SEARCH · Search NASA

Results for “Microbiome optimization”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

43 records · Page 3

All sources NASA NTRS DOE OSTI

DOE OSTI2021

An evolutionary algorithm for designing microbial communities via environmental modification

Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents

The lack of genomic data on pathogens from wildlife severely limits our ability to track transmission patterns and trace the origins of an outbreak. There are currently millions of wildlife samples in biobanks around the world, including blood samples. Blood has traditionally been viewed as a sterile environment in healthy individuals, but recent evidence suggests that this is not the case, especially for wild animals. Our goal was to determine whether frozen plasma samples can be surveyed using 16S sequencing to provide information about potential hosts for pathogens for a more complete understanding of disease systems. We sequenced blood plasma from wild North American deer mice ( Peromyscus maniculatus ) and American kestrels ( Falco sparverius ) that were cryogenically stored for 7 and 13 years, respectively, and compared two DNA extraction kits. The kestrel samples contained a very high number of reads that could not be identified to phylum compared to the mouse samples. The two kits differed in the phyla and genera that were detected, and the Zymo kit, which is optimized for plasma and serum, produced more high-quality reads for both kestrel and mouse samples. We identified several pathogenic genera, including Mycoplasma, Escherichia-Shigella , and Bartonella . Sequencing blood samples for pathogens could potentially have broad applications for identifying important reservoir hosts for pathogen transmission and provide a reduced set of species on which to follow up.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models

Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing (i) the KL divergence between prior and posterior and (ii) the Stein’s loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Biomanufacturing and Scale-Up: Pathways to Biochemicals, Biofuels, and Biomaterials

Advancing the bioeconomy requires the development of large-scale microbial bioprocesses capable of converting waste carbon streams into biofuels, biochemicals, and biomaterials at industrially relevant scales. While biomanufacturing has been successfully demonstrated at the laboratory scale for a wide range of chemicals, only a few have reached industrial-scale production. This is partly due to the inherent complexity of microbial systems, which rely on living cells with intricate metabolic pathways that are highly sensitive to environmental changes, making large-scale production difficult to optimize and predict. As a result, scaling-up bioprocesses remains a high-stakes challenge that requires deeper exploration. This involves integrating feedstock and microbial selection, upstream and downstream processes, and computational modelling, among other research efforts. Bulk and specialty chemicals derived from biological processes also face competition from fossil-based production routes, which have been refined through decades of technological advancements. While biologically derived molecules may offer more environmentally friendly production pathways than traditional chemical manufacturing, their widespread adoption depends on achieving cost parity-or superiority-relative to fossil-based methods. This emphasizes the importance of holistic research, including techno-economic analyses and life cycle assessments, to ensure both economic viability and environmental sustainability. This editorial and special issue explores state-of-the-art strategies for converting waste carbon sources into valuable products. It discusses how enzymes, single microbes (e.g., extremophiles), and microbiomes (e.g., through division of labor) can be integrated with upstream and downstream process innovations-such as consolidated bioprocessing and in situ product recovery-to improve the efficiency and scalability of biomanufacturing. The editorial further highlights the role of computational modelling in understanding, predicting, and controlling bioprocess performance across scales, and concludes by emphasizing the importance of techno-economic modelling to identify technologies that can move to market.

09 BIOMASS FUELS↗

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 OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗