Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MICROBIOME”

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.

At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro

Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep’s blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere

Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States ( n = 0–876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.

Plant Sciences↗
DOE OSTI2024

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data

Abstract Background The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first comprehensive investigations into the predictive potential of machine learning models for understanding the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant performance from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. Results Prediction improves when we add environmental features, such as soil properties and microbial density, along with microbiome data. Different preprocessing strategies show that human decisions significantly impact predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is one of the optimal strategies to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level, or model characteristics. ML performance is limited when humans can’t classify samples accurately. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Conclusions Our study highlights the importance of incorporating diverse environmental features and careful data preprocessing in enhancing the predictive power of machine learning models for soil and biological phenotype connections. This approach can significantly contribute to advancing agricultural practices and soil health management.

Aghdam, Rosa↗
DOE OSTI2023

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗
DOE OSTI2020

A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice

The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host–microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7 m +/+ Lepr db /J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Understanding grapevine-microbiome interactions: implications for viticulture industry

Until recently, the analysis of complex communities such as that of the grapevine-microbe holobiont has been limited by the fact that most microbes are not culturable under laboratory conditions (less than 1%). However, metagenomics, the study of the genetic material recovered directly from environmental samples without the need for enrichment or of culturing, has led to open an unprecedented era in the field of microbiology. Importantly, this technological advance has now become so pervasive that it is being regularly applied to explore soils and plants of agricultural interest. Interestingly, many large companies are taking notice, with significant financial investment being used to exploring ways to manipulate the productivity, disease resistance and stress tolerance for crops by influencing the microbiome. To understand which microbes one needs to manipulate to influence this valuable characteristics, we need to sequence the microbiome and capture the genetic and hence functional metabolic information contained therein. For viticulture and other agricultural fields where the crop is also associated to particular flavor properties that may also be manipulated, understanding how the bacteria, fungi and viruses influence the development and hence chemical makeup of the crop is essential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Organic nutrient chemistry and the marine microbiome

Vast expanses of the ocean are characterized by extraordinarily low concentrations of nutrients but nevertheless support vibrant communities of marine microbes. In aggregate, these communities drive many of the important elemental cycles that sustain life on Earth. Microbial communities are organized to maximize nutrient and energy transfer between cells, and efficiently recycle organic carbon, nitrogen, phosphorus and trace metals. Energy and nutrient transfer occurs across a broad range of spatial scales. Large-sized marine algae and bacteria support epibiont communities that are physically in contact, exchanging nutrients and energy across cell membranes, while other communities that are physically far apart, rely on the horizontal mixing of ocean currents or the vertical pull of gravity to transfer nutrient and energy containing organic matter. Marine organic geochemists are making rapid progress in understanding the chemistry of the marine microbiome. These advances have benefited from parallel developments in analytical chemistry, microbial isolation and culture techniques, and advances in microbial genomics, transcriptomics, and proteomics. The combination of all three approaches has proven to be quite powerful. Here we highlight two aspects of the chemistry of organic phosphorus and trace metal cycling and the marine microbiome. In each study, advances in chemical analyses, microbial culture, and microbial genomics played key roles in understanding how microbial communities interact to facilitate nutrient cycling in the open ocean.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2018

Interagency Strategic Plan for Microbiome Research, FY 2018-2022

This plan was developed by the Microbiome Interagency Working Group (MIWG), an interagency working group under the Life Sciences Subcommittee (LSSC) of the National Science and Technology Council (NSTC) Committee on Science (CoS). The MIWG is a successor to the Fast Track Action Committee on Mapping the Microbiome (FTAC-MM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

COVID-19 biomarkers based on respiratory microbiome content

COVID-19 patient care management would greatly benefit from new tools that enable accurate assessment of disease severity and stage, potentially enabling a personalized medicine approach. Detection of the SARS-CoV-2 virus itself, or even quantitation of viral loads, is not sufficient for accurate assessment of disease state beyond diagnosis of infection [eg, doi:10.1093/cid/ciaa344]. Levels of usual suspect protein biomarkers associated with host response to infection [eg, C-reactive protein (CRP); cytokines like IL-6, TNF-alpha, and IL-10; complement proteins like C3a and C5a], and of individual blood cell types (eg, leukocytes, lymphocytes, and subsets thereof), show limited correlation with disease severity and stage, with high patient-to-patient and study-to-study variability [eg, doi:10.1093/cid/ciaa248]. High-dimensional panels of biomarkers should have greater predictive power and resilience to unavoidable sources of variability; however, their assembly from proteins and cell types is extremely difficult, due to technical limitations in analyte measurement, especially with regard to starting material requirements and detection sensitivity. Host response profiling through Next Generation Sequencing (NGS) of gene expression patterns (ie, RNA-Seq) is a promising approach, but at the time of this project there were only two publicly available datasets of relevance [doi:10.1093/cid/ciaa203, doi:10.1080/22221751.2020.1747363], and close inspection of them revealed that each had at least one major flaw that severely undermined its value in supporting robust analysis of host response to SARS-CoV- 2 infection. However, the first of these studies [doi:10.1093/cid/ciaa203] fortuitously collected NGS data not only from host cells, but also from bacteria present in bronchoalveolar lavage fluid (BALF) recovered from COVID-19 patients; and because the respiratory microbiome (in terms of bacterial species content) is far less complex than the human transcriptome, the NGS data collected were sufficient to provide coverage depth supporting robust analysis. Surprisingly, the authors of the study did not carry out a detailed analysis of these data and their potential for revealing important new information about COVID-19. Therefore, we carried out a meta-analysis of the dataset as a first step in evaluating the potential for profiling of respiratory microbiome dynamics as a means of accurately assessing COVID-19 disease state.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Use of imaging and mass spectrometry-based capabilities to describe microbiome interactions (Q4 Performance Metric Report, 2021)

The LLNL “Microbes Persist” Soil Microbiome Scientific Focus Area (SFA) seeks to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues and formation of soil carbon (C). In much of our research, we use imaging, mass spectrometry, and related methods to study plantmicrobe-mineral interactions, viral and microbial particles from soil, and the signatures plant and microbial necromass contribute as part of soil organic matter (SOM). Our project’s signature techniques include NanoSIMS-enabled approaches (to understand cell-cell and OM-mineral interactions at the single cell and even viral particle scale), radiocarbon (14C) analyses (to determine both the age and turnover time of soil organic matter), and a suite of soil chemical characterization techniques we describe below, and collectively refer to as ‘Multi- dimensional SOM-mineral characterization’ (SEM, TEM, STXM, NEXAFS, NMR, FTICR-MS, LC-MS). In this report, we focus on how imaging, NMR, beamline and mass spectrometry approaches can deepen our understanding of soil microbiomes and their engagement with the soil matrix.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Microbiome Metadata Management

Tremendous amounts of microbiome omics data have been generated in recent years, which holds great potential for large-scale studies and metaanalyses. The utility of these datasets is unfortunately limited by their lack of searchability and interoperability. Thorough, standardized metadata is essential for unlocking the scientific discovery potential of disparate datasets. Several national and international initiatives exist to gather and standardize microbiome omics data to improve accessibility and reusability. Continuing to improve consistency in metadata will allow advances in automation and reduction in manual mapping between databases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes that impact on ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Terrestrial plants benefit from many well-understood mutualistic relationships with root and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗
NASA NTRS2018

Plant Growth Research for Future Food Production - Seed Microbiome Project

Humanity is currently on the precipice of a new era: one where human civilization is no longer bound to the confines of a single planet. Now, organizations like the National Aeronautics and Space Administration (NASA) have extended their areas of research and are beginning to focus not just on getting humans into space, but also to keep them safe, healthy, and sane. This focus falls under the Human Research Program (HRP). A focus of this program is "dedicated to discovering the best methods and technologies to support safe, productive human space travel" [1]. For "safe and productive space travel" to occur, astronauts must have proper nutrition [1]. While sending up large amounts of dried and packaged food with every shuttle might work fairly well in the short term, when only a few people need to be fed, it will not be sustainable, especially as NASA looks toward longer space journeys beyond the Earth's orbit. Research into this area falls under Advanced Life Support (ALS), whose mission is to develop regenerative life support systems to support future NASA long-duration missions [2]. This would involve growing crops in space to supplement astronaut diets [2]. An important, yet often overlooked, part of growing crops in any environment is the microbial organisms that inhabit the plants' microbiomes. The Seed Microbiome Project aims to investigate the microbial presence throughout the life stages of three crops, Mizuna Mustard, 'Outredgeous' Red Romaine Lettuce, and 'Red Robin' Tomato, that have either been or will be grown on the ISS.

Birtell, Eva↗
NASA NTRS2019

Does Seed Sanitization Affect the Plant Rhizosphere Microbiome and Its Ability to Compete with the Human Associated Pathogen, E. coli on Salad Crops?

Cultivation of crops in controlled environmental agricultural systems may limit microbial colonization and reduce diversity of the microbial communities. Practices like seed and growth medium sanitization may further impact microbial communities in the mature plant and the plant’s capacity to limit the growth of pathogens through competition. As humans expand their travels to space, understanding plant growth, health, and development in closed environments will be critical to the success of producing a safe, supplemental food source for astronauts. To determine the persistence of a potential human pathogen in plant growth and development, sanitized and unsanitized seeds from, mizuna (Brassica rapa var japonica) and red romaine lettuce (Lactuca sativa cultivar ‘Outredgeous’), were inoculated with Escherichia coli, ATCC 21445, germinated under simulated International Space Station (ISS) environmental conditions and harvested every 7 days until maturity. The persistence of E. coli in the rhizosphere was determined by plating on selective media, real time PCR (Polymerase Chain Reaction) and community sequencing of the rhizosphere communities. E. coli was detected in the crops’ roots and leaves for several weeks post germination. At day 28, plants from sanitized seeds had significantly higher counts of E. coli on the roots than those from unsanitized seeds. E. coli was also detected on a few uninoculated plants indicating airborne cross contamination among plants in the same growth chamber and suggesting an influence of the natural microbiome on human pathogen survival and persistence in leafy greens. Sequencing analysis revealed variations in composition and diversity between the communities. Understanding the microbial community of the rhizospheric microbiome is only the first step in determining the relationships between plants. Additional studies to include genotypic and phenotypic variations in the plants should be considered to determine if the natural microbes in the rhizosphere may contribute to the health and therefore, safety of the edible plants.

Khodadad, Christina L. M.↗