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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States

The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

Utility of correlation techniques in gravity and magnetic interpretation

Internal correspondence uses Poisson's Theorem in a moving-window linear regression analysis between the anomalous first vertical derivative of gravity and total magnetic field reduced to the pole. The regression parameters provide critical information on source characteristics. The correlation coefficient indicates the strength of the relation between magnetics and gravity. Slope value gives delta j/delta sigma estimates of the anomalous source. The intercept furnishes information on anomaly interference. Cluster analysis consists of the classification of subsets of data into groups of similarity based on correlation of selected characteristics of the anomalies. Model studies are used to illustrate implementation and interpretation procedures of these methods, particularly internal correspondence. Analysis of the results of applying these methods to data from the midcontinent and a transcontinental profile shows they can be useful in identifying crustal provinces, providing information on horizontal and vertical variations of physical properties over province size zones, validating long wavelength anomalies, and isolating geomagnetic field removal problems.

Chandler, V. W.↗
NASA NTRS1992

Self-organization of cosmic radiation pressure instability. II - One-dimensional simulations

The clustering of statistically uniform discrete absorbing particles moving solely under the influence of radiation pressure from uniformly distributed emitters is studied in a simple one-dimensional model. Radiation pressure tends to amplify statistical clustering in the absorbers; the absorbing material is swept into empty bubbles, the biggest bubbles grow bigger almost as they would in a uniform medium, and the smaller ones get crushed and disappear. Numerical simulations of a one-dimensional system are used to support the conjecture that the system is self-organizing. Simple statistics indicate that a wide range of initial conditions produce structure approaching the same self-similar statistical distribution, whose scaling properties follow those of the attractor solution for an isolated bubble. The importance of the process for large-scale structuring of the interstellar medium is briefly discussed.

Hogan, Craig J.↗
DOE OSTI2023

Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates

Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. Here, we isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Shape effects on the local dynamics of suspensions of spheroidal particles

The effect of shape on the dynamics of suspensions of non-spherical heavy particles is examined by fully resolved numerical simulations of oblate and prolate spheroids, as well as spheres, for a density ratio of ten, volume fractions ranging from 0.5% to 5%, and Reynolds numbers between 20 and 30. The dynamics is determined both by the interactions of the particles with the fluid as well as by collisions, with the number and importance of collisions increasing with volume fractions. A single isolated oblate or prolate spheroid falling under gravity generally falls broadside on, for the governing parameters examined here, and at low-volume fractions, the majority of particles in a suspension fall that way. At higher-volume fractions, the orientation is more random. The slip velocity decreases as the volume fraction increases for all shapes, as expected, but the effect of the shape is much less than seen for a single particle. Furthermore, this seems to be due to two effects. For all volume fractions, the most deformed particles cluster more than spheres and less deformed particles, which increases their slip velocity. As the concentration increases, the increased particle interactions also causes more particles to fall short side-on, which reduces the frontal area and the resulting drag, increasing the slip velocity. This second effect is, of course, absent for spherical particles.

42 ENGINEERING↗
DOE OSTI2024

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Reconstructing Emission from Pre-Reionization Sources with Cosmic Infrared Background Fluctuation Measurements by the JWST

We present new methodology to use cosmic infrared background (CIB) fluctuations to probe sources at 10 less than or approx. equal to z less than or approx. equal to 30 from a James Webb Space Telescope (JWST) NIRCam configuration that will isolate known galaxies to 28 AB mag at 0.55 m. At present significant mutually consistent source-subtracted CIB fluctuations have been identified in the Spitzer and AKARI data at 25 m, but we demonstrate internal inconsistencies at shorter wavelengths in the recent CIBER data. We evaluate CIB contributions from remaining galaxies and show that the bulk of the high-z sources will be in the confusion noise of the NIRCam beam, requiring CIB studies. The accurate measurement of the angular spectrum of the fluctuations and probing the dependence of its clustering component on the remaining shot noise power would discriminate between the various currently proposed models for their origin and probe the flux distribution of its sources. We show that the contribution to CIB fluctuations from remaining galaxies is large at visible wavelengths for the current instruments precluding probing the putative Lyman-break of the CIB fluctuations. We demonstrate that with the proposed JWST configuration such measurements will enable probing the Lyman-break. We develop a Lyman-break tomography method to use the NIRCam wavelength coverage to identify or constrain, via the adjacent two-band subtraction, the history of emissions over 10 less than or approx. equal to z less than or approx. equal to 30 as the universe comes out of the Dark Ages. We apply the proposed tomography to the current SpitzerIRAC measurements at 3.6 and 4.5 m, to find that it already leads to interestingly low upper limit on emissions at z greater than or approx. equal to 30.

NIRCam beam↗
DOE OSTI2023

A New Sodium Thioborate Fast Ion Conductor: Na 3 B 5 S 9

Abstract We report a new sodium fast‐ion conductor, Na 3 B 5 S 9 , that exhibits a high Na ion total conductivity of 0.80 mS cm −1 (sintered pellet; cold‐pressed pellet=0.21 mS cm −1 ). The structure consists of corner‐sharing B 10 S 20 supertetrahedral clusters, which create a framework that supports 3D Na ion diffusion channels. The Na ions are well‐distributed in the channels and form a disordered sublattice spanning five Na crystallographic sites. The combination of structural elucidation via single crystal X‐ray diffraction and powder synchrotron X‐ray diffraction at variable temperatures, solid‐state nuclear magnetic resonance spectra and ab initio molecular dynamics simulations reveal high Na‐ion mobility (predicted conductivity: 0.96 mS cm −1 ) and the nature of the 3D diffusion pathways. Notably, the Na ion sublattice orders at low temperatures, resulting in isolated Na polyhedra and thus much lower ionic conductivity. This highlights the importance of a disordered Na ion sublattice—and existence of well‐connected Na ion migration pathways formed via face‐sharing polyhedra—in dictating Na ion diffusion.

Zhou, Laidong↗
DOE OSTI2023

A New Sodium Thioborate Fast Ion Conductor: Na 3 B 5 S 9

Abstract We report a new sodium fast‐ion conductor, Na 3 B 5 S 9 , that exhibits a high Na ion total conductivity of 0.80 mS cm −1 (sintered pellet; cold‐pressed pellet=0.21 mS cm −1 ). The structure consists of corner‐sharing B 10 S 20 supertetrahedral clusters, which create a framework that supports 3D Na ion diffusion channels. The Na ions are well‐distributed in the channels and form a disordered sublattice spanning five Na crystallographic sites. The combination of structural elucidation via single crystal X‐ray diffraction and powder synchrotron X‐ray diffraction at variable temperatures, solid‐state nuclear magnetic resonance spectra and ab initio molecular dynamics simulations reveal high Na‐ion mobility (predicted conductivity: 0.96 mS cm −1 ) and the nature of the 3D diffusion pathways. Notably, the Na ion sublattice orders at low temperatures, resulting in isolated Na polyhedra and thus much lower ionic conductivity. This highlights the importance of a disordered Na ion sublattice—and existence of well‐connected Na ion migration pathways formed via face‐sharing polyhedra—in dictating Na ion diffusion.

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

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15 N 2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.

15 N-tracking metabolomics↗
NASA NTRS2000

A Study of Bubble and Slug Gas-Liquid Flow in a Microgravity Environment

The influence of gravity on the two-phase flow dynamics is obvious.As the gravity level is reduced,there is a new balance between inertial and interfacial forces, altering the behavior of the flow. In bubbly flow,the absence of drift velocity leads to spherical-shaped bubbles with a rectilinear trajectory.Slug flow is a succession of long bubbles and liquid slug carrying a few bubbles. There is no flow reversal in the thin liquid film as the long bubble and liquid slug pass over the film. Although the flow structure seems to be simpler than in normal gravity conditions,the models developed for the prediction of flow behavior in normal gravity and extended to reduced gravity flow are unable to predict the flow behavior correctly.An additional benefit of conducting studies in microgravity flows is that these studies aide the development of understanding for normal gravity flow behavior by removing the effects of buoyancy on the shape of the interface and density driven shear flows between the gas and the liquid phases. The proposal calls to study specifically the following: 1) The dynamics of isolated bubbles in microgravity liquid flows will be analyzed: Both the dynamics of spherical isolated bubbles and their dispersion by turbulence, their interaction with the pipe wall,the behavior of the bubbles in accelerated or decelerated flows,and the dynamics of isolated cylindrical bubbles, their deformation in accelerated/decelerated flows (in converging or diverging channels), and bubble/bubble interaction. Experiments will consist of the use of Particle Image Velocimetry (PIV) and Laser Doppler Velocimeters (LDV) to study single spherical bubble and single and two cylindrical bubble behavior with respect to their influence on the turbulence of the surrounding liquid and on the wall 2) The dynamics of bubbly and slug flow in microgravity will be analyzed especially for the role of the coalescence in the transition from bubbly to slug flow (effect of fluid properties and surfactant), to identify clusters that promote coalescence and transition the void fraction distribution in bubbly and slug flow,to measure the wall friction in bubbly flow. These experiments will consist of multiple bubbles type flows and will utilize hot wire and film anemometers to measure liquid velocity and wall shear stress respectively and double fiber optic probes to measure bubble size and velocity as a function of tube radius and axial location.

McQuillen, J.↗
NASA NTRSDate not supplied

Coordinated analyses of hydrated Kuiper Belt dust

We report on coordinated mineralogical, chemical, and isotopic analyses of hydrated carbon-rich interplanetary dust particles (IDPs). We focus on hydrated IDPs that contain high solar flare track densities consistent with an origin in outer Solar System bodies such as Edgeworth-Kuiper belt objects (EKBOs) [1]. We are searching for evidence of the heavy water reservoir predicted by self-shielding models [2]. The IDPs were embedded in sulfur and microtome thin sections were obtained for Fourier-transform infrared (FTIR), transmission electron microscopy (TEM), and nanoSIMS analyses. The IDPs were only partly microtomed and the remainder was extracted from the sulfur and pressed into In or Au for high precision O isotopic analyses. The hydrated IDPs in this study are compact low-porosity objects with a mineralogy dominated by fine-grained saponite and lesser serpentine, Fe-Ni sulfides, Mg-Fe carbonates, rare crystaline silicates, and abundant organic matter. The C in the IDPs is abundant (typically >4X CI) and occurs as isolated nanoglobules and finely disseminated within the phyllosilicate matrix of the IDPs. TEM analyses of the nanoglobules show O-rich, S-depleted rims with higher carbonyl functionality than their cores. FTIR spectra show strong aliphatic C-H stretches consistent with the presence of short-chain aliphatic hydrocarbons in these IDPs. The oxygen isotopic compositions measured in 6 IDPs all plot within error of the CCAM line [3]. For several of the IDPs we were able to obtain multiple analyses. The ∆^(17)O values range from -23‰ up to +3.4‰ with most analyses clustering above the terrestrial fractionation line. The O isotopic compositions and the high C contents of these IDPs are distinct from known hydrated carbonaceous chondrites. The track-rich hydrated IDPs record parent body aqueous alteration effects through interactions with 16O-poor H2O on a EKBO parent body. The aqueous alteration activity likely resulted from the heat generated by collisional processes among EKBOs given that these objects are believed to have accreted late after the decay of 26Al [4].

Lindsay P. Keller↗
NASA NTRS1990

Trompe L'Oeil 'binary' pulsars

A freely precessing pulsar produces pulse phase residuals which can mimic those of a pulsar in a binary orbit. In particular, discrete sets of phase residuals due to precessional motion of an isolated pulsar are sampled; it is shown that this data is well fit by residuals from a binary pulsar in a sufficiently tight orbit. Analytic and numerical relationships between the projected orbital size, a(p) sin i, and the orbital eccentricity, e, of a misidentified binary pulsar; are found the observations that would distinguish between these models are discussed. Regardless of the mechanism that causes the precession, the maximum amplitude of the phase residual is pi/2: consequently, a(p)sin i is (approximately) bounded by cP(puls)/4. The newly discovered 'binary' millisecond pulsars in the globular cluster 47 Tuc is discussed, and it is shown that the periodic frequency modulation reported cannot be explained by free precession.

Nelson, Robert W.↗
NASA NTRS1995

Artificial neural network application for space station power system fault diagnosis

This study presents a methodology for fault diagnosis using a Two-Stage Artificial Neural Network Clustering Algorithm. Previously, SPICE models of a 5-bus DC power distribution system with assumed constant output power during contingencies from the DDCU were used to evaluate the ANN's fault diagnosis capabilities. This on-going study uses EMTP models of the components (distribution lines, SPDU, TPDU, loads) and power sources (DDCU) of Space Station Alpha's electrical Power Distribution System as a basis for the ANN fault diagnostic tool. The results from the two studies are contrasted. In the event of a major fault, ground controllers need the ability to identify the type of fault, isolate the fault to the orbital replaceable unit level and provide the necessary information for the power management expert system to optimally determine a degraded-mode load schedule. To accomplish these goals, the electrical power distribution system's architecture can be subdivided into three major classes: DC-DC converter to loads, DC Switching Unit (DCSU) to Main bus Switching Unit (MBSU), and Power Sources to DCSU. Each class which has its own electrical characteristics and operations, requires a unique fault analysis philosophy. This study identifies these philosophies as Riddles 1, 2 and 3 respectively. The results of the on-going study addresses Riddle-1. It is concluded in this study that the combination of the EMTP models of the DDCU, distribution cables and electrical loads yields a more accurate model of the behavior and in addition yielded more accurate fault diagnosis using ANN versus the results obtained with the SPICE models.

Momoh, James A.↗
NASA NTRS2013

Intragroup and Galaxy-linked Diffuse X-ray Emission In Hickson Compact Groups

Isolated compact groups (CGs) of galaxies present a range of dynamical states, group velocity dispersions, and galaxy morphologies with which to study galaxy evolution, particularly the properties of gas both within the galaxies and in the intragroup medium. As part of a large, multiwavelength examination of CGs, we present an archival study of diffuse X-ray emission in a subset of nine Hickson compact groups (HCGs) observed with the Chandra X-Ray Observatory. We find that seven of the groups in our sample exhibit detectable diffuse emission. However, unlike large-scale emission in galaxy clusters, the diffuse features in the majority of the detected groups are linked to the individual galaxies, in the form of both plumes and halos likely as a result of vigourous star formation or activity in the galaxy nucleus, as well as in emission from tidal features. Unlike previous studies from earlier X-ray missions, HCGs 31, 42, 59, and 92 are found to be consistent with the L(sub X-Tau) relationship from clusters within the errors, while HCGs 16 and 31 are consistent with the cluster L(sub X-sigma) relation, though this is likely coincidental given that the hot gas in these two systems is largely due to star formation. We find that L(sub X) increases with decreasing group Hi to dynamical-mass ratio with tentative evidence for a dependence in X-ray luminosity on Hi morphology whereby systems with intragroup Hi indicative of strong interactions are considerably more X-ray luminous than passively evolving groups. We also find a gap in the L(sub X) of groups as a function of the total group specific star formation rate. Our findings suggest that the hot gas in these groups is not in hydrostatic equilibrium and these systems are not low-mass analogs of rich groups or clusters, with the possible exception of HCG 62.

Desjardins, Tyler D.↗
DOE OSTI2022

Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces—Recommendations for Two New Genera and One Species

National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was identified as a member of Dothideomycetes incertae sedis and is closely related to the family Kirschsteiniotheliaceae according to a phylogenetic analysis. The polyphasic taxonomic approach supported the recommendation for establishing two novel genera and one novel species. The names Aaosphaeria pasadenensis (FJI-L9-BK-P1 = NRRL 64424 = DSM 114621), Pasadenomyces melaninifex (FJII-L3-CM-DR1 = NRRL 64433 = DSM 114623), and Floridaphiala radiotolerans (FKI-L1-BK-DR1 = NRRL 64434 = DSM 114624) are proposed as type species. Furthermore, resistance to ultraviolet-C and presence of specific biosynthetic gene cluster(s) coding for metabolically active compounds are unique to these strains.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group

Bacillus anthracis, the causative agent of the human disease anthrax, Bacillus cereus, a food-borne pathogen capable of causing human illness, and Bacillus thuringiensis, a well-characterized insecticidal toxin producer, all cluster together within a very tight clade (B. cereus group) phylogenetically and are indistinguishable from one another via 16S rDNA sequence analysis. As new pathogens are continually emerging, it is imperative to devise a system capable of rapidly and accurately differentiating closely related, yet phenotypically distinct species. Although the gyrB gene has proven useful in discriminating closely related species, its sequence analysis has not yet been validated by DNA:DNA hybridization, the taxonomically accepted "gold standard". We phylogenetically characterized the gyrB sequences of various species and serotypes encompassed in the "B. cereus group," including lab strains and environmental isolates. Results were compared to those obtained from analyses of phenotypic characteristics, 16S rDNA sequence, DNA:DNA hybridization, and virulence factors. The gyrB gene proved more highly differential than 16S, while, at the same time, as analytical as costly and laborious DNA:DNA hybridization techniques in differentiating species within the B. cereus group.

Phylogeny↗
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further 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. Methods To identify 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. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗