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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Gut microbiome changes with micronutrient supplementation in children with attention–deficit/hyperactivity disorder: the MADDY study

Micronutrients have demonstrated promise in managing inattention and emotional dysregulation in children with attention-deficit/hyperactivity disorder (ADHD). The biological mechanism by which micronutrients improve these symptoms remains unclear. One plausible pathway is through the gut-brain axis, the bi-directional communication network that links the gastrointestinal tract with the brain. This study examines changes in gut microbiome composition and diversity after micronutrients supplementation in children with ADHD (N=44) and sheds light on potential mechanisms responsible for the response to micronutrients as measured by clinician-rated global impression. Participants from this investigation represent a sub-group of the Micronutrients for ADHD in Youth (MADDY) study, a double blind randomized controlled study in which participants received either micronutrients or a placebo for 8 weeks, followed by an 8-week open label extension with micronutrients for all participants. Stool samples collected at baseline, week 8, and week 16 were analyzed using 16S rRNA amplicon sequencing targeting the V4 hypervariable region. Pairwise compositional analyses served as the primary means for investigating changes in gut microbiome composition between micronutrients versus placebo groups and responders versus non-responders. A significant change in microbial evenness, as measured by alpha diversity, was observed following micronutrients, and the phylum Actinobacteriota decreased in the micronutrients group compared to placebo. Additionally, two bacterial families: Rikenellaceae and Oscillospiraceae, exhibited a significant increase in change of gut microbiome composition following micronutrients between responders and non-responders. These findings suggest that micronutrients modulated the composition of the gut microbiome and point towards specific bacterial changes associated with response to micronutrients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus

The microbiome associated with ornamental plants has largely been neglected, despite its potential for impacting plant health. This work characterized the composition, diversity, and microbial co-associations in the soil microbiome associated with species and cultivars of plant in the genus Buxus (common name boxwood), a group of woody perennial shrubs commonly used in residential landscapes and found in native ecosystems. Soil was collected from 82 individual curated boxwood accessions at the U.S. National Arboretum National Boxwood Collection. Amplicon libraries targeting archaea, bacteria, and fungi were generated and sequenced using the Illumina MiSeq platform. Identification of individual sequence variants resulted in 275 archaeal, 15,580 bacterial, and 7,525 fungal taxa. Neither spatial distance among samples nor association with different types of boxwood were significant predictors of soil microbiome composition. However, archaeal and bacterial diversity was significantly different in soil from distinct types of boxwood. Co-association networks indicated that archaea and bacteria show greater evidence of being keystone taxa than fungi. Overall, this work demonstrates the potential for targeting specific keystone taxa to shift the soil microbiome associated with these boxwood accessions and that planting different species or cultivars in the landscape may shift the diversity of prokaryotic microorganisms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Characterization of phthalate-degrading bacteria from Asian carp microbiomes and riverine sediments

Phthalates are ubiquitous in the environment due to widespread production and distribution. The carcinogenic compounds dimethyl phthalate (DMP), diethyl phthalate (DEP), and dibutyl phthalate (DBP) are non-covalently bonded to plastics; thus prone to dispersal in various environments. Phthalates not only sorb to riverine sediments, but are also taken up by a variety of aquatic organisms. Asian carp species silver (Hypophthalmichthys molitrix) and bighead (Hypophthaltnichthys nobilis) are exposed to phthalates by ingestion and absorption.,The biodegradation of phthalates has been extensively investigated; however, no studies have isolated phthalate degrading bacteria from aquatic species. The purpose of this study was to characterize the growth and biodegradation kinetics of phthalate-degrading bacteria isolated from the gut, gill, and scale microbiomes of Asian carp, and riverine sediments. 16S rRNA sequencing identified similar genera in sediment and H. molitrix gut microbiome inoculated phthalate enrichments. Achromobacter aegrifaciens strain SKTGEO1 and Pseudomonas japonica strain SKEO1 were enriched from sediments; Bacillus subtilis strain SK18, Pseudomonas putida strain SKTG1, and Consortium SK-1 were enriched from Asian carp microbiomes. Each bacteria isolated was shown to eliminate phthalates from experimental systems. This is the first study documenting the biodegradation of phthalates by bacteria isolated from Asian carp gut and H. molitrix scale microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways

The lung has a diverse microbiome that is modest in biomass. This microbiome differs in asthmatic patients compared with control subjects, but the effects of clinical characteristics on the microbial community composition and structure are not clear. OBJECTIVES: We examined whether the composition and structure of the lower airway microbiome correlated with clinical characteristics of chronic persistent asthma, including airflow obstruction, use of corticosteroid medications, and presence of airway eosinophilia. METHODS: DNA was extracted from endobronchial brushings and bronchoalveolar lavage fluid collected from 39 asthmatic patients and 19 control subjects, along with negative control samples. 16S rRNA V4 amplicon sequencing was used to compare the relative abundance of bacterial genera with clinical characteristics. RESULTS: Differential feature selection analysis revealed significant differences in microbial diversity between brush and lavage samples from asthmatic patients and control subjects. Lactobacillus, Pseudomonas, and Rickettsia species were significantly enriched in samples from asthmatic patients, whereas Prevotella, Streptococcus, and Veillonella species were enriched in brush samples from control subjects. Generalized linear models on brush samples demonstrated oral corticosteroid use as an important factor affecting the relative abundance of the taxa that were significantly enriched in asthmatic patients. In addition, bacterial α-diversity in brush samples from asthmatic patients was correlated with FEV1 and the proportion of lavage eosinophils. CONCLUSION: The diversity and composition of the bronchial airway microbiome of asthmatic patients is distinct from that of nonasthmatic control subjects and influenced by worsening airflow obstruction and corticosteroid use. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

16S ribosomal RNA↗
DOE OSTI2021

Predicting measures of soil health using the microbiome and supervised machine learning

Soil health encompasses a range of biological, chemical, and physical soil properties that sustain the commercial and ecological value of agroecosystems. Monitoring soil health requires a comprehensive set of diagnostics that can be cost-prohibitive for routine analyses. The soil microbiome provides a rich source of information about soil properties, which can be assayed in a high-throughput, cost-effective way. We evaluated the accuracy of random forest (RF) and support vector machine (SVM) regression and classification models in predicting 12 measures of soil health, tillage status, and soil texture from 16S rRNA gene amplicon data with an operationally relevant sample set. We validated the efficacy of the best performing models against independent datasets and also tested best practices for processing microbiome data for use in machine learning. Soil health metrics could be predicted from microbiome data with the best models achieving a Kappa value of ~0.65, for categorical assessments, and a R2 value of ~0.8, for numerical scores. Biological health ratings were better predicted than chemical or physical ratings. Validation with independent datasets revealed that models had general predictive value for soil properties, including yield. The ecological profiles of several taxa important for model accuracy matched the observed relationships with soil health, including Pyrinomonadaceae, Nitrososphaeraceae, and Candidatus Udeaobacter. Models trained at the highest taxonomic resolution proved most accurate, with losses in accuracy resulting from rarefying, sparsity filtering, and aggregating at higher taxonomic ranks. Furthermore, our study provides the groundwork for developing scalable technology to use microbiome-based diagnostics for the assessment of soil health.

16S rRNA gene↗
DOE OSTI2016

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Qiita: rapid, web-enabled microbiome meta-analysis

Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.

microbiome, bioinformatics software, open source s↗
DOE OSTI2018

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Laboratory colonization by Dirofilaria immitis alters the microbiome of female Aedes aegypti mosquitoes

Background: The ability of blood-feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered with, or enhanced by, the arthropod’s native microbiome. Mosquitoes transmit viruses, protozoan and filarial nematodes, the majority of which contribute to the 17% of infectious disease cases worldwide. Diroflaria immitis, a mosquito-transmitted filarial nematodes of dogs and cats, is vectored by several mosquito species including Aedes aegypti. Methods: In this study, we investigated the impact of D. immitis colonization on the microbiome of laboratory reared female Ae. aegypti. Metagenomic analysis of the V3–V4 variable region of the microbial 16S RNA gene was used for identification of the microbial differences down to species level. Results: We generated a total of 1068 OTUs representing 16 phyla, 181 genera and 271 bacterial species. Overall, in order of abundance, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the most represented phylum with D. immitis-infected mosquitoes having more of Proteobacteria (71%) than uninfected mosquitoes (56.9%). An interesting finding in this study is the detection of Klebsiella oxytoca in relatively similar abundance in infected and uninfected mosquitoes, suggesting a possible endosymbiotic relationship, and has been previously shown to indirectly compete for nutrients with fungi on domestic housefly eggs and larvae. While D. immitis colonization has no effect on the overall species richness, we identified significant differences in the composition of selected bacterial genera and phyla between the two groups. We also reported distinct compositional and phylogenetic differences in the individual bacterial species when commonly identified bacteria were compared. Conclusions: To the best of our knowledge, this is the first study to understand the impact of a filarial infection on the microbiome of its mosquito vector. Further studies are required to identify bacteria species that could play an important role in the mosquito biology. While the microbiome composition of Ae. aegypti mosquito have been previously reported, our study shows that in an effort to establish itself, a filarial nematode modifies and alters the overall microbial diversity within its mosquito host.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Abstract Background Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor. Results We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO 2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor. Conclusions The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Investigation of Spaceflight Induced Changes to Astronaut Microbiomes

The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts’ time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts’ saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts’ time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut’s microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor’s microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus , Populus with Pinus , and Pinus with Pinus . Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus -associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl 2 ) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia , (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Altogether, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs

The gut microbiome plays an important role in the health of dogs. Both beneficial microbes and overall diversity can be modulated by diet. Fermentable sources of fiber in particular often increase the abundance of beneficial microbes. Banded crickets ( Gryllodes sigillatus ) contain the fermentable polysaccharides chitin and chitosan. In addition, crickets are an environmentally sustainable protein source. Considering crickets as a potential source of both novel protein and novel fiber for dogs, four diets ranging from 0% to 24% cricket content were fed to determine their effects on healthy dogs’ ( n = 32) gut microbiomes. Fecal samples were collected serially at 0, 14, and 29 days, and processed using high-throughput sequencing of 16S rRNA gene PCR amplicons. Microbiomes were generally very similar across all diets at both the phylum and genus level, and alpha and beta diversities did not differ between the various diets at 29 days. A total of 12 ASVs (amplicon sequence variants) from nine genera significantly changed in abundance following the addition of cricket, often in a dose-response fashion with increasing amounts of cricket. A net increase was observed in Catenibacterium , Lachnospiraceae [ Ruminococcus ], and Faecalitalea , whereas Bacteroides , Faecalibacterium , Lachnospiracaeae NK4A136 group and others decreased in abundance. Similar changes in Catenibacterium and Bacteroides have been associated with gut health benefits in other studies. However, the total magnitude of all changes was small and only a few specific taxa changed in abundance. Overall, we found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. These results support crickets as a potential healthy, novel food ingredient for dogs.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2025

The Microbiome of A Tomato Crop Grown Under Different Lighting Regimes on the International Space Station

The VEG-05 experiment presented here investigated the effect of red-rich and blue-rich light recipes in Veggie on the microbiome of the Veggie facility and the plant tissues of a dwarf tomato variety, Solanum lycopersicum cv. Red Robin. For food safety, the plants were screened using culture-based methods for potential human pathogens that may cause infection by consumption of the fruit. The microbiome was investigated using bacterial 16S and fungal ITS sequencing methods to enumerate and identify bacterial and fungal communities on tomato fruit, roots, leaves, rooting substrate, and Veggie facility surfaces grown under blue-rich or red-rich lighting. Comparisons of microbial communities were made between lighting treatments, as well as for flight and ground controls. This analysis determined the core microbiome and microbiological composition for tomato plants grown under a blue-rich or red-rich lighting treatment and microgravity conditions. Culture-based pathogen screening, corroborated by 16S and ITS sequencing, yielded negative results. Bacterial and fungal counts were lower for ground controls than in-flight samples. However, there were no differences in microbial counts between lighting treatments. Regardless of lighting treatment, plant components shared a core microbiome, although some differences were observed in genera between lighting treatments.

Veggie↗
DOE OSTI2017

Microbiomes Have the Power to Help or Hinder Your Health

They are everywhere: countless microorganisms that inhabit our world—even in your skin, mouth, gut and other parts of your body. Called microbiomes, these communities play a fundamental role in our ecosystem and our bodies, influencing everything from climate to human health. And scientists at PNNL are studying microbiomes to better understand how they influence our daily lives. Scientist Janet Jansson studies complex microbiomes in soil and the human intestine to understand changes in the composition or function of microbes. In the soil, these microbes are associated with carbon cycling and degrading pollutants, as well as plant health. In the intestine, they are responsible for digestion of our food and protection from pathogens. When they go awry, they can be associated with numerous inflammatory bowel diseases, such as Crohn’s. Understanding the factors underlying these microbiome changes will ultimately help researchers develop solutions to problems encountered within our world and our bodies.

54 ENVIRONMENTAL SCIENCES↗