Dori Tools v2.1.0
Dori Tools is a set of useful programs that support running a mid-range HPC cluster for BioInformatics workloads.
Rath, Georg [Lawrence Berkeley National Laboratory↗
SEARCH · Search NASA
Results for “DORIS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Potential Adoption and Benefits of Co-Optimized Multimode Engines and Fuels for U.S. Light-Duty Vehicles
Exploring a diverse portfolio of technologies for decarbonization is crucial to understanding the potential impacts of different technological solutions and their associated environmental implications. Using high-octane, high-sensitivity biofuel blends in co-optimized multimode engines can increase engine efficiency and reduce vehicle emissions. Here, the multimode engine research focuses on the benefits of light-duty vehicle engines, which can operate in multiple modes depending on the vehicle's load. Low-temperature combustion can improve efficiency and reduce emissions (such as those from oxides of nitrogen and particulate matter) during low-load operation, while spark ignition performance is maintained in high-load operation. These advanced engines can be optimized to run on blends of biobased fuels. This analysis models scenarios for potential market adoption of co-optimized multimode vehicles fueled by three different bioblendstocks: ethanol, isopropanol, and isobutanol. An integrated modeling approach is used to forecast the energy and environmental impacts of the deployment of co-optimized multimode vehicles and fuels in the light-duty sector over the 2020-to-2050 time horizon. The multidisciplinary approach combines vehicle sales modeling, system dynamics modeling of the biorefining industry, and life cycle assessment to estimate the emissions and energy benefits. The models consider market forces such as consumer preferences for vehicle attributes, biofuel supply and demand dynamics subject to biorefinery capacity build-out and bioresource constraints, and forecasted changes to the U.S. bulk energy system over time. Market adoption of co-optimized vehicles is evaluated across a wide parameter space for incremental vehicle cost and engine efficiency improvement. This analysis reveals that the deployment of co-optimized multimode fuels and vehicles results in up to a 5% reduction in annual sector-wide life cycle greenhouse gas (GHG) emissions by 2050, relative to a business-as-usual scenario, but is also indicates environmental trade-offs, such as higher life cycle water-use. Emission benefits could potentially increase beyond 2050, as the new technologies penetrate the market and gain a foothold. Results also show that, under certain circumstances, vehicles with engines co-optimized for use with high-octane, high-sensitivity biofuel blends can be cost-competitive with conventional gasoline, while reducing GHG emissions. Our modeling results indicate that co-optimized multimode fuels and engines can be strategically leveraged in tandem with electrification to decarbonize the light-duty sector. Co-optimized vehicles could play a role in the early years of the time horizon, while electric vehicles (EVs) could become more competitive in the later years, highlighting the complementary benefits of these technologies for GHG reductions.
Oke, Doris↗
Gramicidin and chlorhexidine encapsulated in bicontinuous microemulsions: Antimicrobial activity performance and their impact on self‐assembly
The utility of bicontinuous microemulsions (BMEs) as carriers of the antimicrobial peptide (AMP) gramicidin D and antiseptic chlorhexidine was investigated for possible topical delivery to chronic wounds. The two water-insoluble solutes dissolved in pre-formed one-phase BMEs of Water/Polysorbate 80/Limonene/Ethanol/Glycerol and Water/Aerosol-OT (AOT)/Polysorbate 85/Isopropyl Myristate and an AOT/Polysorbate 85 Winsor-III system, achieving gramicidin and chlorhexidine concentrations of 1.0 wt% and 0.5% individually and 0.5% and 0.3% in mixtures at 22°C, respectively. Small-angle neutron scattering measurements demonstrated that both solutes decreased surfactant interfacial activity and increased interfacial fluidity for the Polysorbate 80 system. For the AOT/Polysorbate 85 systems, ellipsoidal aggregates consisting of gramicidin and likely adsorbed surfactant and oil formed, while chlorhexidine enhanced the surface activity of surfactants. According to bioassays performed on artificial skin, the incorporation of melittin, gramicidin, and chlorhexidine in general enhanced the bioactivity of Polysorbate 80 BMEs for 24 h treatment against relevant antibiotic-resistant bacteria found on skin relative to controls. Yet, BME treatments were less effective than aqueous melittin control, in contrast to well diffusion bioassays performed previously. The results reflect the strong impact of AMPs and antiseptics on BME structure and dynamics and the complexity of formulating BMEs for optimal antimicrobial activity.
antimicrobial peptides↗
Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme Fe II enzymes
Carotenoid cleavage dioxygenases (CCDs) are non-heme Fe II enzymes that catalyze the oxidative cleavage of alkene bonds in carotenoids, stilbenoids, and related compounds. How these enzymes control the reaction of dioxygen (O 2 ) with their alkene substrates is unclear. Here, we apply spectroscopy in conjunction with X-ray crystallography to define the iron coordination geometry of a model CCD, CAO1 (Neurospora crassa carotenoid oxygenase 1), in its resting state and following substrate binding and coordination sphere substitutions. Resting CAO1 exhibits a five-coordinate (5C), square pyramidal Fe II center that undergoes steric distortion toward a trigonal bipyramidal geometry in the presence of piceatannol. Titrations with the O 2 -analog, nitric oxide, show a >100-fold increase in iron–nitric oxide affinity upon substrate binding, defining a crucial role for the substrate in activating the Fe II site for O 2 reactivity. The importance of the 5C Fe II structure for reactivity was probed through mutagenesis of the second-sphere Thr151 residue of CAO1, which occludes ligand binding at the sixth coordination position. A T151G substitution resulted in the conversion of the iron center to a six-coordinate state and a 135-fold reduction in apparent catalytic efficiency toward piceatannol compared with the wildtype enzyme. Substrate complexation resulted in partial six-coordinate to 5C conversion, indicating solvent dissociation from the iron center. Additional substitutions at this site demonstrated a general functional importance of the occluding residue within the CCD superfamily. Taken together, these data suggest an ordered mechanism of CCD catalysis occurring via substrate-promoted solvent replacement by O 2 . CCDs thus represent a new class of mononuclear non-heme Fe II enzymes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Technology Impact and Resource Assessment of Existing and Planned U.S. Biofuel Production: Life Cycle Water Consumption, Water Stress, Land Use, and Criteria Air Pollutants
Biofuels have the potential to strengthen the U.S. energy supply, enhance energy security, and promote economic development. As the United States continues to expand biofuel production, quantifying resource requirements and location-specific constraints is crucial for planning, siting, and technology development to support long-term viability. Accordingly, this work assesses the life cycle resource consumption (water consumption, and land use), water stress and criteria air pollutants associated with expanded U.S. biofuel production over the 2020–2035 period, based on producers’ plans. We perform a bottom-up technology impact assessment and resource assessment by integrating facility-level production statistics with Argonne’s Research and Development (R&D) GREET model and county-level water-stress characterization factors from Available Water Remaining for the United States (AWARE-US) model. Results suggest that by 2035, biofuels could meaningfully contribute to U.S. energy demand, driven primarily by first-generation and waste-based feedstocks with plans for substantial capacity expansion, although cellulosic and e-fuel technologies remain limited. However, growth must be managed to minimize impacts on water resources and land use. These impacts vary by fuel type and facility location, specifically, projected expansion increases water consumption and can elevate water-stress impacts in certain regions like Nebraska, Kansas, Colorado, Idaho, California and North Texas. Direct land use also increases overall, particularly for first-generation feedstocks such as corn and soybeans. These findings underscore the need for continued technological improvements and innovative strategies to manage resource demands as the industry scales and to support complementary deployment within the evolving U.S. energy system.
09 BIOMASS FUELS↗
Evaluation of Subetadex-α-methyl, a Polyanionic Cyclodextrin Scaffold, as a Medical Countermeasure against Fentanyl and Related Opioids
Subetadex-α-methyl (SBX-Me), a modified, polyanionic cyclodextrin scaffold, has been evaluated for its utilization as a medical countermeasure (MCM) to neutralize the effects of fentanyl and related opioids. Initial in vitro toxicity assays demonstrate that SBX-Me has a nontoxic profile, comparable to the FDA-approved cyclodextrin-based drug Sugammadex. Pharmacokinetic analysis showed rapid clearance of SBX-Me with an elimination half-life of ~7.4 h and little accumulation in major organs. SBX-Me was also evaluated for its ability to counteract the effects of fentanyl, carfentanil, and remifentanil in rats. Recovery times in rats exposed to sublethal fentanyl doses were found to be shorter when treated with SBX-Me after opioid exposure. The recovery times were reduced from ~35 to ~17 min for fentanyl, ~172 to ~59 min for carfentanil, and ~18 to ~12 min for remifentanil. SBX-Me increased the elimination half-life for fentanyl and remifentanil from 5.37 to 6.42 h and 8.24 to 9.74 h, respectively. These data support SBX-Me as a solid platform from which further research can be launched for the development of a MCM against the effects of fentanyl and its analogs. Furthermore, the data suggests that SBX-Me and other analogs are attractive candidates as broad spectrum opioids targeting MCMs.
Chemistry↗
Nature of the Reactive Biferric Peroxy Intermediate P′ in the Arylamine Oxygenases and Related Binuclear Fe Enzymes
Binuclear nonheme iron enzymes activate O 2 to perform a wide range of chemical transformations. The process of O 2 activation typically involves a biferric peroxy-level intermediate P. It has been previously found that this intermediate undergoes further activation, either protonation or rearrangement to form P′ or further oxidation to form high-valent intermediates Q or X. Here, this study defines the structure of the P′ intermediate in the N-oxygenases CmlI (and AurF based on previous data) using nuclear resonance vibrational spectroscopy (NRVS) in conjugation with density functional theory (DFT) calculations. These results, combined with variable temperature variable field (VTVH) magnetic circular dichroism (MCD) spectroscopy on the 1-electron cryoreduced P′, define the structure of the P′ intermediate as a μ-1,2-hydroxoperoxo biferric site with a second hydroxide bridge. Reaction coordinate calculations demonstrate that single electron transfer (SET) is facilitated by protonation of the peroxo, activating its reductive cleavage, and that the additional hydroxide bridge does not impact this reaction. VTVH MCD studies further reveal that the hydroxide bridge is absent in the biferrous site, suggesting that during the O 2 reaction with the biferrous site, a water molecule forms the hydroxide bridge in providing the proton that activates the peroxide in P′ for reactivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Baltimore Community Weather Station Network: Filling the Urban Measurement Desert
Quantification and understanding of how heat, rainfall, and air quality vary within cities are needed to identify the area with the worst conditions, develop solutions to extreme weather, and assess the impact of proposed policies. However, neighborhood-level variability is not well quantified because there are few environmental measurement stations within cities. In Baltimore City, a community-based network of weather stations to address this issue has been developed through a partnership between universities, state agencies, and Baltimore residents. The weather stations are hosted by community partners, and the data collected are enabling the mapping of urban weather across the city and the testing of models and proposed mitigation strategies. In addition, the network provides direct community involvement, with resulting benefits of increased community engagement, education, and empowerment. Researchers have an opportunity to democratize the scientific process and ensure that local knowledge and lived experiences of city residents inform future decision-making. The approach could be used as a model for other cities that apply similar monitoring instruments for other environmental exposures.
community↗
Assessing the deployment of solar-driven hydrogen from biomass at scale in the U.S.
Solar hydrogen from biomass gasification is a promising technology to sustainably produce hydrogen, responsibly dispose biomass waste, and reduce reliance on fossil fuels. However, its large-scale deployment faces challenges due to the geospatial misalignment between biomass resources and solar intensity, which introduces additional supply chain logistics costs. We analyze the logistics cost burden imposed by this misalignment and its impact on successful large-scale deployment of solar-driven hydrogen from biomass in the United States. We also consider associated carbon emissions and explore how the mix of deployed technologies evolves under externally imposed carbon penalties. Our findings show that while economies of scale are known to apply at the processing facility level, the reverse effect occurs at the broader systems-level, driven by logistics. Also, at current technology costs, high carbon penalties would be required to favor deployment of solar based technologies over conventional and hybrid alternatives. We further illustrate strategies and system-level changes to reduce logistics costs and enable sustainable, low-cost hydrogen for decarbonizing different industrial sectors.
Iloeje, Chukwunwike O. [Argonne National Laborator↗
Life cycle greenhouse gas emissions and carbon intensity of U.S. fuel use and projection for the next 10 years-based on built capacity and expansion plans
The U.S. Inflation Reduction Act of 2022 supports biofuel production expansion through the 45Z clean fuel production tax credit, replacing previous 40A and 40B credits. This follows on the Renewable Fuel Standard from the Energy Policy Act of 2005 and its expansion in 2007. States like California, Oregon, and Washington also offer clean fuel credits. Meanwhile, federal agencies, including the U.S. Department of Energy, have advanced alternative fuel technologies through research and development funding. The surging interest in the biofuel industry has spurred the demand for biofuel supplies in the markets, although achieving profitability for advanced biofuels and low-carbon e-fuels remains challenging. This study aims to track U.S. alternative fuel production capacity expansion plans over the next 10 years and estimate impacts on greenhouse gas (GHG) emissions. By tracking built capacity and industry announcements of planned expansion, this study complements other studies which use models to predict changes in energy technologies and the associated GHG implications. Modeled projections of future technologies are often criticized for over or underestimating the cost and potential role of new technologies. The study focuses on sustainable aviation fuel, renewable diesel, ethanol, biodiesel, and renewable natural gas. Using facility-level data, we conducted a bottom-up analysis linking biofuel production pathways with corresponding pathways and parameterizations in the Argonne R&D GREET model. Results indicate that biofuel capacity could reach 3.8 exajoules in 2035, potentially reducing U.S. GHG emissions by 179 million tonnes, including the full life cycle. This corresponds to a 20% reduction in transportation and 5% in industry sector emissions by 2035, or a 3.6% reduction in economy-wide emissions. Overall, this study shows that while biofuel production capacity in the U.S. is expanding, the capacities remain limited compared to fuel demand. Uncertainty regarding the durability and extension of incentives may be dampening the pace of growth. Meanwhile, demonstrating the commercial potential for alternative fuels and climbing the learning curve for new technologies could lead to an increased pace of expansion in later years. This study offers insights for bioenergy stakeholders, highlighting biofuel technologies' contribution to U.S. energy system and emissions reduction over time based on producers' plans.
Biofuel Producers↗
The stellar origins of 96 Zr excesses in presolar graphites from the Murchison meteorite
Context. Zirconium-96 is a stable isotope that can be synthesized under different neutron-rich nucleosynthetic conditions. Astrophysical models predict its production to occur in various stellar environments: from low-to-intermediate-mass asymptotic giant branch (AGB) stars to massive stars and core-collapse supernovae. Aims. Detections of 96Zr excesses, in combination with other isotopic measurements from presolar grains can provide unique constraints on its stellar origin. Presolar grains are microscopic particles found in primitive Solar System materials, which formed in stellar winds and supernova ejecta. The isotopic composition of each grain can provide us a snapshot of the nucleosynthetic processes that took place during the parent star’s lifetime. Methods. In this study, we measured the stable isotopes of C, N, O, Mo, Zr, and Ru in high-density presolar graphite grains from the Murchison meteorite and found four grains that contain positive isotopic anomalies in 96 Zr carried by their internal subgrains. We analyzed multi-element isotopic datasets from each grain to explore the source of the observed 96 Zr excesses. Results. Comparisons with stellar models indicate that two grains likely condensed in an intermediate-mass AGB star with initial metallicity of Z ≤ 0.014. Their 96 Zr/ 94 Zr ratios also match those predicted for born-again AGB stars undergoing a very late thermal pulse and rapidly accreting white dwarfs. After comparing the relative populations of the aforementioned dust-producing stars, we propose rapidly accreting white dwarfs as a new, and more likely, stellar source for one of the presolar grains. The remaining two grains could have originated in the supernova ejecta of massive stars, due to correlated excesses in the p-nuclides, 92, 94 Mo. Thus, grains with 96 Zr anomalies can have a variety of stellar origins, in agreement with theoretical studies. Conclusions. Our study highlights the importance of multi-element analysis in constraining the types of stars where presolar grains have condensed. These data will help improve our understanding of various nucleosynthesis processes in different stellar phases.
79 ASTRONOMY AND ASTROPHYSICS↗
ATLAS HL-LHC Demonstrators with Data Carousel: Dataon-Demand and Tape Smart Writing
The High Luminosity upgrade to the LHC (HL-LHC) is expected to deliver scientific data at the multi-exabyte scale. To tackle this unprecedented data storage challenge, the ATLAS experiment initiated the Data Carousel project in 2018. Data Carousel is a tape-driven workflow in which bulk production campaigns with input data resident on tape are executed by staging and promptly processing a sliding window to disk buffer such that only a small fraction of inputs are pinned on disk at any one time. Put in ATLAS production before Run3, Data Carousel continues to be our focus for seeking new opportunities in disk space savings, and enhancing tape usage throughout the ATLAS Distributed Computing (ADC) environment. These efforts are highlighted by two recent ATLAS HL-LHC demonstrator projects: data-on-demand and tape smart writing. In this paper, we will discuss the recent studies and outcomes from these projects. The research was conducted together with site experts at CERN and Tier-1 centers.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
American cities in a time of global environmental change: the case of the Baltimore Social-Environmental Collaborative
The Baltimore Social-Environmental Collaborative (BSEC) Urban Integrated Field Laboratory seeks a new paradigm for urban climate research. Motivated by deep uncertainties in urban climate and the future of urban systems, BSEC works collaboratively across institutions and stakeholder groups to co-generate the science needed to advance energy security and resilience to extreme events across the city of Baltimore, Maryland, USA, and to do so in a manner that can inform similar efforts in other cities. BSEC begins with stakeholder priorities (health, affordable energy, etc) and designs observation networks and models to deliver climate science to address them. This takes the form of an iterative collaborative cycle, in which an initial research strategy is repeatedly updated in conversation with community partners, and researchers and stakeholders learn from each other. To date, this cycle has included multiple rounds of collaborative deliberation on urban heat mitigation, in which a multicriteria decision tool has been updated with more community-relevant spatial structure and modified optimization metrics. The guiding objective of this cycle is to inform potential ‘secure and resilient pathways’ for energy and infrastructure. In doing so, BSEC addresses fundamental urban science questions in natural and social sciences. It also tests our ability to integrate this science in a manner that advances participatory decision-making for urban resilience.
climate↗
Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource
Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.
Biochemistry & Molecular Biology↗
The seventh blind test of crystal structure prediction: structure generation methods
A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.
Chemistry↗
The seventh blind test of crystal structure prediction: structure ranking methods
A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.
Chemistry↗
What Is the Best Use of Biomass? A Harmonized LCA-TEA Framework Quantifying Economic and Environmental Metrics for Bioenergy Pathways
Bioresource utilization is expected to play a pivotal role in complementing existing energy pathways and enhancing energy resilience. This study develops a harmonized life cycle assessment (LCA) and techno-economic analysis (TEA) framework to evaluate the greenhouse gas (GHG) reduction potential, minimum fuel selling price (MFSP), and marginal abatement cost (MAC) of bioenergy pathways. We analyze 19 pathways, including liquid biofuels (via catalytic fast pyrolysis, Fischer–Tropsch synthesis, and gasification), bioelectricity, and biomass-to-hydrogen, with and without carbon capture and storage (CCS). The GHG impacts are assessed using the GREET 2022 model, while U.S. Billion-Ton 2016 biomass availability projections are used to estimate scale-up potential. Additionally, we evaluate the influence of a low-carbon electricity grid on pathway performance. Our results show that CCS implementation reduces carbon intensities (CI) to net-negative values for several pathways, with MAC ranging from $\$$32 to $\$$600 per metric ton (MT) CO2e avoided. Bioelectricity pathways with CCS achieve the lowest MAC ($\$$32–$\$$68/tCO2e), while liquid biofuels and hydrogen pathways remain critical for hard-to-abate sectors like aviation and heavy industry. Pathways with net-positive electricity demand benefit from a low-carbon grid, whereas those co-producing electricity experience increased MAC under lower electricity grid CI scenarios. This open-source framework provides a robust tool for harmonized evaluation of bioenergy pathways, enabling policymakers and stakeholders to identify cost-effective strategies for biomass utilization and carbon abatement at scale. The findings underscore the importance of CCS, co-product credits, and feedstock availability in optimizing bioenergy deployment for a low-carbon economy.
09 BIOMASS FUELS↗
Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans
Abstract Background Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism. Results 13 CO 2 breath tests with germ-free C57BL/6 mice gavaged with 13 C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance ofAgathobacter rectalisandBilophila wadsworthiain cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice.Escherichia coliandEnterocloster clostridioformiswere identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although someE. clostridioformisgenomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derivedE. clostridioformisstrain. Conclusions Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.
Microbiology↗