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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

Amylases in the Human Vagina

ABSTRACT Dominance of Lactobacillus species in vaginal communities is a hallmark of healthy conditions in the female genital tract. Key nutrients for lactobacilli include sugars produced when glycogen is degraded by α-amylase in the vagina. While α-amylase activity has been demonstrated in vaginal fluids, it is unclear whether α-amylases are produced solely by the host, bacteria in the vagina, or both. We screened cervicovaginal mucus from 23 reproductive-age women, characterized the species composition of vaginal communities, measured vaginal pH, and determined levels of amylase activity, glycogen, and lactic acid. Based on differences in these measured variables, one sample from each of four individual donors was selected for metagenomic and proteomic analyses. Of eight putative bacterial amylases identified in the assembled bacterial metagenomes, we detected four in vaginal fluids. These amylases were produced by various bacteria in different vaginal communities. Moreover, no two communities were the same in terms of which bacteria were producing amylases. Although we detected bacterial amylases in vaginal fluids, there was no clear association between the bacterial species that was dominant in a community and the level of amylase activity. This association was likely masked by the presence of human α-amylase, which was also detected in vaginal fluids. Finally, the levels of amylase activity and glycogen were only weakly associated. Our findings show, for the first time, that multiple amylases from both bacterial and human origins can be present simultaneously in the vagina. This work also suggests that the link between glycogen, amylase, and Lactobacillus in the vagina is complex. IMPORTANCE In this study, we show that multiple bacteria in the vaginal community produce amylases that hydrolyze glycogen into simpler sugars (i.e., maltose and maltotriose). These sugars serve as “common goods” that sustain bacterial populations in vaginal communities. Given the temporal changes that are observed in the human vaginal microbiome, we expect the kinds of bacterial amylases produced will also vary over time. These differences influence the pool of resources that are broadly shared and shape the species composition of the vaginal bacterial community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host–microbiome metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Abstract Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Abstract The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Terabase Metagenome Sequencing of Grassland Soil Microbiomes

ABSTRACT To enable an in-depth survey of the metabolic potential of complex soil microbiomes, we performed ultra-deep metagenome sequencing, collecting >1 Tb of sequence data from three grassland soils representing different precipitation regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Impacts of The Wetland Sedge Carex aquatilis on Microbial Community and Methane Metabolisms

Microbial activity in the soil of wetlands is responsible for the emission of more methane to the atmosphere than all other natural sources combined. This microbial activity is heavily impacted by plant roots, which influence the microbial community by exuding organic compounds and by leaking oxygen into an otherwise anoxic environment. This study compared the microbial communities of planted and unplanted wetland soil from an Alaskan bog to elucidate how plant growth influences populations and metabolisms of methanogens and methanotrophs. A common boreal wetland sedge, Carex aquatilis, was grown in the laboratory and DNA samples were sequenced from the rhizosphere, unplanted bulk soil, and a simulated rhizosphere with oxygen input but no organic carbon. The abundance of both methanogens and methanotrophs were positively correlated with methane emissions. Among the methanotrophs, both aerobic and anaerobic methane oxidizing microbes were more common in the rhizosphere of mature plants than in unplanted soil, while facultative methanotrophs capable of utilizing either methane or other molecules became relatively less common. Furthermore, these trends indicate that the roots in this experiment created an environment which favored highly specialized microbial metabolisms over generalist approaches. One aspect of this specialized microbiome is the presence of both aerobic and anaerobic metabolisms, which indicates that oxygen is present but is a limiting resource controlling competition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A symbiotic bacterium of Antarctic fish reveals environmental adaptability mechanisms and biosynthetic potential towards antibacterial and cytotoxic activities

Antarctic microbes are important agents for evolutionary adaptation and natural resource of bioactive compounds, harboring the particular metabolic pathways to biosynthesize natural products. However, not much is known on symbiotic microbiomes of fish in the Antarctic zone. In the present study, the culture method and whole-genome sequencing were performed. Natural product analyses were carried out to determine the biosynthetic potential. We report the isolation and identification of a symbiotic bacterium Serratia myotis L7-1, that is highly adaptive and resides within Antarctic fish, Trematomus bernacchii . As revealed by genomic analyses, Antarctic strain S. myotis L7-1 possesses carbohydrate-active enzymes (CAZymes), biosynthetic gene clusters (BGCs), stress response genes, antibiotic resistant genes (ARGs), and a complete type IV secretion system which could facilitate competition and colonization in the extreme Antarctic environment. The identification of microbiome gene clusters indicates the biosynthetic potential of bioactive compounds. Based on bioactivity-guided fractionation, serranticin was purified and identified as the bioactive compound, showing significant antibacterial and antitumor activity. The serranticin gene cluster was identified and located on the chrome. Furthermore, the multidrug resistance and strong bacterial antagonism contribute competitive advantages in ecological niches. Our results highlight the existence of a symbiotic bacterium in Antarctic fish largely represented by bioactive natural products and the adaptability to survive in the fish living in Antarctic oceans.

Xiao, Yu↗
DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome

The human gut microbiome, which develops and stabilizes during the early stages of infant life, plays an essential role in host health through the production of metabolic resources and the stimulation and training of the immune system. To study colonization and community functional dynamics of the microbiota based on responses to host immune processes during the normal and dysbiotic establishment of the gut, metaproteomics was conducted on 91 fecal samples collected over the first 90 days of life from 17 hospitalized premature infants. Microbial responses to antibiotic administration and host-imposed metal bactericidal control correlated with community assembly and resiliency of microbes in the developing preterm gut. Specifically, proteins related to antibiotic resistance and metal homeostasis mechanisms were predominant in persisting members in the infant gut environment over the first several weeks of life. Overall, this metaproteomics study provides a unique approach to examine the temporal expansion and resilience of microbial colonization, as it allows simultaneous examination of both host and microbial metabolic activities. Understanding the interplay between host and microbes may elucidate the microbiome’s potential immunomodulatory roles relevant to necrotizing enterocolitis and other dysbiotic conditions in preterm infants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Climate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients

Less carbon-intensive energy sources are needed to reduce greenhouse gas emissions and their predicted role in climate change. There is growing interest in the potential of biofuels for meeting this need. A critical question is whether large-scale biofuel production can be sustainable over the time scales needed to mitigate our carbon debt from fossil fuel consumption. The carbon balance and ultimately the sustainability of biofuel feedstock production is the result of complex climate-coupled interactions between carbon fixation, sequestration, and release through combustion. Similarly, the long-term productivity of biofuels depends on the environmental factors limiting plant growth. These factors are often related to soil resources which involve complex interactions at the plant-microbe-soil interface impacting their availability and cycling. Our collaborative project addressed sustainable switchgrass (Panicum virgatum) production by exploring Plant Systems, Plant-Microbiome Interactions, and Ecosystem Processes through the integrating lens of Multi-Scale Modeling. Our research was based on detailed characterization of genetically diverse switchgrass genotypes planted in common gardens across a continental latitudinal gradient. The underlying theme of our Plant Systems research was the use of locally adapted plant material to explore plant function, to understand the mechanistic basis of environmental interactions, and to discover the plant genes important for adaptation and sustainability in the face of climate change. Our Plant-Microbiome Interaction project characterized the microbial communities associated with switchgrass using genomic tools. Our Ecosystem Processes research focused on carbon cycle responses at the ecosystem level using stand level plantings. Finally, our Multi-Scale Modeling helped to define conditions of a sustainable biofuel system and identify key tradeoffs between genetic diversity, productivity, and ecosystem services. Genome-wide association analyses were used to identify alleles that contribute to successful establishment and biomass production across North America. Together, our work provided a baseline analyses of the potential of switchgrass as a biofuel feedstock. Our project resulted in a number of successful outcomes. First, we were successful in collecting switchgrass germplasm across the species range, propagating the material, and establishing common garden experiments across the species range. In collaboration with DOE JGI, we successfully assembled the first tetraploid switchgrass genome and published this resource with an analyses of the genetic basis local adaptation from our gardens (Lowry et al. 2019, Lovell et al. 2021). The gardens were used to characterize the genetic architecture for a number of important plant phenotypes. Our project also conducted extensive sampling and sequencing to characterize the bacterial and fungal associates of switchgrass roots and leaves. We showed that host genotype, location, and harvesting practices can play a role in microbiome assembly (Singer et al. 2019 & 2022, Van Wallendael et al. 2020 & 2022, Edwards et al. 2023). Our ecosystem processes work created baseline dataset of carbon and nutrient cycling in realistic stand plantings of switchgrass. Data from this experiment provided new insight into the role of plant traits, phenology, and local environments in ecosystem processes like soil respiration, net-ecosystem exchange, and dynamics of soil and plant nutrients (Ricketts et al. 2023). Finally, our crop modelling experiments help to characterize the sensitivity of common modeling frameworks to parameters, identify key limiters of productivity across large geographic scales, and leverage patterns of local adaptation in prediction. Ultimately, these studies help to identify critical plant-microbe-soil traits that may be manipulated, through breeding or agronomic management, to improve the sustainability of biofuel feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports large-scale data generation efforts across its two divisions: Biological Systems Science and Earth and Environmental Systems Sciences. These efforts include user facilities in atmospheric radiation measurements, genomics, metabolomics, proteomics, compute, and imaging. In addition, BER supports the development of plant-based fuels; research in biosystems design, environmental microbiomes, and atmospheric systems; energy flux monitoring; climate-based ecosystem experiments; pathogen biopreparedness; and modeling of climate, urban interfaces, and interactions between people and energy resources. For data access, BER supports community data services at its user facilities, along with specialized data initiatives for Earth and environmental science, climate modeling, genomic and microbial analysis, and multisector dynamics modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

GROWdb US River Systems - Samples

GROW Overview We developed the Genome Resolved Open Watersheds database (GROWdb), which aims to increase genomic sampling and understanding of global river microbiomes. An emphasis of GROWdb is to create a publicly available and ever-expanding microbial genome database that is focused on rivers while being interoperable with databases from other ecosystems. GROWdb is based on a network-of-networks approach to move beyond a small collection of well-studied rivers, towards a spatially distributed, global network of systematic observations. GROWdb represents the first microbial, river-focused resource parsed at various scales from genes to MAGs to community level including expression and potential based measurements that will be of interest to microbiologists, ecologists, geochemists, hydrologists, and modelers. Dataset Acknowledgement GROWdb contains data from various research campaigns, please acknowledge the following data generators, as appropriate: WHONDRS derived genomes or samples - include this statement in your acknowledgements: “This study used data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) under the River Corridor Science Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL) that was generated at the U.S. Department of Energy (DOE) Joint Genome Institute User Facility. PNNL is operated by Battelle Memorial Institute for the U.S. DOE under Contract No. DE-AC05-76RL01830. The SFA is supported by the U.S. DOE, Office of Biological and Environmental Research (BER), Environmental System Science (ESS) Program.” Total Samples loaded onto this Narrative: 178 Note: Not all GROW samples may be loaded into KBase Data Availability The data underlying GROWdb are accessible across various platforms to ensure all levels of data structure are widely available. First, all reads and MAGs are publicly hosted on National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. Second, all data related data presented here including MAG annotations, extended data tables, phylogenetic tree files, antibiotic resistance gene database files, and MAG abundance tables are available in Zenodo (link). Beyond the flat database files listed above, our aim for GROWdb was to maximize data use by making the data available in searchable and interactive platforms including the National Microbiome Data Collaborative (NMDC) data portal, the Department of Energy’s Systems Biology Knowledgebase (KBase), and a GROW specific user interface released here, GROWdb Explorer. Each platform provides different ways to interact with GROWdb: NMDC GROWdb formed a pilot project for the NMDC. Specifically, individual GROWdb datasets (metagenomes, metatranscriptomes, etc) are easily accessible and searchable through the NMDC data portal, where they are systematically connected to each other and to a rich suite of sample information and standard analysis results, following Findable, Accessible, Interoperable, and Reusable (FAIR) data practices. KBase GROWdb is publicly available within KBase, including samples (this Narrative), MAGs, and corresponding genome scale metabolic models. Access within KBase allows for immediate access and reuse of data, including comparison to private data using KBase’s 500+ analysis tools. Other linked narratives in KBase: GROW Metagenome Assembled Genomes (MAGs) GROW Metabolic Models GROWdb Explorer GROWdb data is also explorable through a graphical user interface built through the Colorado State University Geospatial Centroid (https://geocentroid.shinyapps.io/GROWdatabase/), allowing users to search and graph microbial and spatial data simultaneously. In summary, this microbial genome resource represents the first publicly available genome collection from rivers and offers data that can be leveraged across microbiome studies. GROWdb is an expanding repository to incorporate and unify global river multi-omic data for the future.

59 BASIC BIOLOGICAL SCIENCES↗