SEARCH · Search NASA

Results for “microbial metabolites”

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

SourceResearch connectionFrom yearThrough year

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

At least 127 records · Page 7

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Data from: Switchgrass rhizosphere metabolite chemistry driven by nitrogen availability

Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. Plants were grown with the inoculum Azotobacter vinelandii DJ for three days before harvest. We found switchgrass root exudate chemistry to be driven by N availability. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment. However, we found little evidence of N treatment and inoculation interaction effects which suggests this response is not directly mediated by N availability.

09 BIOMASS FUELS↗

NASA NTRS1971

Continuous propagation of microalgae. III.

Data are presented which give the specific photosynthetic rate and the specific utilization rates of urea and carbon dioxide as functions of specific growth rate for Chlorella. A mathematical model expresses a set of mass balance relations between biotic and environmental materials. Criteria of validity are used to test this model. Predictive procedures are complemented by a particular model of microbial growth. Methods are demonstrated for predicting substrate utilization rates, production rates of extracellular metabolites, growth limiting conditions, and photosynthetic quotients from propagator variables.

Hanson, D. T.↗

DOE OSTI2021

Electrochemical and spectroelectrochemical characterization of bacteria and bacterial systems

Microbes, such as bacteria, can be described, at one level, as small, self-sustaining chemical factories. Based on the species, strain, and even the environment, bacteria can be useful, neutral or pathogenic to human life, so it is increasingly important that we be able to characterize them at the molecular level with chemical specificity and spatial and temporal resolution in order to understand their behavior. Bacterial metabolism involves a large number of internal and external electron transfer processes, so it is logical that electrochemical techniques have been employed to investigate these bacterial metabolites. In this mini-review, we focus on electrochemical and spectroelectrochemical methods that have been developed and used specifically to chemically characterize bacteria and their behavior. First, we discuss the latest mechanistic insights and current understanding of microbial electron transfer, including both direct and mediated electron transfer. Second, we summarize progress on approaches to spatiotemporal characterization of secreted factors, including both metabolites and signaling molecules, which can be used to discern how natural or external factors can alter metabolic states of bacterial cells and change either their individual or collective behavior. Finally, we address in situ methods of single-cell characterization, which can uncover how heterogeneity in cell behavior is reflected in the behavior and properties of collections of bacteria, e.g. bacterial communities. Recent advances in (spectro)electrochemical characterization of bacteria have yielded important new insights both at the ensemble and the single-entity levels, which are furthering our understanding of bacterial behavior. Furthermore, these insights, in turn, promise to benefit applications ranging from biosensors to the use of bacteria in bacteria-based bioenergy generation and storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota

Abstract Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, includingLachnospiraceaeandEnterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.

Environmental Sciences & Ecology↗

DOE OSTI2025

Multi-technique characterization of iron reduction by an Antarctic Shewanella : an analog system for putative Martian biosignature identification

ABSTRACT Microbes from terrestrial extreme environments enable testing of biosignature production in conditions relevant to astrobiological targets. Mars, which was likely more conducive to life during early warmer and wetter epochs, has inspired missions that search for signs of early life in the surficial rock record, including mineral or organic biosignatures. Microbial iron reduction is a common and ancient metabolism that may have also operated on other rocky celestial bodies. To investigate biosignature production during iron reduction, aShewanellasp. (strain BF02_Schw) isolated from a subglacial discharge known as Blood Falls, Antarctica, was incubated with the electron acceptor ferrihydrite (Fh). Biosignatures associated with Fh reduction were identified using a suite of techniques currently utilized or proposed for Mars missions, including X-ray diffraction and infrared, Mössbauer, and Raman spectroscopy. The biotic origin of features was validated by transcriptional changes observed between treatments with and without Fh and comparison to killed controls. In live treatments, Fh was reduced to magnetite and goethite, both detected in Martian lacustrine basins. Several soluble and volatile metabolites were also detected, including riboflavin and dimethyl sulfide (DMS), which could be astrobiological indicators of active microbial processes. While none of the identified biosignatures individually would serve as definitive proof of life (past or present), detecting concomitant features associated with known terrestrial biotic processes would provide compelling rationale for more targeted life detection missions. Terrestrial extremophiles can support the exploration of astrobiologically relevant microbial processes, validation of life detection instrumentation, and potentially the discovery of new biomarkers. IMPORTANCE Culture-based experiments with terrestrial extremophiles can elucidate biosignatures that may be analogous to those produced under extraterrestrial conditions, and thus inform sampling and technology strategies for future missions. Here, we demonstrate the production of several biosignatures under iron-reducing conditions byShewanellasp. BF02_Schw, originally isolated from an Antarctic analog feature. These biosignatures could be detectable using flight-ready instrumentation. Growth experiments with terrestrial extremophiles can identify biosignatures measurable by current methodologies and inform the development and optimization of techniques for detecting extant or extinct life on other worlds.

Biotechnology & Applied Microbiology↗

DOE OSTI2024

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Evolutionary and functional relationships between plant and microbial C 1 metabolism in terrestrial ecosystems

One-carbon (C 1 ) metabolism, centered on the universal methyl donor S-adenosyl methionine (SAM), plays critical roles in biosynthesis, redox regulation, and stress responses across plants and microbes. A recently proposed photosynthetic C 1 pathway links SAM methyl groups directly to RuBisCO-mediated CO 2 assimilation and integrates with nitrogen and sulfur metabolism. Light-dependent SAM synthesis may regulate the methylation of biopolymers and specialized metabolites and help mitigate photorespiratory stress under elevated temperature and drought. Phylogenetic analysis of two core enzymes suggests evolutionary continuity from methylotrophic microbes to land plants, supporting microbial origins via endosymbiotic gene transfer. Beyond intracellular roles, C 1 metabolism drives biosphere–atmosphere exchange via gases such as methane, methanol, formic acid, and formaldehyde, and numerous specialized volatiles synthesized through SAM methylation. S-methylmethionine, a mobile C 1 metabolite, may mediate phloem transport of reduced sulfur, nitrogen, and methyl groups, linking above- and belowground C 1 cycling in plants. Advances in real-time gas sensing now allow the high-frequency quantification of C 1 fluxes from leaves, stems, and soils, highlighting C 1 metabolism as a critical and underrecognized component of terrestrial carbon and nutrient cycling. Given its microbial ancestry and the production of diverse volatile biosignatures, C 1 metabolism may also offer unique insights into life's origins and biosignature detection on exoplanets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Vertical movement of soluble carbon and nutrients from biocrusts to subsurface mineral soils

Dryland ecosystems can be constrained by low soil fertility. Within drylands, the soil nutrient and organic carbon (C) cycling that does occur is often mediated by soil surface communities known as biological soil crusts (biocrusts), which cycle C and nutrients in the top ca. 0–2 cm of soil. However, the degree to which biocrusts are influencing soil fertility and biogeochemical cycling in deeper, subsurface mineral soils is unclear. The movement of dissolved resources from biocrusts to deeper soil layers in leachate may be one of the main mechanisms through which biocrust fertility is transferred downward towards deeper microbial communities and plant roots occurring within mineral soil. Here, in this study, we examined the role of biocrust leachate in contributing to subsurface nutrient and soluble C pools and subsurface microbial cycling. We collected biocrusts from three biocrust successional stages and explored resource pools in situ at multiple soil depths, while collecting leachate and measuring nutrient and organic C concentrations and metabolite composition from each successional stage in the laboratory. After four leachate collections, we conducted an incubation of mineral soil collected from below each biocrust successional stage to measure heterotrophic microbial CO 2 flux and biomass. Overall, our findings observed that the degree of nutrient and C connectivity between biocrusts and the sub-crust mineral soil depended on the biocrust successional stage and the element being considered, and the influence of biocrust successional stage on mineral soil CO 2 flux is likely related to long-term resource build up. Together, our results suggest that the influence of biocrust leachate on subsurface mineral soil is complex and context dependent, but, over longer time periods and at later successional stages, can have measurable effects on dryland soil biogeochemical cycling with feedbacks to resource availability and CO 2 flux.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2018

Transitory Microbial Habitat in the Hyperarid Atacama Desert

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Schulze-Makuch, Dirk↗

DOE OSTI2026

1H-NMR characterization of soil dissolved organic matter from soil samples in control and warming plots in Blodgett Forest, CA (2014 and 2018)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of Lawrence Berkeley National Laboratory Terrestrial Ecosystem Science Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM (soil organic matter) decomposition and stabilization. This package contains metabolite data obtained through 1H nuclear magnetic resonance (NMR) spectroscopy on water-extracted soils. Soil samples were collected in 2014/06/03 and 2018/06/04 from 3 replicated paired plots that had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. The following files are included: (1) nmr_h2o_data_raw.csv: raw data, (2) nmr_h2o_data_processed.csv: computed compound concentrations and metadata, (3) nmr_h2o_compound_metadata.csv: compound metadata, (4) nmr_h2o_sample_metadata.csv: sample metadata

1H-NMR (nucleic magnetic resonance) spectroscopy↗

DOE OSTI2021

The Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by Phaeodactylum tricornutum (Bacillariophyceae)

Here, to examine the impact of heterotrophic bacteria on microalgal physiology, we co-cultured the diatom Phaeodactylum tricornutum with six bacterial strains to quantify bacteria-mediated differences in algal biomass, total intracellular lipids, and for a subset, extracellular metabolite accumulation. A Marinobacter isolate significantly increased algal cell concentrations, dry biomass, and lipid content compared to axenic algal cultures. Two other bacterial strains from the Bacteroidetes order, of the genera Algoriphagus and Muricauda, significantly lowered P. tricornutum biomass, leading to overall decreased lipid accumulation. These three bacterial co-cultures (one mutualistic, two competitive) were analyzed for extracellular metabolites via untargeted liquid chromatography mass spectrometry to compare against bacteria-free cultures. Over 80% of the extracellular metabolites differentially abundant in at least one treatment were in higher concentrations in the axenic cultures, in agreement with the hypothesis that the co-cultured bacteria incorporated algal-derived organic compounds for growth. Furthermore, the extracellular metabolite profiles of the two growth-inhibiting cultures were more similar to one another than the growth-promoting co-culture, linking metabolite patterns to ecological role. Our results show that algal–bacterial interactions can influence the accumulation of intracellular lipids and extracellular metabolites, and suggest that utilization and accumulation of compounds outside the cell play a role in regulating microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

ABSTRACT Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Differential Gene Expression in A Cross-Feeding Two-Species Model Microbial Community Under Simulated Microgravity and Deep-Space Radiation

A long-term goal of space biology is to understand interspecies microbial interactions in space. Presently, little is known about the combined effect of microgravity and ionizing radiation on bacterial community response when species are interdependent through exchange of metabolites in fluid medium (cross-feeding). Microgravity is expected to slow interspecies mass transfer and growth in cross-feeding communities in the low-shear, diffusion-limited environment, while ionizing radiation may influence stress response to direct (DNA damage) and indirect damage (ROS). Using a well-understood, two-species (Escherichia coli and Salmonella enterica) microbial community engineered to be a model for studying cross-feeding, we simulated galactic cosmic rays (GCRsim) and microgravity to test the hypothesis: exposure to ionizing radiation causes cell damage or stress, altering transcriptomic community responses in metabolically interdependent cells, which is exacerbated by microgravity. We expect to see differential gene expression between cross-feeding and non-cross-feeding communities. We measured GCRsim effects on growth and gene expression in well-mixed versus simulated-microgravity conditions and in cross-feeding and non-cross-feeding medium. Microbial cultures were inoculated into liquid medium in rotating wall vessels (RWV) with different rotation rates: 5 RPM (simulated microgravity) and 50 RPM (well-mixed). The E. coli-S. enterica consortium, under simulated microgravity, were exposed to 500 mGy of Simplified 5-ion Galactic Cosmic Ray Simulation for 2 hours at Brookhaven National Lab. We harvested samples 40 minutes after irradiation for extraction and sequencing (NASA GeneLab). Here we present the differential gene expression analysis results, which reveal altered transcriptomic community responses, even where growth rate differences are not observed. Gene expression of these actively metabolizing microbial communities in GCRsim may illuminate molecular mechanisms of microbial interactions in space. Understanding how microbial community gene expression, metabolism, and other cellular processes are influenced by spaceflight stressors can inform the use of microbes in human life support for low Earth orbit missions and beyond.

microgravity↗

NASA NTRSDate not supplied

Evolutionary Stability of Microbial Mutualism in Simulated Microgravity

Sustainable long-term space travel will require astronauts to live in built environments cohabited by microbes. Though much of space biology research has focused on microbial monocultures, microbes naturally live in multispecies communities in which they compete and cooperate. Understanding how communities experience spaceflight over generations can influence sanitation measures and the design of synthetic communities for applications in spaceflight. In this study, we investigated the evolutionary stability of mutualism in multispecies communities in microgravity using a model system of cooperating microbes. Our model consisted of bioengineered strains of mutually dependent E. coli and S. enterica. E. coli metabolized lactose and produced a carbon source for S. enterica, which secreted methionine for E. coli. By introducing a noncooperative ("cheater") strain of S. enterica, we tested the dynamic stability of mutualism. Using a rotating wall vessel, we simulated microgravity, specifically a low-shear, diffusion-limited environment where metabolite transfer is limited compared to 1g conditions. Fluorescent motile and non-motile strains were used to assess how motility affects the microbial experience of microgravity. We hypothesized that mutualism in non-motile cocultures would be favored in microgravity due to the diffusion-limited spatial structure, while motile strains would show less difference between simulated microgravity and other conditions. We cultured communities for approximately 20 generations and assessed community composition over time using flow cytometry. We compared simulated microgravity to cultures grown in agar plates as spatially structured controls, shaken flasks as well-mixed controls, and still flasks representing the convective mixing of 1g. A high, sustained cooperator-to-cheater ratio represented stable mutualism within the community. Our results show that microbial communities may better maintain mutualism in microgravity compared to their counterparts in 1g conditions and that the motility of a community’s constituents influences how the community experiences microgravity on generational timescales.

Nathan Moreno↗

DOE OSTI2021

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes

Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Swimming and the human microbiome at the intersection of sports, clinical, and environmental sciences: A scoping review of the literature

The human microbiota is comprised of more than 10–100 trillion microbial taxa and symbiotic cells. Two major human sites that are host to microbial communities are the gut and the skin. Physical exercise has favorable effects on the structure of human microbiota and metabolite production in sedentary subjects. Recently, the concept of “athletic microbiome” has been introduced. To the best of our knowledge, there exists no review specifically addressing the potential role of microbiomics for swimmers, since each sports discipline requires a specific set of techniques, training protocols, and interactions with the athletic infrastructure/facility. Therefore, to fill in this gap, the present scoping review was undertaken. Four studies were included, three focusing on the gut microbiome, and one addressing the skin microbiome. It was found that several exercise-related variables, such as training volume/intensity, impact the athlete’s microbiome, and specifically the non-core/peripheral microbiome, in terms of its architecture/composition, richness, and diversity. Swimming-related power-/sprint- and endurance-oriented activities, acute bouts and chronic exercise, anaerobic/aerobic energy systems have a differential impact on the athlete’s microbiome. Therefore, their microbiome can be utilized for different purposes, including talent identification, monitoring the effects of training methodologies, and devising ad hoc conditioning protocols, including dietary supplementation. Microbiomics can be exploited also for clinical purposes, assessing the effects of exposure to swimming pools and developing potential pharmacological strategies to counteract the insurgence of skin infections/inflammation, including acne. In conclusion, microbiomics appears to be a promising tool, even though current research is still limited, warranting, as such, further studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

Background: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. Results: A high quality draft genome (7.8Mb) of S. yeochonensis CN732 was obtained with a G+C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. Conclusions: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.

59 BASIC BIOLOGICAL SCIENCES↗