Molecular Conformation, Generic health relevance, Organic Chemistry, Chemical Sciences, Biological Sciences, Medical and Health Sciences
Abstract

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Published
2019

8. Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Author

McAlpine, James B, Chen, Shao-Nong, Kutateladze, Andrei, MacMillan, John B, Appendino, Giovanni, Barison, Andersson, Beniddir, Mehdi A, Biavatti, Maique W, Bluml, Stefan, Boufridi, Asmaa, Butler, Mark S, Capon, Robert J, Choi, Young H, Coppage, David, Crews, Phillip, Crimmins, Michael T, Csete, Marie, Dewapriya, Pradeep, Egan, Joseph M, Garson, Mary J, Genta-Jouve, Grégory, Gerwick, William H, Gross, Harald, Harper, Mary Kay, Hermanto, Precilia, Hook, James M, Hunter, Luke, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, Rivera-Chávez, José, Robien, Wolfgang, Saunders, Carla M, Schmidt, Thomas J, Seger, Christoph, Shen, Ben, Steinbeck, Christoph, Stuppner, Hermann, Sturm, Sonja, Taglialatela-Scafati, Orazio, Tantillo, Dean J, Verpoorte, Robert, Wang, Bin-Gui, Williams, Craig M, Williams, Philip G, Wist, Julien, Yue, Jian-Min, Zhang, Chen, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Organic Chemistry, Chemical Sciences, Clinical Research, Biological Sciences, Medical and Health Sciences, Medicinal and biomolecular chemistry, Traditional, complementary and integrative medicine
Abstract

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

Published
2019

9. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients

Author

Sala, Samuele, primary, Nitschke, Philipp, additional, Masuda, Reika, additional, Gray, Nicola, additional, Lawler, Nathan G., additional, Wood, James M., additional, Buckler, Joshua N., additional, Berezhnoy, Georgy, additional, Bolaños, Jose, additional, Boughton, Berin A., additional, Lonati, Caterina, additional, Rössler, Titus, additional, Singh, Yogesh, additional, Wilson, Ian D., additional, Lodge, Samantha, additional, Morillon, Aude-Claire, additional, Loo, Ruey Leng, additional, Hall, Drew, additional, Whiley, Luke, additional, Evans, Gary B., additional, Grove, Tyler L., additional, Almo, Steven C., additional, Harris, Lawrence D., additional, Holmes, Elaine, additional, Merle, Uta, additional, Trautwein, Christoph, additional, Nicholson, Jeremy K., additional, and Wist, Julien, additional

Published
2024
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10. Exploring the Interactions between Obesity and Diabetes: Implications for Understanding Metabolic Dysregulation in a Saudi Arabian Adult Population

Author

Ahmad, Muhammad Saeed, primary, Minaee, Novia, additional, Serrano-Contreras, Jose Ivan, additional, Kaluarachchi, Manuja, additional, Shen, Eric Yi-Liang, additional, Boulange, Claire, additional, Ahmad, Sultan, additional, Phetcharaburanin, Jutarop, additional, Holmes, Elaine, additional, Wist, Julien, additional, Albaloshi, Ahmed Hakem, additional, Alaama, Tareef, additional, Damanhouri, Zoheir Abdullah, additional, and Lodge, Samantha, additional

Published
2024
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12. Altered dietary behaviour during pregnancy impacts systemic metabolic phenotypes

Author

Rowley, Charlotte E., primary, Lodge, Samantha, additional, Egan, Siobhon, additional, Itsiopoulos, Catherine, additional, Christophersen, Claus T., additional, Silva, Desiree, additional, Kicic-Starcevich, Elizabeth, additional, O’Sullivan, Therese A., additional, Wist, Julien, additional, Nicholson, Jeremy, additional, Frost, Gary, additional, Holmes, Elaine, additional, and D’Vaz, Nina, additional

Published
2023
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14. Nonsevere Burn Induces a Prolonged Systemic Metabolic Phenotype Indicative of a Persistent Inflammatory Response Postinjury

Author

Ryan, Monique J., Raby, Edward, Whiley, Luke, Masuda, Reika, Lodge, Samantha, Nitschke, Philipp, Maker, Garth L., Wist, Julien, Holmes, Elaine, Wood, Fiona M., Nicholson, Jeremy K., Fear, Mark W., and Gray, Nicola

Abstract

Globally, burns are a significant cause of injury that can cause substantial acute trauma as well as lead to increased incidence of chronic comorbidity and disease. To date, research has primarily focused on the systemic response to severe injury, with little in the literature reported on the impact of nonsevere injuries (<15% total burn surface area; TBSA). To elucidate the metabolic consequences of a nonsevere burn injury, longitudinal plasma was collected from adults (n= 35) who presented at hospital with a nonsevere burn injury at admission, and at 6 week follow up. A cross-sectional baseline sample was also collected from nonburn control participants (n= 14). Samples underwent multiplatform metabolic phenotyping using 1H nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry to quantify 112 lipoprotein and glycoprotein signatures and 852 lipid species from across 20 subclasses. Multivariate data modeling (orthogonal projections to latent structures-discriminate analysis; OPLS-DA) revealed alterations in lipoprotein and lipid metabolism when comparing the baseline control to hospital admission samples, with the phenotypic signature found to be sustained at follow up. Univariate (Mann–Whitney U) testing and OPLS-DA indicated specific increases in GlycB (p-value < 1.0e–4), low density lipoprotein-2 subfractions (variable importance in projection score; VIP > 6.83e–1) and monoacyglyceride (20:4) (p-value < 1.0e–4) and decreases in circulating anti-inflammatory high-density lipoprotein-4 subfractions (VIP > 7.75e–1), phosphatidylcholines, phosphatidylglycerols, phosphatidylinositols, and phosphatidylserines. The results indicate a persistent systemic metabolic phenotype that occurs even in cases of a nonsevere burn injury. The phenotype is indicative of an acute inflammatory profile that continues to be sustained postinjury, suggesting an impact on systems health beyond the site of injury. The phenotypes contained metabolic signatures consistent with chronic inflammatory states reported to have an elevated incidence postburn injury. Such phenotypic signatures may provide patient stratification opportunities, to identify individual responses to injury, personalize intervention strategies, and improve acute care, reducing the risk of chronic comorbidity.

Published
2024
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16. Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD+ pathway and SIRT1 activation.

Author

Lonati, Caterina, Berezhnoy, Georgy, Lawler, Nathan, Masuda, Reika, Kulkarni, Aditi, Sala, Samuele, Nitschke, Philipp, Zizmare, Laimdota, Bucci, Daniele, Cannet, Claire, Schäfer, Hartmut, Singh, Yogesh, Gray, Nicola, Lodge, Samantha, Nicholson, Jeremy, Merle, Uta, Wist, Julien, and Trautwein, Christoph

Subjects
NAD (Coenzyme), LIQUID chromatography-mass spectrometry, NICOTINAMIDE, ANTIVIRAL nucleosides, METABOLOMICS, SIRTUINS, SARS-CoV-2
Abstract

The stratification of individuals suffering from acute and post-acute SARS-CoV-2 infection remains a critical challenge. Notably, biomarkers able to specifically monitor viral progression, providing details about patient clinical status, are still not available. Herein, quantitative metabolomics is progressively recognized as a useful tool to describe the consequences of virus-host interactions considering also clinical metadata. The present study characterized the urinary metabolic profile of 243 infected individuals by quantitative nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography mass spectrometry (LC–MS). Results were compared with a historical cohort of noninfected subjects. Moreover, we assessed the concentration of recently identified antiviral nucleosides and their association with other metabolites and clinical data. Urinary metabolomics can stratify patients into classes of disease severity, with a discrimination ability comparable to that of clinical biomarkers. Kynurenines showed the highest fold change in clinically-deteriorated patients and higher-risk subjects. Unique metabolite clusters were also generated based on age, sex, and body mass index (BMI). Changes in the concentration of antiviral nucleosides were associated with either other metabolites or clinical variables. Increased kynurenines and reduced trigonelline excretion indicated a disrupted nicotinamide adenine nucleotide (NAD+) and sirtuin 1 (SIRT1) pathway. Our results confirm the potential of urinary metabolomics for noninvasive diagnostic/prognostic screening and show that the antiviral nucleosides could represent novel biomarkers linking viral load, immune response, and metabolism. Moreover, we established for the first time a casual link between kynurenine accumulation and deranged NAD+/SIRT1, offering a novel mechanism through which SARS-CoV-2 manipulates host physiology. [ABSTRACT FROM AUTHOR]

Published
2024
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17. A community-built calibration system: The case study of quantification of metabolites in grape juice by qNMR spectroscopy

Author

Musio, Biagia, Ragone, Rosa, Todisco, Stefano, Rizzuti, Antonino, Latronico, Mario, Mastrorilli, Piero, Pontrelli, Stefania, Intini, Nicola, Scapicchio, Pasquale, Triggiani, Maurizio, Di Noia, Tommaso, Acquotti, Domenico, Airoldi, Cristina, Assfalg, Michael, Barge, Alessandro, Bateman, Lorraine, Benevelli, Francesca, Bertelli, Davide, Bertocchi, Fabio, Bieliauskas, Aurimas, Borioni, Anna, Caligiani, Augusta, Callone, Emanuela, Čamra, Ales, Cesare Marincola, Flaminia, Chalasani, Dinesh, Consonni, Roberto, Dambruoso, Paolo, Davalli, Silvia, David, Taylor, Diehl, Bernd, Donarski, James, Gil, Ana M., Gobetto, Roberto, Goldoni, Luca, Hamon, Erwann, Harwood, John S., Kobrlová, Andrea, Longobardi, Francesco, Luisi, Renzo, Mallamace, Domenico, Mammi, Stefano, Martin-Biran, Magali, Mazzei, Pierluigi, Mele, Andrea, Milone, Salvatore, Molero Vilchez, Dolores, Mulder, Roger J., Napoli, Claudia, Ragno, Daniele, Randazzo, Antonio, Rossi, Maria Cecilia, Rotondo, Archimede, Šačkus, Algirdas, Sáez Barajas, Elena, Schievano, Elisabetta, Sitaram, Bhavaraju, Stevanato, Livio, Takis, Panteleimon G., Teipel, Jan, Thomas, Freddy, Torregiani, Elisabetta, Valensin, Daniela, Veronesi, Marina, Warren, John, Wist, Julien, Zailer-Hafer, Elina, Zuccaccia, Cristiano, and Gallo, Vito

Published
2020
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18. Nonsevere Burn Induces a Prolonged Systemic Metabolic Phenotype Indicative of a Persistent Inflammatory Response Postinjury

Author

Ryan, Monique J., primary, Raby, Edward, additional, Whiley, Luke, additional, Masuda, Reika, additional, Lodge, Samantha, additional, Nitschke, Philipp, additional, Maker, Garth L., additional, Wist, Julien, additional, Holmes, Elaine, additional, Wood, Fiona M., additional, Nicholson, Jeremy K., additional, Fear, Mark W., additional, and Gray, Nicola, additional

Published
2023
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19. Rapid and Self-Administrable Capillary Blood Microsampling Demonstrates Statistical Equivalence with Standard Venous Collections in NMR-Based Lipoprotein Analysis

Author

Roberts, Jayden Lee, primary, Whiley, Luke, additional, Gray, Nicola, additional, Gay, Melvin, additional, Nitschke, Philipp, additional, Masuda, Reika, additional, Holmes, Elaine, additional, Nicholson, Jeremy Kirk, additional, Wist, Julien, additional, and Lawler, Nathan, additional

Published
2023
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20. Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD+ pathway and SIRT1 activation

Author

Lonati, Caterina, primary, Berezhnoy, Georgy, additional, Lawler, Nathan, additional, Masuda, Reika, additional, Kulkarni, Aditi, additional, Sala, Samuele, additional, Nitschke, Philipp, additional, Zizmare, Laimdota, additional, Bucci, Daniele, additional, Cannet, Claire, additional, Schäfer, Hartmut, additional, Singh, Yogesh, additional, Gray, Nicola, additional, Lodge, Samantha, additional, Nicholson, Jeremy, additional, Merle, Uta, additional, Wist, Julien, additional, and Trautwein, Christoph, additional

Published
2023
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22. Stratification of Sepsis Patients on Admission into the Intensive Care Unit According to Differential Plasma Metabolic Phenotypes

Author

Lodge, Samantha, Litton, Edward, Gray, Nicola, Ryan, Monique, Millet, Oscar, Fear, Mark, Raby, Edward, Currie, Andrew, Wood, Fiona, Holmes, Elaine, Wist, Julien, and Nicholson, Jeremy K.

Abstract

Delayed diagnosis of patients with sepsis or septic shock is associated with increased mortality and morbidity. UPLC-MS and NMR spectroscopy were used to measure panels of lipoproteins, lipids, biogenic amines, amino acids, and tryptophan pathway metabolites in blood plasma samples collected from 152 patients within 48 h of admission into the Intensive Care Unit (ICU) where 62 patients had no sepsis, 71 patients had sepsis, and 19 patients had septic shock. Patients with sepsis or septic shock had higher concentrations of neopterin and lower levels of HDL cholesterol and phospholipid particles in comparison to nonsepsis patients. Septic shock could be differentiated from sepsis patients based on different concentrations of 10 lipids, including significantly lower concentrations of five phosphatidylcholine species, three cholesterol esters, one dihydroceramide, and one phosphatidylethanolamine. The Supramolecular Phospholipid Composite (SPC) was reduced in all ICU patients, while the composite markers of acute phase glycoproteins were increased in the sepsis and septic shock patients within 48 h admission into ICU. We show that the plasma metabolic phenotype obtained within 48 h of ICU admission is diagnostic for the presence of sepsis and that septic shock can be differentiated from sepsis based on the lipid profile.

Published
2024
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23. Gut microbiota and metabolomics profiles in patients with chronic stable angina and acute coronary syndrome.

Author

Ahmad, Adilah F., Caparros-Martin, Jose A., Gray, Nicola, Lodge, Samantha, Wist, Julien, Lee, Silvia, O'Gara, Fergal, Dwivedi, Girish, and Ward, Natalie C.

Subjects
GUT microbiome, ACUTE coronary syndrome, BACTERIAL metabolites, ANGINA pectoris, METABOLOMICS, BACTERIAL diversity
Abstract

Cardiovascular disease (CVD) is the leading cause of death worldwide. The gut microbiota and its associated metabolites may be involved in the development and progression of CVD, although the mechanisms and impact on clinical outcomes are not fully understood. This study investigated the gut microbiome profile and associated metabolites in patients with chronic stable angina (CSA) and acute coronary syndrome (ACS) compared with healthy controls. Bacterial alpha diversity in stool from patients with ACS or CSA was comparable to healthy controls at both baseline and follow-up visits. Differential abundance analysis identified operational taxonomic units (OTUs) assigned to commensal taxa differentiating patients with ACS from healthy controls at both baseline and follow-up. Patients with CSA and ACS had significantly higher levels of trimethylamine N-oxide compared with healthy controls (CSA: 0.032 ± 0.023 mmol/L, P < 0.01 vs. healthy, and ACS: 0.032 ± 0.023 mmol/L, P ¼ 0.02 vs. healthy, respectively). Patients with ACS had reduced levels of propionate and butyrate (119 ± 4 vs. 139 ± 5.1 lM, P ¼ 0.001, and 14 ± 4.3 vs. 23.5 ± 8.1 lM, P < 0.001, respectively), as well as elevated serum sCD14 (2245 ± 75.1 vs. 1834 ± 45.8 ng/mL, P < 0.0001) and sCD163 levels (457.3 ± 31.8 vs. 326.8 ± 20.7 ng/mL, P ¼ 0.001), compared with healthy controls at baseline. Furthermore, a modi- fied small molecule metabolomic and lipidomic signature was observed in patients with CSA and ACS compared with healthy controls. These findings provide evidence of a link between gut microbiome composition and gut bacterial metabolites with CVD. Future time course studies in patients to observe temporal changes and subsequent associations with gut microbiome composition are required to provide insight into how these are affected by transient changes following an acute coronary event. NEW & NOTEWORTHY The study found discriminative microorganisms differentiating patients with acute coronary syndrome (ACS) from healthy controls. In addition, reduced levels of certain bacterial metabolites and elevated sCD14 and sCD163 were observed in patients with ACS compared with healthy controls. Furthermore, modified small molecule metabolomic and lipidomic signatures were found in both patient groups. Although it is not known whether these differences in profiles are associated with disease development and/or progression, the findings provide exciting options for potential new disease-related mechanism(s) and associated therapeutic target(s). [ABSTRACT FROM AUTHOR]

Published
2024
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24. Clinical prediction of wound re-epithelisation outcomes in non-severe burn injury using the plasma lipidome

Author

Ryan, Monique J., primary, Raby, Edward, additional, Masuda, Reika, additional, Lodge, Samantha, additional, Nitschke, Philipp, additional, Maker, Garth L., additional, Wist, Julien, additional, Fear, Mark W., additional, Holmes, Elaine, additional, Nicholson, Jeremy, additional, Gray, Nicola, additional, Whiley, Luke, additional, and Wood, Fiona M., additional

Published
2023
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25. Integrative Plasma Metabolic and Lipidomic Modelling of SARS-CoV-2 Infection in Relation to Clinical Severity and Early Mortality Prediction

Author

Lodge, Samantha, primary, Lawler, Nathan G., additional, Gray, Nicola, additional, Masuda, Reika, additional, Nitschke, Philipp, additional, Whiley, Luke, additional, Bong, Sze-How, additional, Yeap, Bu B., additional, Dwivedi, Girish, additional, Spraul, Manfred, additional, Schaefer, Hartmut, additional, Gil-Redondo, Rubén, additional, Embade, Nieves, additional, Millet, Oscar, additional, Holmes, Elaine, additional, Wist, Julien, additional, and Nicholson, Jeremy K., additional

Published
2023
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26. Meta-analysis of the microbial diversity cultured in bioreactors simulating the gut microbiome: another key to unlocking the microbial dark matter

Author

Garcia Mendez, David Felipe, Egan, Siobhon, Wist, Julien, Holmes, Elaine, and Sanabria, Janeth

Subjects
in vitro gut, faecal microbiome, simulation, Hill numbers, diversity
Abstract

Background The challenges surrounding the mechanistic study of the gut ecosystem have motivated the development and use of multiple in vitro models, such as microbial cultures and bioreactors, that simulate some of the features of the gut environment. The control technology, integrated into bioreactors, allowing tuning of pH, redox potential, and retention time, has allowed the recovery and isolation of microorganisms that are hard to culture with conventional methods opening access to hitherto unexplored microbial species - microbial “dark matter”. Although multiple bioreactor platforms have been developed, there is a lack of studies describing and comparing the microbial diversity cultivated in these devices. This study aimed to characterise and compare the microbial diversity of 1,619 samples from 19 studies in which various in vitro models were used to cultivate faecal microbiota. Results The community structure differed between the 19 studies based on β-diversity analysis using t-SNE and the Hellinger distance, with inter-individual variation between the faecal inoculum donors contributing the most influence. Moreover, there was no overlap between samples from studies that used the same bioreactor model. Studies with more than one donor showed higher variations than those with pooled samples. The diversity profiles of the samples within each study based on α-diversity (Hill numbers) were not dependent on the complexity of the bioreactors. Nevertheless, further analyses of the samples of five studies showed Amplicon Sequence Variants enrichment in the bioreactors compared to the faecal inoculum, two of which provided a mucosal component. Finally, a comparative analysis of the taxonomy at family level in the 19 studies versus those listed in the Data Repository for Human Gut Microbiota (GMRepo) revealed 30 families that were unique to bioreactor models. This finding highlights the potential of bioreactors to uncover a hidden diversity, which is not detected with culture-independent methods. Conclusions: This study shows that bioreactors can sustain stable communities and recover the most abundant taxa from faecal samples. Additionally, we highlight the potential of bioreactors as a tool to enrich species that are difficult to cultivate, allowing insights into their role in host-microbiome interactions.

Published
2023
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27. SARS-CoV-2 Infection Biomarkers Reveal an Extended RSAD2 Dependant Metabolic Pathway

Author

Sala, Samuele, primary, Nitschke, Philipp, additional, Masuda, Reika, additional, Gray, Nicola, additional, Lawler, Nathan, additional, Wood, James M., additional, Berezhnoy, Georgy, additional, Bolanos, Alejandro, additional, Boughton, Berin A., additional, Lonati, Caterina, additional, Roessler, Titus, additional, Singh, Yogesh, additional, Wilson, Ian D., additional, Lodge, Samantha, additional, Morillon, Aude-Claire, additional, Loo, Ruey Leng, additional, Hall, Drew, additional, Whiley, Luke, additional, Evans, Gary B., additional, Grove, Tyler L., additional, Almo, Steven C., additional, Harris, Lawrence D., additional, Holmes, Elaine, additional, Merle, Uta, additional, Trautwein, Christoph, additional, Nicholson, Jeremy K., additional, and Wist, Julien, additional

Published
2023
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28. Metabolic consequences of non-severe burn injury are associated with increased plasma markers of inflammation and cardiovascular disease risk.

Author

Ryan, Monique J, primary, Raby, Edward, additional, Masuda, Reika, additional, Lodge, Samantha, additional, Nitschke, Philipp, additional, Maker, Garth L, additional, Wist, Julien, additional, Holmes, Elaine, additional, Whiley, Luke, additional, Wood, Fiona M, additional, Nicholson, Jeremy K, additional, Fear, Mark W, additional, and Gray, Nicola, additional

Published
2023
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31. SARS-CoV-2 Infection Biomarkers Reveal Adaptive Evolutionary Chemistry of Antiviral Nucleoside Metabolism

Author

Sala, Samuele, Nitschke, Philipp, Masuda, Reika, Gray, Nicola, Lawler, Nathan, Wood M., James, Berezhnoy, Georgy, Bolaños, Alejandro, Boughton A., Berin, Lonati, Caterina, Roessler, Titus, Singh, Yogesh, Wilson D., Ian, Lodge, Samantha, Morillon, Aude-Claire, Loo, Ruey Leng, Hall, Drew, Whiley, Luke, Evans B., Gary, Grove L., Tyler, Almo C., Steven, Harris D., Lawrence, Holmes, Elaine, Merle, Uta, Trautwein, Christoph, Nicholson K., Jeremy, and Wist, Julien

Subjects
deoxydidehydronucleosides, NMR spectroscopy, antivirals, SARS-CoV-2, biomarkers, COVID-19, polypharmacy, urine, nucleosides
Abstract

We present compelling evidence for the existence of an evolutionary adaptive response to viral agents such as SARS-CoV-2, that results in the human in vivo biosynthesis of a family of compounds with potential antiviral activity. Using nuclear magnetic resonance (NMR) spectroscopy, we detected a characteristic spin-system motif indicative of the presence of an extended panel of urinary and serum metabolites during the acute viral phase. The structure of eight of nucleoside analogues was elucidated (six of which have not previously been reported in human urine), and subsequently confirmed by total-synthesis and matrix spiking. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ and IL-10, suggest an association with the viperin enzyme contributing to an endogenous innate immune defense mechanism against viral infection., Acknowledgements: Acknowledgements: We thank The Spinnaker Health Research Foundation, WA, The McCusker Foundation, WA, The Western Australian State Government and the Medical Research Future Fund (EPCD000037 and MRF2014349) for financial support. We thank the Department of Jobs, Tourism, Science and Innovation, Government of a Western Australian Premier's Fellowship for RLL and the ARC for Laureate Fellowship funding for EH. JW thanks Ministerio de Ciencia, Tecnología e Innovación (Minciencias), Ministerio de Educación Nacional, Ministerio de Industria, Comercio y Turismo e ICETEX (792–2017) 2a Convocatoria Ecosistema Científico - Colombia Científica para la Financiación de Proyectos de I + D + i), World Bank and Vicerrectoría de Investigaciones, Pontificia Universidad Javeriana, Bogotá, Colombia (contract no. FP44842 - 221-2018). We gratefully thank the Werner Siemens Imaging Center under direction of Prof. Bernd Pichler for supporting this project as well as Aditi Kulkarni and Daniele Bucci for excellent technical assistance. JMW, GBE and LDH thank the New Zealand Ministry of Business Innovation & Employment for support (Endeavour Fund program contract UOOX1904 (NZ)).

Published
2023
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32. Integrative Metabolic, Lipidomic and Lipoproteomic Modelling of SARS-CoV-2 Infections in Relation to Clinical Severity and Early Mortality Prediction

Author

Lodge, Samantha, Lawler, Nathan, Gray, Nicola, Masuda, Reika, Nitschke, Philipp, Whiley, Luke, Sze-How Bong, Yeap, Bu B., Girish Dwivedi, Spraul, Manfred, Schaefer, Hartmut, Gil-Redondo, Rubén, Embade, Nieves, Millet, Oscar, Holmes, Elaine, Wist, Julien, and Nicholson, Jeremy K.

Subjects
lipoproteins, NMR spectroscopy, metabolic phenotyping, SARS-CoV-2, COVID-19, plasma IVDr, lipidomics, diagnostic modelling, patient stratification, mortality prediction, metabolomics, mass spectrometry
Abstract

An integrative multi-modal metabolic phenotyping model was developed to assess the systemic plasma sequelae of SARS-CoV-2 (rRT-PCR positive) induced COVID-19 disease in patients with different respiratory severity levels. Plasma samples from 306 unvaccinated COVID-19 patients were collected in 2020 and classified into four levels of severity ranging from mild symptoms to severe ventilated cases. These samples were investigated using a combination of quantitative Nuclear Magnetic Resonance (NMR) spectroscopy and Mass Spectrometry (MS) platforms to give broad lipoprotein, lipidomic and amino acid, tryptophan-kynurenine pathway and biogenic amine pathway coverage. All platforms revealed highly significant differences in metabolite patterns between patients and controls (n=89) that had been collected prior to the COVID-19 pandemic. The total number of significant metabolites increased with severity with 344 out of the 1034 quantitative variables being common to all severity classes. Metabolic signatures showed a continuum of changes across the respiratory severity levels with the most significant and extensive changes being in the most severely affected patients. Even mildly affected respiratory patients showed multiple highly significant abnormal biochemical signatures reflecting serious metabolic deficiencies of the type observed in Post acute COVID -19 syndrome patients. The most severe respiratory patients had a high mortality (56.1%) and we found that we could predict mortality in this patient sub-group with high accuracy in some cases up to 61 days prior to death, based on a separate metabolic model, which highlighted a different set of metabolites to those defining the basic disease. Specifically, hexosylceramides (HCER 16:0, HCER 20:0, HCER 24:1, HCER 26:0, HCER 26:1) were markedly elevated in the non-surviving patient group (Cliff’s delta 0.91-0.95) and two phosphoethanolamines (PE.O 18:0/18:1, Cliff’s delta=-0.98 and PE.P 16:0/18:1, Cliff’s delta=-0.93) were markedly lower in the non-survivors. These results indicate that patient morbidity to mortality trajectories are determined relatively soon after infection, opening the opportunity to select more intensive therapeutic interventions to these “high risk” patients in the early disease stages.&nbsp

Published
2023
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33. Comprehensive Lipidomic Workflow for Multicohort Population Phenotyping Using Stable Isotope Dilution Targeted Liquid Chromatography-Mass Spectrometry

Author

Ryan, Monique J., primary, Grant-St James, Alanah, additional, Lawler, Nathan G., additional, Fear, Mark W., additional, Raby, Edward, additional, Wood, Fiona M., additional, Maker, Garth L., additional, Wist, Julien, additional, Holmes, Elaine, additional, Nicholson, Jeremy K., additional, Whiley, Luke, additional, and Gray, Nicola, additional

Published
2023
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34. An NMR-Based Model to Investigate the Metabolic Phenoreversion of COVID-19 Patients throughout a Longitudinal Study

Author

Gil-Redondo, Rubén, primary, Conde, Ricardo, additional, Bizkarguenaga, Maider, additional, Bruzzone, Chiara, additional, Laín, Ana, additional, González-Valle, Beatriz, additional, Iriberri, Milagros, additional, Ramos-Acosta, Carlos, additional, Anguita, Eduardo, additional, Arriaga Lariz, Juan Ignacio, additional, España Yandiola, Pedro Pablo, additional, Moran, Miguel Ángel, additional, Jiménez-Mercado, Mario Ernesto, additional, Egia-Mendikute, Leire, additional, Seco, María Luisa, additional, Schäfer, Hartmut, additional, Cannet, Claire, additional, Spraul, Manfred, additional, Palazón, Asís, additional, Embade, Nieves, additional, Lu, Shelly C., additional, Wist, Julien, additional, Nicholson, Jeremy K., additional, Mato, José M., additional, and Millet, Oscar, additional

Published
2022
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41. Exploration of Human Serum Lipoprotein Supramolecular Phospholipids Using Statistical Heterospectroscopy in n-Dimensions (SHY-n): Identification of Potential Cardiovascular Risk Biomarkers Related to SARS-CoV-2 Infection

Author

Masuda, Reika, primary, Lodge, Samantha, additional, Whiley, Luke, additional, Gray, Nicola, additional, Lawler, Nathan, additional, Nitschke, Philipp, additional, Bong, Sze-How, additional, Kimhofer, Torben, additional, Loo, Ruey Leng, additional, Boughton, Berin, additional, Zeng, Annie X., additional, Hall, Drew, additional, Schaefer, Hartmut, additional, Spraul, Manfred, additional, Dwivedi, Girish, additional, Yeap, Bu B., additional, Diercks, Tammo, additional, Bernardo-Seisdedos, Ganeko, additional, Mato, José M., additional, Lindon, John C., additional, Holmes, Elaine, additional, Millet, Oscar, additional, Wist, Julien, additional, and Nicholson, Jeremy K., additional

Published
2022
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44. J-Edited DIffusional Proton Nuclear Magnetic Resonance Spectroscopic Measurement of Glycoprotein and Supramolecular Phospholipid Biomarkers of Inflammation in Human Serum

Author

Nitschke, Philipp, primary, Lodge, Samantha, additional, Kimhofer, Torben, additional, Masuda, Reika, additional, Bong, Sze-How, additional, Hall, Drew, additional, Schäfer, Hartmut, additional, Spraul, Manfred, additional, Pompe, Nils, additional, Diercks, Tammo, additional, Bernardo-Seisdedos, Ganeko, additional, Mato, José M., additional, Millet, Oscar, additional, Susic, Daniella, additional, Henry, Amanda, additional, El-Omar, Emad M, additional, Holmes, Elaine, additional, Lindon, John C., additional, Nicholson, Jeremy K., additional, and Wist, Julien, additional

Published
2022
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50. Diagnostic Potential of the Plasma Lipidome in Infectious Disease: Application to Acute SARS-CoV-2 Infection

Author

Gray, Nicola, primary, Lawler, Nathan, additional, Zeng, Annie, additional, Ryan, Monique, additional, Bong, Sze, additional, Boughton, Berin, additional, Bizkarguenaga, Maider, additional, Bruzzone, Chiara, additional, Embade, Nieves, additional, Wist, Julien, additional, Holmes, Elaine, additional, Millet, Oscar, additional, Nicholson, Jeremy, additional, and Whiley, Luke, additional

Published
2021
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