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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents

The lack of genomic data on pathogens from wildlife severely limits our ability to track transmission patterns and trace the origins of an outbreak. There are currently millions of wildlife samples in biobanks around the world, including blood samples. Blood has traditionally been viewed as a sterile environment in healthy individuals, but recent evidence suggests that this is not the case, especially for wild animals. Our goal was to determine whether frozen plasma samples can be surveyed using 16S sequencing to provide information about potential hosts for pathogens for a more complete understanding of disease systems. We sequenced blood plasma from wild North American deer mice ( Peromyscus maniculatus ) and American kestrels ( Falco sparverius ) that were cryogenically stored for 7 and 13 years, respectively, and compared two DNA extraction kits. The kestrel samples contained a very high number of reads that could not be identified to phylum compared to the mouse samples. The two kits differed in the phyla and genera that were detected, and the Zymo kit, which is optimized for plasma and serum, produced more high-quality reads for both kestrel and mouse samples. We identified several pathogenic genera, including Mycoplasma, Escherichia-Shigella , and Bartonella . Sequencing blood samples for pathogens could potentially have broad applications for identifying important reservoir hosts for pathogen transmission and provide a reduced set of species on which to follow up.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. Here, a similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk

Production of trimethylamine- N -oxide (TMAO), a biomarker of CVD risk, is dependent on intestinal microbiota, but little is known of dietary conditions promoting changes in gut microbial communities. Resistant starches (RS) alter the human microbiota. We sought to determine whether diets varying in RS and carbohydrate (CHO) content affect plasma TMAO levels. We also assessed postprandial glucose and insulin responses and plasma lipid changes to diets high and low in RS. In a cross-over trial, fifty-two men and women consumed a 2-week baseline diet (41 percentage of energy (%E) CHO, 40 % fat, 19 % protein), followed by 2-week high- and low-RS diets separated by 2-week washouts. RS diets were assigned at random within the context of higher (51–53 %E) v . lower CHO (39–40 %E) intake. Measurements were obtained in the fasting state and, for glucose and insulin, during a meal test matching the composition of the assigned diet. With lower CHO intake, plasma TMAO, carnitine, betaine and γ -butyrobetaine concentrations were higher after the high- v . low-RS diet ( P <0·01 each). These metabolites were not differentially affected by high v . low RS when CHO intake was high. Although the high-RS meal reduced postprandial insulin and glucose responses when CHO intake was low ( P <0·01 each), RS did not affect fasting lipids, lipoproteins, glucose or insulin irrespective of dietary CHO content. In conclusion, a lower-CHO diet high in RS was associated with higher plasma TMAO levels. These findings, together with the absence of change in fasting lipids, suggest that short-term high-RS diets do not improve markers of cardiometabolic health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome

Increasing evidence has shown that microorganisms present in the mammalian gut have a major impact on the metabolism of xenobiotics – chemicals foreign to the body including drugs and environmental contaminants – either by modulating host metabolism or by transforming xenobiotics or their metabolites directly. Being able to predict these interactions will be critical to develop precision medicine strategies utilizing the gut microbiota. However, current knowledge of which microbes are responsible for a given activity is severely limited and is further complicated by the sheer diversity of gut microbes between individuals. Current approaches including metagenomic and metatranscriptomic analyses can only identify enzymes and organisms that have the potential to catalyze a specific reaction, but cannot determine if an enzyme is truly active within the gut. To identify the microorganisms that are directly responsible for an activity in the gut of an individual, new functional approaches are needed. Here, we present an activity-based probe (ABP) approach to define the microbial populations responsible for a specific xenobiotic metabolizing activity. We developed an ABP for β-glucuronidases, enzymes capable of reversing a major pathway in phase II metabolism that is responsible for xenobiotic elimination. Using this ABP, we covalently labelled active β-glucuronidases both in vitro and in bacterial cells in the mouse gut microbiota. Cells possessing β-glucuronidase activity were then fluorescently labeled, isolated using fluorescence-activated cell sorting (FACS), and identified by sequencing. We found that glucuronidase active bacteria in the murine gut are taxonomically diverse, and even within phyla the taxa displaying function are highly disparate. Perturbation of the gut microbiota with vancomycin decreased but did not eliminate β-glucuronidase activity, which corresponded to a shift in the β-glucuronidase active population. These data demonstrate that the metabolic activity of the gut microbiota can be plastic and that during perturbation, functional capacity may be maintained by phylogenetically disparate populations. This work highlights the utility of ABPs to identify currently unknown functional microbial subpopulations responsible for a specific activity of interest within the gut of an individual.

Whidbey, Christopher↗
DOE OSTI2016

Strategies to improve reference databases for soil microbiomes

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 928 genomes of soil-associated organisms (888 bacteria, 34 archaea, and 6 fungi). Using this database as a representation of the current state of knowledge of soil microbes that are well-characterized, we evaluated its composition and compared it to broader microbial databases, specifically NCBI’s RefSeq, as well as 3,035 publicly available soil amplicon datasets. These comparisons identified phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. For example, RefSoil was observed to have increased representation of Firmicutes despite its low abundance in soil environments and also lacked representation of Acidobacteria and Verrucomicrobia, which are abundant in soils. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to recover 14 genomes from the "most wanted" list, which improved RefSoil's representation of EMP sequences by 7% by abundance. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗