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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.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Organic Microbial Electrochemical Transistor Monitoring Extracellular Electron Transfer

Abstract Extracellular electron transfer (EET) denotes the process of microbial respiration with electron transfer to extracellular acceptors and has been exploited in a range of microbial electrochemical systems (MESs). To further understand EET and to optimize the performance of MESs, a better understanding of the dynamics at the microscale is needed. However, the real‐time monitoring of EET at high spatiotemporal resolution would require sophisticated signal amplification. To amplify local EET signals, a miniaturized bioelectronic device, the so‐called organic microbial electrochemical transistor (OMECT), is developed, which includes Shewanella oneidensis MR‐1 integrated onto organic electrochemical transistors comprising poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) combined with poly(vinyl alcohol) (PVA). Bacteria are attached to the gate of the transistor by a chronoamperometric method and the successful attachment is confirmed by fluorescence microscopy. Monitoring EET with the OMECT configuration is achieved due to the inherent amplification of the transistor, revealing fast time‐responses to lactate. The limits of detection when using microfabricated gates as charge collectors are also investigated. The work is a first step toward understanding and monitoring EET in highly confined spaces via microfabricated organic electronic devices, and it can be of importance to study exoelectrogens in microenvironments, such as those of the human microbiome.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2020

Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus

Although the COVID-19 pandemic is caused by a single virus, the rest of the human microbiome appears to be involved in the disease and could influence vaccine responses while offering opportunities for microbiome-directed therapeutics. The newly formed Microbiome Centers Consortium (MCC) surveyed its membership and identified four ways to leverage the strengths and experience of microbiome centers in the response to the COVID-19 pandemic. To meet these needs, the MCC will provide a platform to coordinate clinical and environmental research, assist with practical obstacles, and help communicate the connections between the microbiome and COVID-19. We ask that microbiome researchers join us in these efforts to address the ongoing pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche

Abstract Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.

Microbiology↗
DOE OSTI2021

Radiation Therapy–Induced Changes of the Nasopharyngeal Commensal Microbiome in Nasopharyngeal Carcinoma Patients

The human commensal microbiome has been suggested to be involved in the regulation of response to anticancer therapies. However, little is known regarding changes in commensal microbes in patients with cancer during radiation therapy. We conducted a prospective, longitudinal proof-of-concept cohort study with patients with newly diagnosed nasopharyngeal carcinoma (NPC) who underwent radiation therapy-based treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Single-Cell Genomics and the Oral Microbiome

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. We conclude studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024

Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12–13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Characterization and Spatial Mapping of the Human Gut Metasecretome

Bacterially secreted proteins are necessary for the proper functioning of bacterial cells and communities. Secreted proteins provide bacterial cells with the ability to harvest resources from the exterior, import these resources into the cell, and signal to other bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes

Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research

Metabolites from the microbiome influence human, animal, and environmental health, but the diversity and functional roles of these compounds have only begun to be elucidated. Comprehensively characterizing these molecules are significant challenges, as it requires expertise in analytical methods, such as mass spectrometry and nuclear magnetic resonance spectroscopy, skills that not many traditional microbiologists or microbial ecologists possess. This creates a gap between microbiome scientists that want to understand the role of microbial metabolites in microbiome systems and the skills required to generate and interpret complex metabolomics data sets. To bridge this gap, microbiome scientists should engage analytical chemists to best understand the underlying chemical principles of the data. Conversely, analytical scientists are encouraged to engage with microbiome scientists to better understand the biological questions being asked with metabolomics and to best communicate its intricacies. Better communication across the chemistry/biology disciplines will further reveal the “dark matter” within microbiomes that maintain healthy humans and environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria

Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, in this work, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.

42 ENGINEERING↗
DOE OSTI2020

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.

Naylor, Dan T.↗
DOE OSTI2025

Effect of in utero and lactational exposure to antiretroviral therapy on the gut microbial composition and metabolic function in aged rat offspring

Despite the highly effective impact of antiretroviral therapy (ART) in reducing mother-to-child transmission of human immunodeficiency virus (HIV), there are concerns of long-term impacts of ART on the health of the offspring. The implications of perinatal exposure to antiviral drugs on the gut bacterial population and metabolic function in the offspring is unclear but may influence health outcomes given the various reported effects of the microbiome in human health. This study aims to gain insight into the potential effect ofin uteroand lactational exposure to ART on gut microbiota populations and short‐chain fatty acids (SCFAs) production in aged rat offspring. Pregnant rats were administered a combination of antiretroviral drugs (abacavir/dolutegravir/lamivudine) at two different dose levels during gestation and throughout lactation, and the fecal bacterial abundance and SCFA levels of the offspring were analyzed when they reached 12 months of age. Our results showed dose-dependent and sex-based differences in fecal microbial abundance at various taxonomic levels. Specifically, we found a decline inFirmicutesin males, and an increase inActinobacteriaamong males and females. Furthermore, a sex-specific distribution reorganization ofLactobacillus,Bifidobacterium, andAkkermansiawas identified. No significant difference in the concentration of prominent SCFAs and IgA levels were identified. These findings provide preliminary information indicating the need to evaluate perinatal effects of ART more comprehensively on the gut bacterial and metabolic function in future studies, and their potential role in offspring health outcomes.

Research & Experimental Medicine↗
DOE OSTI2025

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↗
DOE OSTI2024

Metalloproteomics Reveals Multi-Level Stress Response in Escherichia coli When Exposed to Arsenite

The arsRBC operon encodes a three-protein arsenic resistance system. ArsR regulates the transcription of the operon, while ArsB and ArsC are involved in exporting trivalent arsenic and reducing pentavalent arsenic, respectively. Previous research into Agrobacterium tumefaciens 5A has demonstrated that ArsR has regulatory control over a wide range of metal-related proteins and metabolic pathways. We hypothesized that ArsR has broad regulatory control in other Gram-negative bacteria and set out to test this. Here, we use differential proteomics to investigate changes caused by the presence of the arsR gene in human microbiome-relevant Escherichia coli during arsenite (AsIII) exposure. We show that ArsR has broad-ranging impacts such as the expression of TCA cycle enzymes during AsIII stress. Additionally, we found that the Isc [Fe-S] cluster and molybdenum cofactor assembly proteins are upregulated regardless of the presence of ArsR under these same conditions. An important finding from this differential proteomics analysis was the identification of response mechanisms that were strain-, ArsR-, and arsenic-specific, providing new clarity to this complex regulon. Given the widespread occurrence of the arsRBC operon, these findings should have broad applicability across microbial genera, including sensitive environments such as the human gastrointestinal tract.

Biochemistry & Molecular Biology↗