MetaboLights

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identify the detected m/z and retention times for the targeted compounds, we developed the  processing method using a mixture of all compounds of interest and L-Leucine-13C3 as the internal standard. Next, all data were processed using this method to identify the compounds and integrate their peak areas.MetaboLightsPublicLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - negative - hilicFor LCMS analysis, samples were resuspended in a mix of acetonitrile:water (1:1 ratio) containing 10 ug/mL of L-Leucine-13C3 as internal standard. Relative metabolite quantification was performed by using an Ultra Performance Liquid Chromatography (UPLC) system (Waters Corp.) coupled with a high-resolution mass-spectrometer (MS) Exploris 240 (Thermo Fisher Scientific Inc.). Compound separation was done on a BEH Amide column (Waters Corp.), using a gradient of 10 mM ammonium formate in 90% water (pH 3.5) (mobile phase A) and 90% acetonitrile (mobile phase B) for 25 minutes. The injection volume was 1 µL, with the column temperature kept at 30 °C and the flow rate at 0.25 mL/min.Core microbes are ecological generalists supporting the host, ecosystem functionality and stability.Omar TovarBen Gurion Universitymixturespent culture mediumGrowth Mediumsolventmass spectrometry assayMetabolite extraction from microbial supernatants was done by mixing 100 uL of each sample with 300 uL of methanol, followed by vortexing for 5 s and incubation at -20 °C for 10 min. Then, samples were centrifuged at 18,213 rcf for 10 min at 4 °C and 300 uL of the supernatant were dried in a centrifugal vacuum concentrator for 4 h and stored at -80 °C until use.Enterococcus faecalisClostridium cadaverisTreponema sp.Prevotella sp.Clostridium paraputrificumBlank transfer 3Bifidobacterium thermophilumBlank transfer 2Succinivibrio dextrinosolvensPseudobutyrivibrio ruminisButyrivibrio fibrisolvensSelenomonas ruminantiumMegasphaera elsdeniiSegatella baroniaeMixed metabolites for transfer 3Methanobrevibacter smithiiPrevotella ruminicolaFibrobacter succinogenesPrevotella albensisButyrivibrio proteoclasticusButyrivibrio fibrinosolvensSolvent_blankRuminococcus flavefaciensNon inoculated mediaRuminococcus gnavusSharpea azabuensisSelenomonas bovisBacteroides thetaiotaomicronTreponema bryantiiReference compoundButyrivibrio hungateihttps://www.ebi.ac.uk/metabolights/MTBLS11446Omar Tovar-Herrera. Ben Gurion University. omaretoh@gmail.com. +9720509563341.Gil Sorek.Ido Lybovits.Ido Grinshpan.Sarah Moraïs.Itzhak Mizrahi. imizrahi@bgu.ac.il.The data analysis was performed using Xcalibur Quan Browser. First, to identify the detected m/z and retention times for the targeted compounds described above, we developed the  processing method using a mixture of all compounds of interest and L-Leucine-13C3 as the internal standard. Next, all data were processed using this method to identify the compounds and integrate their peak areas. Finally, normalized relative concentrations of each target were calculated by obtaining the ratio between its peak area and the peak area of the internal standard.Experiment typeReplicateCore Gut MicrobesTimepointomaretoh@gmail.comWe analyzed the supernatant of bacterial isolates through targeted metabolomics. Sample collection was done after growing the microbial isolates culture media for 24-48 °C at 39 °C. After incubation, the samples were obtained by centrifuging the spent media at 11,292 rcf for 10 min and 4 °C. The supernatant was then transferred into an eppendorf tube and stored at -80 °C.MetabolomicsMicrobial EcologyRumenuntargeted metabolitesMicrobiomeMicrobial EcologyRumenuntargeted metabolitesMicrobiomeHigh-resolution mass spectra were acquired using electrospray ionization (ESI) in positive mode (full scan, 70-700 m/z), with a resolution of 24,000 full width at half-maximum (FWHM). The MS parameters were: ion spray voltage 3500, sheath gas 50, aux gas 1, ion transfer tube temperature 325 °C and vaporizer temperature 350 °C. Data were acquired under the control of Xcalibur software version 4.5.455 (Thermo Fisher Scientific Inc.).falseCore microbes are ecological generalists supporting the host and ecosystem functionality and stabilityCore gut microbes persist across diverse gut ecosystems, raising the central question in microbiome research of what defines core microbes and the factors driving their persistence across hosts? Using the rumen microbiome as a model system, our study reveals that core microbes exhibit distinct attributes of ecological generalists, including greater strain variability and broader functional capacity, linked to larger genome sizes. These traits enable core microbes to be metabolically independent while also supporting non-core microbes and the host. Core taxa produce essential metabolites, such as amino acids and vitamins, and encode fiber-degrading enzymes crucial for host nutrition. Additionally, they engage in cross-feeding, providing non-core microbes with vital nutrients. This independence positions core microbes as foundational pillars of gut ecosystem stability. Our findings offer valuable insights into the functional essence of core microbes, with implications that extend beyond ecology to microbiome-based interventions in food security and environmental sustainability.2025-05-232024-11-06MTBLS11446