MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/m_MTBLS13315_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/m_MTBLS13315_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/m_MTBLS13315_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/m_MTBLS13315_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/a_MTBLS13315_LC-MS_negative_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/s_MTBLS13315.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/a_MTBLS13315_LC-MS_positive_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/a_MTBLS13315_LC-MS_negative_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315/a_MTBLS13315_LC-MS_positive_hilic_metabolite_profiling.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13315Compound identification was conducted with MS-DIAL by comparing chromatographic and spectrometric characteristics with both in-house and publicly available databases (MassBank, ReSpect, RIKEN, GNPS, Fiehn libraries, CASMI2016, MetaboBASE, BMDMS-NP, and PFAS). Additional identifiers were obtained using MS-FINDER (ver. 3.60) to compare acquired MS/MS spectra with in silico-generated records for known compounds. All metabolite annotations followed the Metabolomics Standards Initiative by the Chemical Analysis Working Group.MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - positive - HILICLiquid Chromatography MS - negative - HILICLiquid Chromatography MS - positive - reverse phaseRPThe samples were analyzed by liquid chromatography-mass spectrometry consisting of a 1290 Infinity II UHPLC (Agilent Technologies, Santa Clara, USA) equipped with Ultra Low Dispersion Kit and 1290 Multisampler (G7167B). Reversed-phase separation was employed using a Zorbax Eclipse XDB-C18 column (2.1 × 100 mm, 1.8 μm, Agilent Technologies, Palo Alto, CA, USA) at 50°C as the stationary phase. The mobile phase consisted of ultra-pure water (eluent A) and MeOH (eluent B), both containing 0.1% (v/v) formic acid. The flow rate of the eluent was 0.4 mL/min. The elution gradient profile was as follows (t [min], %B): (0, 2), (10, 100), (14.5, 100), (14.51, 2), (16.5, 2). Injection volume was to 2 µL. HILIC The samples were analyzed by liquid chromatography-mass spectrometry consisting of a 1290 Infinity II UHPLC (Agilent Technologies, Santa Clara, USA) equipped with Ultra Low Dispersion Kit and 1290 Multisampler (G7167B). HILIC separation was employed using an Acquity UPLC® BEH Amide column (2.1 × 100 mm, 1.7 μm, Waters Corporation, Milford, MA, USA) at 45°C as the stationary phase. The mobile phase consisted of 50% v/v ACN in water (eluent A) and 90% v/v ACN in water (eluent B), both containing 20 mM ammonium formate buffer containing 0.25% (v/v) formic acid. The flow rate of the eluent was 0.6 mL/min. The elution gradient profile was as follows (t [min], %B): (0,100), (2.5,100), (10, 0), (10.01, 100), (12.5, 100). Injection volume was to 2 µL.Differential effects of synbiotic delivery route (feed, water, combined) in broilers challenged with Salmonella Infantis. 10.1016/j.psj.2025.104890. PMID:40048980Afekta Technologies Ltd.Topi Meuronencaecumblankmass spectrometryFrozen chicken caecum tissue and digesta samples were weighed in homogenizer tubes (1). For the metabolite extraction and protein precipitation, cold methanol (2) (80% v/v) was added in a ratio of 1000 µl per 100 mg of a tissue sample and 1500 µl per 100 mg of a digesta sample. Blank samples contained 1000 µl of extraction solvent per tube and were handled similarly to the samples from now on. The tubes were shaken by hand to mix solid samples to solvent. The tissue samples were homogenized (3) at 2 ± 2 °C at the speed 7.45 m/s for 60 s running the program twice while the digesta samples were homogenized (3) at 2 ± 2 °C at the speed 6.0 m/s for 30 s. The samples were incubated on ice for 15 min and mixed once for 10 sec by vortexing during incubation. This was followed by centrifugation at 17,000×g for 10 min at 4 °C. The supernatants were transferred into a filter plate (4) which was centrifuged at 700×g for 5 min at 4 °C. The pooled quality control (QC) samples were prepared by collecting 30 µl from each tissue and digesta supernatant and combining the sample materials in their respective tubes. The QC samples were mixed by vortexing and filtered through the filter plate as the sample supernatants. Materials:1. Bead Ruptor Pre-Filled Bead Tubes, 2 ml, metal beads, Omni International2. Methanol, CHROMASOLV™ LC–MS Ultra, Riedel-de Haën™, Honeywell. Ultrapure water (Type 1) water (Direct-Q® Water Purification System)3. Bead Ruptor 24 Elite homogenizer, Omni International4. Captiva ND filter plate 0.2 µm, AgilentblankGallus gallushttps://www.ebi.ac.uk/metabolights/MTBLS13315Antton Alberdi. University of Copenhagen. antton.alberdi@sund.ku.dk.Mahdi Ghanbari. mahdi.ghanbari@dsm-firmenich.com.Michael Hess. Histovac GmbH, Klosterneuburg, Austria. michael.hess@histovac.com.Soile Turunen. soile.turunen@afekta.com.Olli Kärkkäinen. Afekta Technologies Ltd.. olli@afekta.com.Topi Meuronen. Afekta Technologies Ltd.. topi.meuronen@afekta.com.Victoria Drauch. Victoria.Drauch@vetmeduni.ac.at.Briefly, peak detection and alignment was performed in MS-DIAL ver. 4.92. For the peak collection, m/z values between 50 and 1600 and all retention times were considered. The amplitude of minimum peak height was set at 2000. The peaks were detected using the linear weighted moving average algorithm. For the alignment of the peaks across samples, the retention time tolerance was 0.2 min and the m/z tolerance was 0.015 Da. Solvent background was removed using solvent blank samples under the condition that to be kept for further data analysis, the maximum signal abundance across the samples had to be at least five times that of the average in the solvent blank samples. Preprocessing was applied separately to both sample types. Low-quality features were flagged and discarded from the FDR correction calculations and multivariate analyses. Molecular features were considered of high quality if they met all the following quality metrics: low number of missing values (present in more than 70% of the QC samples, present in at least 50% of samples in at least one study group), not present in blank samples (sample max/blank mean > 5), and RSD* below 20%, D-ratio* below 10%. In addition, if either RSD* or D-ratio* was above the threshold, the features were still considered good quality if their classic RSD, RSD* and basic D-ratio were all below 10%. All analyses were conducted with R version 4.2.3 and notame version 0.3.1.TreatmentSamply typeBioSamples accessiontopi.meuronen@afekta.comThe full study description is published in detail before:Poult Sci. 2025 Feb 6;104(4):104890. doi: 10.1016/j.psj.2025.104890“Differential effects of synbiotic delivery route (Feed, water, combined) in broilers challenged with Salmonella Infantis” Animal were euthanized and samples from caecum tissue (N) and caecum content (M) were collected on Days 7 (a), 14 (b), 21 (c), 28 (d) and 28 (e) from 5 different Treatments (SI, Control, SynW_SI, SynFW_SI, SynF_SI). MetabolomicsMetabolomicsSynbiotic SupplementGallus gallusMetabolomicsSynbiotic SupplementGallus gallusRP POSMass spectrometry analysis was performed on Agilent 6546 QTOF with a Dual Jet Stream ESI ionization source. Positive ionization mode was used for data acquisition in a 10 GHz extended dynamic range mode scanning from m/z 50 to 1600. The data was collected in the centroid mode at an acquisition rate of 1.67 spectra/s (i.e., 600 ms/spectrum) with an abundance threshold of 150. The following conditions for Dual Jet Stream ESI source were applied: drying gas temperature 325 °C and flow 10 L/min, sheath gas temperature 350 °C with a flow of 11 L/min, nebulizer pressure 45 psi, capillary voltage 3500 V, nozzle voltage 1000 V, fragmentor voltage 100 V and skimmer 45 V.For fragmentation spectra, tandem mass spectrometry methods (MS/MS) were applied. Data dependent acquisition (DDA) was conducted by automatically selecting the four most abundant precursor ions for MS/MS fragmentation. Each precursor was excluded from further selection after two MS/MS spectra had been acquired and released again from the exclusion list after 0.25 min. MS/MS scan rate was set to 3.33 spectra/sec with the precursor isolation width set to 1.3 Da. The collision energies used for the MS/MS analysis were 10, 20, and 40 eV in mass range 50-1600 m/z.  RP NEGMass spectrometry analysis was performed on Agilent 6546 QTOF with a Dual Jet Stream ESI ionization source. Negative ionization mode was used for data acquisition in a 10 GHz extended dynamic range mode scanning from m/z 50 to 1600. The data was collected in the centroid mode at an acquisition rate of 1.67 spectra/s (i.e., 600 ms/spectrum) with an abundance threshold of 150. The following conditions for Dual Jet Stream ESI source were applied: drying gas temperature 325 °C and flow 10 L/min, sheath gas temperature 350 °C with a flow of 11 L/min, nebulizer pressure 45 psi, capillary voltage 3500 V, nozzle voltage 1000 V, fragmentor voltage 100 V and skimmer 45 V.For fragmentation spectra, tandem mass spectrometry methods (MS/MS) were applied. Data dependent acquisition (DDA) was conducted by automatically selecting the four most abundant precursor ions for MS/MS fragmentation. Each precursor was excluded from further selection after two MS/MS spectra had been acquired, and released again from the exclusion list after 0.25 min. MS/MS scan rate was set to 3.33 spectra/sec with the precursor isolation width set to 1.3 Da. The collision energies used for the MS/MS analysis were 10, 20, and 40 eV in mass range 50-1600 m/z.  HILIC POSMass spectrometry analysis was performed on Agilent 6546 QTOF with a Dual Jet Stream ESI ionization source. Positive ionization mode was used for data acquisition in a 10 GHz extended dynamic range mode scanning from m/z 50 to 1600. The data was collected in the centroid mode at an acquisition rate of 1.67 spectra/s (i.e., 600 ms/spectrum) with an abundance threshold of 150. The following conditions for Dual Jet Stream ESI source were applied: drying gas temperature 325 °C and flow 10 L/min, sheath gas temperature 350 °C with a flow of 11 L/min, nebulizer pressure 45 psi, capillary voltage 3500 V, nozzle voltage 1000 V, fragmentor voltage 100 V and skimmer 45 V.For fragmentation spectra, tandem mass spectrometry methods (MS/MS) were applied. Data dependent acquisition (DDA) was conducted by automatically selecting the four most abundant precursor ions for MS/MS fragmentation. Each precursor was excluded from further selection after two MS/MS spectra had been acquired, and released again from the exclusion list after 0.25 min. MS/MS scan rate was set to 3.33 spectra/sec with the precursor isolation width set to 1.3 Da.  The collision energies used for the MS/MS analysis were 10, 20, and 40 eV in mass range 50-1600 m/z.  HILIC NEGMass spectrometry analysis was performed on Agilent 6546 QTOF with a Dual Jet Stream ESI ionization source. Negative ionization mode was used for data acquisition in a 10 GHz extended dynamic range mode scanning from m/z 50 to 1600. The data was collected in the centroid mode at an acquisition rate of 1.67 spectra/s (i.e., 600 ms/spectrum) with an abundance threshold of 150. The following conditions for Dual Jet Stream ESI source were applied: drying gas temperature 325 °C and flow 10 L/min, sheath gas temperature 350 °C with a flow of 11 L/min, nebulizer pressure 45 psi, capillary voltage 3500 V, nozzle voltage 1000 V, fragmentor voltage 100 V and skimmer 45 V.For fragmentation spectra, tandem mass spectrometry methods (MS/MS) were applied. Data dependent acquisition (DDA) was conducted by automatically selecting the four most abundant precursor ions for MS/MS fragmentation. Each precursor was excluded from further selection after two MS/MS spectra had been acquired, and released again from the exclusion list after 0.25 min. MS/MS scan rate was set to 3.33 spectra/sec with the precursor isolation width set to 1.3 Da. The collision energies used for the MS/MS analysis were 10, 20, and 40 eV in mass range 50-1600 m/z. FA 20:0SM d34:1NaringeninFA 20:4FA 22:4Syringic AcidFA 12:1;O2Medicagenic acidDihydrocaffeic acid 3-sulfate7-Sulfocholic acid3,5-Dihydroxybenzoic acid3-hydroxybenzoic acidPhthalic acidGallic acidAllocholic acid6-Hydroxynicotinic acid4-Hydroxybenzoic acidCatecholVanillic acid 4-O-sulfateSyringic acid sulfateFA 11:1;O23-Dehydroquinic acidOxidized glutathionePC 18:2/18:2N6-Succinyl Adenosine2-(Malonylamino)benzoic acidChenodeoxycholic acidAdipic acid4-HydroxybenzaldehydeHomovanillic acid sulfateSuberic acid3,4-Dihydroxyhydrocinnamic acidPC O-16:1_18:23-Hydroxymethylglutaric acidAzelaic acidGentisic acidGlutaric acidFA 16:1Salisylic acidPC 18:1/18:1FA 16:0FA 18:02-Hydroxybutyric acidFA 18:2PC 14:0_18:2FA 10:1;O2N-AcetylphenylalanineHydroxyphenyllactic acid3-[3-(Sulfooxy)phenyl]propanoic acid3-Hydroxy-2-methylpyridine-4,5-dicarboxylateTauromuricholic acidAlpha-Muricholic acidFA 22:6DaidzeinSalmonella enterica subsp. enterica serovar Infantis (S. Infantis) presents a persistent and multi-drug-resistant threat to poultry production, highlighting the need for effective control strategies. This study evaluated the impact of a S. Infantis infection in broiler chickens across various parameters, including organ colonization, gut microbiota, and immune function. We also assessed the mitigation potential of a synbiotic, multispecies feed additive, administered via three routes applicable for the field: feed only, drinking water only, and a combination of both. Our results demonstrated that the combined administration route yielded notably positive effects on several parameters, followed by the drinking-water only administration. This approach resulted in significant improvements in gut microbiota health, characterized by increased levels of beneficial microbes such as Lactobacillus, Ligilactobacillus, and Butyricicoccus, and a decrease in potentially harmful genera from the Proteobacteria phylum. Reduction of S. Infantis load was observed in caecum, ileum, and spleen over time albeit shedding was not influenced. The drinking water-only administration showed a significant reduction of S. Infantis colonization in the caecum on the last sampling day. Immune response analysis indicated no significant differences in serum antibody levels between control and treatment groups. These findings underscore the impact of both combined and drinking water-only synbiotic, multispecies feed additive administration on the gut microbiota and a possible route for reducing S. Infantis in poultry production. The obtained data provide valuable guidance for optimizing synbiotic use in commercial poultry management, enabling enhanced pathogen control and improved gut health.Differential effects of synbiotic delivery route (feed, water, combined) in broilers challenged with Salmonella Infantis.Drauch Victoria V, Ghanbari Mahdi M, Reisinger Nicole N, Mohnl Michaela M, Hess Claudia C, Hess Michael Mfalse3D'omics: Salmonella challenge chicken trialBioProject PRJEB86258 at https://www.ebi.ac.uk/ena/browser/view/PRJEB86258 The full study description is published in detail before:Poult Sci. 2025 Feb 6;104(4):104890. doi: 10.1016/j.psj.2025.104890“Differential effects of synbiotic delivery route (Feed, water, combined) in broilers challenged with Salmonella Infantis”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