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This is a list of publications using the SIRIUS software framework to get the most out of their metabolomics data.

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Gastroprotective effect of Artemisia absinthium L.: A medicinal plant used in the treatment of digestive disorders

Boeing, Thaise; de Souza, Josiane; de Cássia Vilhena da Silva, Rita; Mariano, Luísa Nathália Bolda; da Silva, Luisa Mota; Gerhardt, Guilherme Moreschi; Cretton, Sylvian; Klein-Junior, Luiz Carlos; de Souza, Priscila

In: Journal of Ethnopharmacology, vol. 312, pp. 116488, 2023.

Summary | Tags: bioactivity, COSMIC, CSI:FingerID, pharmacology, plants, SIRIUS | Links:

This study investigated the potential protective effect of extracts from Artemisia absinthium (wormwood) on the stomach. They tested two extracts obtained through hot and room temperature maceration of A. absinthium aerial parts in rats and found that the room temperature extract was more effective. It reduced gastric ulcers and prevented inflammation. The extract seemed to maintain the stomach's protective barrier. Using SIRIUS they putatively identified with a high level of confidence (COSMIC score at least 80%) eight main peaks as tuberonic acid glycoside, rupicolin, 2-hydroxyeupatolide, yangabin, sesartemin, artemetin, isoalantodiene, and dehydroartemorin. These findings support the traditional use of A. absinthium for stomach problems.


Activity labelled molecular networking fuels the antioxidation active molecules profile of Ginger

Wang, Qiqi; Chen, Tao; La, Mencuo; Song, Zhibo; Gao, Mengze; Yang, Tingqin; Li, Yulin; He, Liangliang; Zou, Denglang


Summary | Tags: antioxidation, CSI:FingerID, food, molecular networks, SIRIUS

Ginger has been used as consumed food spice and folk medicine in daily life for thousands of years in various regions of the world. It is known to exhibit health-promoting effects due to its considerable antioxidation activity. This bioinformatic workflow was developed to generate activity labelled molecular networking (ALMN) to generate antioxidation active molecules profile of Ginger. SIRIUS + CSI:FIngerID was used to conduct high confidence structure annotations of antioxidation active molecules. Consequently, 48 molecules were prioritized as antioxidation active molecules from 11,720 metabolite molecules of Ginger in a systematical way.


Endophytic bacteria as biological agents to control fusarium wilt disease and promote tomato plant growth

Sriwati, Rina; Maulidia, Vina; Intan, Nurainun; Oktarina, Hartati; Syamsuddin,; Khairan, Khairan; Skala, Leigh; Mahmud, Taifo

In: Physiological and Molecular Plant Pathology, vol. 125, pp. 101994, 2023.

Summary | Tags: bacteria, biocontrol, crop protection, CSI:FingerID, molecular networks, plants, SIRIUS | Links:

Endophytic bacteria are capable of controlling fusarium wilt disease and promoting the growth of tomato plants. Bioactive secondary metabolites produced by the bacteria take part in their biocontrol activity. Sriwati et al explored those metabolites using molecular networks that were annotated through SIRIUS and CSI:FingerID: Clusters were annotated by compound class and many possible structures of secondary metabolites produced by these bacteria were elucidated. Although the active compounds of the bacterial extracts could not be identified, many compounds have the potential to exhibit antibacterial or antifungal activity (containing azole or allylamine subunits).


Identification of Antimicrobial Metabolites from the Egyptian Soil-Derived Amycolatopsis keratiniphila Revealed by Untargeted Metabolomics and Molecular Docking.

Hamed, Ahmed A.; Mohamed, Osama G.; Aboutabl, Elsayed A.; Fathy, Fify I.; Fawzy, Ghada A.; El-Shiekh, Riham A.; Al-Karmalawy, Ahmed A.; Al-Taweel, Areej M.; Tripathi, Ashootosh; Elsayed, Tarek R.

In: Metabolites, vol. 13, iss. 5, pp. 620, 2023.

Summary | Tags: antibiotics, bacteria, CSI:FingerID, drug discovery, SIRIUS | Links:

Researchers are searching for natural antimicrobial agents due to the prevalence of multidrug-resistant pathogens. A rare actinobacteria strain was isolated from Egyptian soil and identified as Amycolatopsis keratiniphila DPA04. Its crude extracts were found to have antimicrobial activity against Gram-positive bacteria. Analysis of the crude extracts using UHPLC-QTOF and SIRIUS + CSI:FingerD led to the identification of 45 metabolites of different chemical classes. ECO-0501 was identified in the cultures with significant antimicrobial activity. Molecular docking studies confirm that it is a promising candidate as MATE (multidrug efflux pump) inhibitor. Natural products from this strain could be useful therapeutic tools for controlling infectious diseases.


Metabolomic Evenness Underlies Intraspecific Differences Among Lineages of a Wetland Grass

Salgado, Ana L.; Glassmire, Andrea E.; Sedio, Brian E.; Diaz, Rodrigo; Stout, Michael J.; Čuda, Jan; Pyšek, Petr; Meyerson, Laura A.; Cronin, James T.

In: J Chem Ecol, 2023.

Summary | Tags: biodiversity, CSI:FingerID, invasive species, plants, SIRIUS | Links:

This study investigates Phragmites australis, a wetland grass, to understand how metabolites contribute to plant invasion success.They analyzed the plant lipidome and metabolome using SIRIUS and CSI:FingerID to predict molecular structures, which in turn were used to classify compounds using ClassyFire and NPClassifier. Using Random Forests, they identified informative features that distinguished five lineages: European native, North American invasive, North American native, Gulf, and Delta. The study found that each lineage had unique phytochemical fingerprints, with some overlap between North American invasive and native lineages. The results suggest that metabolomic evenness may be a critical trait within plant species.


On the Fate of Butyl Methoxydibenzoylmethane (Avobenzone) in Coral Tissue and Its Effect on Coral Metabolome

Clergeaud, Fanny; Giraudo, Maeva; Rodrigues, Alice M. S.; Thorel, Evane; Lebaron, Philippe; Stien, Didier

In: Metabolites, vol. 13, iss. 4, pp. 533, 2023.

Summary | Tags: animals, corals, CSI:FingerID, ecotoxicity, marine, SIRIUS | Links:

The use of sunscreen is essential for public health, but the ultraviolet filters in these products can harm marine organisms, including coral. Butyl methoxydibenzoylmethane (BM) is a UV filter that has already been tested for coral inflammation which is not caused by BM. However, coral exposed to BM is subject to a metabolomic shift. Exploring the metabolism of corals exposed to increasing concentrations of BM, SIRIUS+CSI:FingerID identified two carotenoids that are required for the formation of photosynthetic pigment–protein complexes of the thylakoid membrane. The decrease in the relative concentration of these two carotenoids might be indicative of an alteration in the photosynthetic capacity of the coral. We need to evaluate the levels of BM contamination in the reefs and surrounding waters of anthropized areas to assess whether BM could contribute locally to coral bleaching.


Effects of Long-Term Storage on the Biobanked Neonatal Dried Blood Spot Metabolome

Ottosson, Filip; Russo, Francesco; Abrahamsson, Anna; MacSween, Nadia; Courraud, Julie; Nielsen, Zaki Krag; Hougaard, David M.; Cohen, Arieh S.; Ernst, Madeleine

In: J Am Soc Mass Spectrom, vol. 34, iss. 4, pp. 685-694, 2023.

Summary | Tags: CANOPUS, CSI:FingerID, human, metabolic degradation, metabolite monitoring, molecular networks, SIRIUS, untargeted metabolomics | Links:

Neonatal dried blood spots are not only important for newborn screening but also a powerful source for investigating the potential metabolic etiologies of various diseases using untargeted LC-MS-based metabolomics. So far it is unclear whether the metabolites in those samples remain stable in storage. CSI:FingerID and CANOPUS help to investigate the stability of metabolites and classes of molecules.


Phenolic Fingerprint, Bioactivity and Nanoformulation of Prunus spinosa L. Fruit Extract for Skin Delivery

Luca, Maria De; Tuberoso, Carlo Ignazio Giovanni; Pons, Ramon; García, María Teresa; del Carmen Morán, María; Ferino, Giulio; Vassallo, Antonio; Martelli, Giuseppe; Caddeo, Carla

In: Maria De Luca and Carlo Ignazio Giovanni Tuberoso and Ramon Pons and María Teresa García and María del Carmen Morán and Giulio Ferino and Antonio Vassallo and Giuseppe Martelli and Carla Caddeo, vol. 15, iss. 4, pp. 1063, 2023.

Summary | Tags: bioactivity, nanoformulation, plants | Links:

Prunus spinosa is a plant with diuretic, laxative, antispasmodic, antimicrobial, anti-inflammatory, and antioxidant properties, recommended for the treatment of various inflammation-related disorders, metabolic diseases, circulatory system disorders, wound healing, and selective growth inhibition of some bacteria strains due to its high content of phenolic acids and flavonoids. Here, an extract from P. spinosa berries was prepared and characterized by identifying compounds commonly known for their biological importance, using SIRIUS+CSI:FingerID and COMSIC. In addition, nanoformulation of the plant extracts in phospholipid vesicles was used to improve extract bioavailability in a potential topical application.


Metabarcoding and Metabolomics Reveal the Effect of the Invasive Alien Tree Miconia calvescens DC. on Soil Diversity on the Tropical Island of Mo’orea (French Polynesia)

Clerissi, Camille; Chaïb, Slimane; Raviglione, Delphine; Espiau, Benoit; Bertrand, Cédric; Meyer, Jean-Yves

In: Microorganisms, vol. 11, iss. 4, pp. 832, 2023.

Summary | Tags: bacteria, biodiversity, CANOPUS, CSI:FingerID, invasive species, plants, SIRIUS | Links:

The invasive tree species Miconia calvescens threatens the biodiversity of French Polynesia. This study investigated the impact of M. calvescens on the rhizosphere of six plant species at both the seedling and tree stages. They used metabarcoding and metabolomics to study the diversity of soil organisms and secondary metabolites. Compounds were identified using SIRIUS+CSI:FingerID. The results showed that M. calvescens had a specific association with microeukaryotes of the Cryptomycota family at the tree stage, and this family was positively correlated with the terpenoids found in the soil. The study suggests that these molecules might contribute to the success of M. calvescens as an invasive species.


Cholinesterase Inhibitors from an Endophytic Fungus Aspergillus niveus Fv-er401: Metabolomics, Isolation and Molecular Docking.

Hamed, Ahmed A.; El-Shiekh, Riham A.; Mohamed, Osama G.; Aboutabl, Elsayed A.; Fathy, Fify I.; Fawzy, Ghada A.; Al-Taweel, Areej M.; Elsayed, Tarek R.; Tripathi, Ashootosh; Al-Karmalawy, Ahmed A.

In: Molecules, vol. 28, iss. 6, pp. 2559, 2023.

Summary | Tags: Alzheimer's, CSI:FingerID, drug discovery, fungi, SIRIUS | Links:

Alzheimer's disease is a neurodegenerative condition that affects cognitive function and is expected to triple in the US by 2060, with treatment costs projected to rise to over $500 billion annually. Cholinesterase inhibitors can improve cognitive decline by increasing the neurotransmitter acetylcholine, but they also have side effects such as bradycardia, nausea, stomach pain, anorexia, and diarrhea. Endophytic fungi live inside plant tissues without harming their host and produce a variety of bioactive secondary metabolites which are a promising source of novel cholinesterase inhibitor candidates. In this study, metabolites of an Aspergillus niveus ethyl acetate extract were annotated using SIRIUS and CSI:FinegrID. While the isolated compounds displayed only moderate activity against cholinesterases, structurally related metabolites yielded considerable anticholinesterase activities and are promising leads for developing new potent cholinesterase inhibitors.


Impact of in vitro phytohormone treatments on the metabolome of the leafy liverwort Radula complanata (L.) Dumort

Blatt-Janmaat, Kaitlyn; Neumann, Steffen; Schmidt, Florian; Ziegler, Jörg; Qu, Yang; Peters, Kristian

In: Metabolomics, vol. 19, no. 3, pp. 17, 2023, ISSN: 1573-3890.

Summary | Tags: CANOPUS, chemical diversity, CSI:FingerID, plants, SIRIUS, stress response, untargeted metabolomics, ZODIAC | Links:

Liverworts are chemically diverse plants with unique cell organelles responsible for the synthesis and storage of specialized metabolites. Untargeted metabolomics was used to analyze the metabolic stress response of liverworts without isolating individual metabolites. CANOPUS classified the affected compounds and helped to map the biochemical pathways of the unique stress response of liverworts compared to vascular plants.


Adding insult to injury: Light competition and allelochemical weapons interact to facilitate grass invasion

Morrison, Colin R.; Rhodes, Aaron C.; Bowman, Elizabeth A.; Plowes, Robert M.; Sedio, Brian E.; Gilbert, Lawrence E.

In: Ecosphere, vol. 14, iss. 3, pp. e4438, 2023.

Summary | Tags: allelopathy, biodiversity, CSI:FingerID, invasive species, plants, SIRIUS | Links:

Morrison et al. used Sirius and CSI:FingerID to describe the metabolome of the invasive Guinea grass for the first time, identifying 37 unique secondary metabolites. They compared the effect of the known allelochemical 2HPAA with that of the whole-plant chemical extract, which had significantly stronger effects than pure 2HPAA.


Metabolic adjustments in response to ATP spilling by the small DX protein in a Streptomyces strain

Apel, Cécile; Levasseur, Marceau; Lejeune, Clara; Korch, Shaleen B.; Guérard, Florence; David, Michelle; Askora, Ahmed; Litaudon, Marc; Roussi, Fanny; Gakière, Bertrand; Chaput, John; and Marie-Joelle Virolle,

In: Front Cell Dev Biol, vol. 11, pp. 1129009, 2023.

Summary | Tags: antibiotics, bacteria, CANOPUS, SIRIUS, stress response | Links:

The strategy of ATP spilling, which involves degrading ATP into ADP to enhance metabolic activity and productivity, has been rarely implemented in Streptomyces species. However, antibiotic production by these microorganisms is known to be triggered in conditions that correlate with low ATP content. Researchers cloned the gene for the DX protein, which dephosphorylates ATP into ADP, and introduced it into Streptomyces albogriseolus/viridodiastaticus. used LC/HRMS2 to analyze the molecules produced by the resulting strain A37 and a control strain A36. Molecular formulas of compounds of interest were predicted with SIRIUS and class annotation was confirmed with CANOPUS. The study demonstrated that DX can be an efficient tool for enhancing specialized metabolic pathways in Streptomyces, potentially leading to the discovery of novel bioactive molecules.


Prioritization of Microorganisms Isolated from the Indian Ocean Sponge Based on Metabolomic Diversity and Biological Activity for the Discovery of Natural Products

Loarer, Alexandre Le; Marcellin-Gros, Rémy; Dufossé, Laurent; Bignon, Jérôme; Frédérich, Michel; Ledoux, Allison; Queiroz, Emerson Ferreira; Wolfender, Jean-Luc; Gauvin-Bialecki, Anne; Fouillaud, Mireille

In: Microorganisms, vol. 11, no. 3, 2023, ISSN: 2076-2607.

Summary | Tags: bacteria, CANOPUS, CSI:FingerID, cytotoxicity, drug discovery, marine, marine natural products, molecular networks, SIRIUS | Links:

Marine microorganisms offer a rich source of bioactive compounds with unique structures and remarkable biological activity. This makes them an important resource for the search for new therapeutic compounds, which is one of the most pressing challenges of our time. To narrow down the search to the most promising microorganisms, SIRIUS is nearly doubling the number of natural products annotated to estimate the chemical potential of microbial extracts.