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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and thirteen genome sequences were used to re-assess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor . The updated core-genome contains 1,401 ortholog groups (average genome size for thirteen species = 2,516 genes). The pan-genome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multi-domain glycoside hydrolases (GH). These include three cellulases with GH48 domains that are co-located in the Glucan Degradation Locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. str. Rt8.B8 (re-named here Caldicellulosiruptor morganii ), Thermoanaerobacter cellulolyticus str. NA10 (re-named here Caldicellulosiruptor naganoensis NA10), and Caldicellulosiruptor sp. str. Wai35.B1 (re-named here Caldicellulosiruptor danielii ) degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than C. bescii in this regard and differed from the other twelve species examined here, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to Caldicellulosiruptor obsidiansis , but there was also evidence for other thermophilic fermentative anaerobes ( Caldanaerobacter , Fervidobacterium , Caloramator , and Clostridium ). One enrichment, containing 89.7% Caldicellulosiruptor and 9.7% Caloramator , had a capacity for switchgrass solubilization comparable to C. bescii . These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction and are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pan-genomes, based on analysis of thirteen species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the Glucan Degradation Locus (GDL), a set of genes encoding glycoside hydrolases (GH), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation

Genomes reveal nutrient stress patterns Within the surface ocean, nitrogen, iron, and phosphorous can all be limiting nutrients for phytoplankton depending on location. Ustick et al. used the prevalence of Prochlorococcus genes involved in nutrient acquisition to develop maps of inferred nutrient stress across the global ocean (see the Perspective by Coleman). They found broad patterns of limitation consistent with an Earth system model and nutrient addition experiments. Leveraging metagenomic data in this manner is an appealing approach that will help to expand our understanding of the biogeochemistry in the vast open ocean. Science , this issue p. 287 ; see also p. 239

Science & Technology - Other Topics↗
DOE OSTI2015

GenomePeek—an online tool for prokaryotic genome and metagenome analysis

As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 x 10 6 reads revealed >3 x 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 x 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria , predominantly Comamonadaceae . The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3% of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Altogether, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae , pathogenic Pseudomonadaceae , and ‘Vibrionales' ) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products

In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome’s taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436–557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

ABSTRACT In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods. IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs

Highlights: • First time to use metagenomic analyze the effects of different milk feeding patterns on gut microbiome of Amur tiger cubs. • Goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger. • Breastfed Amur tiger cubs and goat milk-fed Amur tiger cubs have distinct microbiotas in their guts. Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. Furthermore, the high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Post Wildfire Soil Bacterial MAGs and Metagenome Analysis

We compare the differences between bacteria in soil affected by a wildfire to an unaffected area from Minnewaska State Park, NY located in the biodiverse northern Shawangunk ridge. We detail our metagenomic sequencing data, relative abundance of bacterial phyla, and the taxonomic classification of three high-quality MAGs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Metagenomic Analysis of Three Samples from the MCU Process

Three Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) Strip Effluent Feed samples were sent from Savannah River National Laboratory (SRNL) to Microbial Insights (MI), Knoxville, TN, for molecular analysis. The objective of the analysis was to profile and identify dominant members of the microbial community in these samples. More effective control of microbial growth in the MCU depends on the fundamental understanding of the microorganisms responsible for system colonization that leads to biofilm formation and coalescer impairment. This analysis entailed Next-generation sequencing (NGS) of DNA, a collective term for advanced technologies that allow the determination of microbial species present. NGS, also commonly called metagenomics, provides for the identification of microorganisms down to the genus level. Although function, e.g. biofilm formation or corrosion, cannot always be predicted from identification, knowledge of the microorganisms present can offer insight into the potential microbial processes that may influence system function occurring in the MCU. Information on microbial identification can also influence control measures, e.g. operational/maintenance parameters or the choice of biocides to employ. This knowledge can help control undesired microbial activity as conventional cleaning and disinfection regimens may also contribute to inefficient biofilm control and dissemination of microbial resistance to remediation efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Shotgun metagenomics analysis indicates Bradyrhizobium spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem

ABSTRACT Ten soil cores were collected from the long-term heavy metal-contaminated Savannah River Site (SRS) and studied using shotgun metagenomics. In-line with our previous reports, Bradyrhizobium spp. dominated the SRS soils, and thus we recommend that SRS bioremediation studies target the Bradyrhizobium genus.

Agashe, Rohan↗
DOE OSTI2018

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Metagenomic Analysis of the Airborne Environment in Urban Spaces

The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Refinement of the “ Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration

Members of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon’s index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

metagenomic↗