DNA extraction and primer choice have a large effect on the observed community structure in all microbial amplicon sequencing analyses. Although the biases are well known, no comprehensive analysis ...has been conducted in activated sludge communities. In this study we systematically explored the impact of a number of parameters on the observed microbial community: bead beating intensity, primer choice, extracellular DNA removal, and various PCR settings. In total, 176 samples were subjected to 16S rRNA amplicon sequencing, and selected samples were investigated through metagenomics and metatranscriptomics. Quantitative fluorescence in situ hybridization was used as a DNA extraction-independent method for qualitative comparison. In general, an effect on the observed community was found on all parameters tested, although bead beating and primer choice had the largest effect. The effect of bead beating intensity correlated with cell-wall strength as seen by a large increase in DNA from Gram-positive bacteria (up to 400%). However, significant differences were present at lower phylogenetic levels within the same phylum, suggesting that additional factors are at play. The best primer set based on in silico analysis was found to underestimate a number of important bacterial groups. For 16S rRNA gene analysis in activated sludge we recommend using the FastDNA SPIN Kit for Soil with four times the normal bead beating and V1-3 primers.
A catalog of the mouse gut metagenome Xiao, Liang; Feng, Qiang; Liang, Suisha ...
Nature biotechnology,
10/2015, Letnik:
33, Številka:
10
Journal Article
Recenzirano
We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse ...strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.
Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in ...healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.
MIRI (the Mid-Infrared Instrument for the James Webb Space Telescope JWST) operates from 5 to 28.5 μm and combines over this range: (1) unprecedented sensitivity levels; (2) subarcsecond angular ...resolution; (3) freedom from atmospheric interference; (4) the inherent stability of observing in space; and (5) a suite of versatile capabilities including imaging, low- and medium-resolution spectroscopy (with an integral field unit), and coronagraphy. We illustrate the potential uses of this unique combination of capabilities with various science examples: (1) imaging exoplanets; (2) transit and eclipse spectroscopy of exoplanets; (3) probing the first stages of star and planet formation, including identifying bioactive molecules; (4) determining star formation rates and mass growth as galaxies are assembled; and (5) characterizing the youngest massive galaxies.
Update on human health effects of boron Nielsen, Forrest H.
Journal of trace elements in medicine and biology,
10/2014, Letnik:
28, Številka:
4
Journal Article
Recenzirano
In vitro, animal, and human experiments have shown that boron is a bioactive element in nutritional amounts that beneficially affects bone growth and central nervous system function, alleviates ...arthritic symptoms, facilitates hormone action and is associated with a reduced risk for some types of cancer. The diverse effects of boron suggest that it influences the formation and/or activity of substances that are involved in numerous biochemical processes. Several findings suggest that this influence is through the formation of boroesters in biomolecules containing cis-hydroxyl groups. These biomolecules include those that contain ribose (e.g., S-adenosylmethionine, diadenosine phosphates, and nicotinamide adenine dinucleotide). In addition, boron may form boroester complexes with phosphoinositides, glycoproteins, and glycolipids that affect cell membrane integrity and function. Both animal and human data indicate that an intake of less than 1.0mg/day inhibits the health benefits of boron. Dietary surveys indicate such an intake is not rare. Thus, increasing boron intake by consuming a diet rich in fruits, vegetables, nuts and pulses should be recognized as a reasonable dietary recommendation to enhance health and well-being.
Animal studies have shown that magnesium deficiency induces an inflammatory response that results in leukocyte and macrophage activation, release of inflammatory cytokines and acute-phase proteins, ...and excessive production of free radicals. Animal and in vitro studies indicate that the primary mechanism through which magnesium deficiency has this effect is through increasing cellular Ca
, which is the signal that results in the priming of cells to give the inflammatory response. Primary pro-inflammatory cytokines such as tumor necrosis factor-α and interleukin (IL)-1; the messenger cytokine IL-6; cytokine responders E-selectin, intracellular adhesion molecule-1 and vascular cell adhesion molecule-1; and acute-phase reactants C-reactive protein and fibrinogen have been determined to associate magnesium deficiency with chronic low-grade inflammation (inflammatory stress). When magnesium dietary intake, supplementation, and/or serum concentration suggest/s the presence of magnesium deficiency, it often is associated with low-grade inflammation and/or with pathological conditions for which inflammatory stress is considered a risk factor. When magnesium intake, supplementation, and/or serum concentration suggest/s an adequate status, magnesium generally has not been found to significantly affect markers of chronic low-grade inflammation or chronic disease. The consistency of these findings can be modified by other nutritional and metabolic factors that affect inflammatory and oxidative stress. In spite of this, findings to date provide convincing evidence that magnesium deficiency is a significant contributor to chronic low-grade inflammation that is a risk factor for a variety of pathological conditions such as cardiovascular disease, hypertension, and diabetes. Because magnesium deficiency commonly occurs in countries where foods rich in magnesium are not consumed in recommended amounts, magnesium should be considered an element of significant nutritional concern for health and well-being in these countries.
Certain pathogens deliver effectors into plant cells to modify host protein targets and thereby suppress immunity. These target modifications can be detected by intracellular immune receptors, or ...Resistance (R) proteins, that trigger strong immune responses including localized host cell death. The accelerated cell death 11 (acd11) "lesion mimic" mutant of Arabidopsis thaliana exhibits autoimmune phenotypes such as constitutive defense responses and cell death without pathogen perception. ACD11 encodes a putative sphingosine transfer protein, but its precise role during these processes is unknown. In a screen for lazarus (laz) mutants that suppress acd11 death we identified two genes, LAZ2 and LAZ5. LAZ2 encodes the histone lysine methyltransferase SDG8, previously shown to epigenetically regulate flowering time via modification of histone 3 (H3). LAZ5 encodes an RPS4-like R-protein, defined by several dominant negative alleles. Microarray and chromatin immunoprecipitation analyses showed that LAZ2/SDG8 is required for LAZ5 expression and H3 lysine 36 trimethylation at LAZ5 chromatin to maintain a transcriptionally active state. We hypothesize that LAZ5 triggers cell death in the absence of ACD11, and that cell death in other lesion mimic mutants may also be caused by inappropriate activation of R genes. Moreover, SDG8 is required for basal and R protein-mediated pathogen resistance in Arabidopsis, revealing the importance of chromatin remodeling as a key process in plant innate immunity.
Crop yields and yield potentials on Danish coarse sandy soils are strongly limited due to restricted root growth and poor water and nutrient retention. We investigated if biochar amendment to subsoil ...can improve root development in barley and significantly increase soil water retention. Spring barley (Hordeum vulgare cv. Anakin) was grown in soil columns (diameter: 30 cm) prepared with 25 cm topsoil, 75 cm biochar‐amended subsoil, and 30 cm un‐amended subsoil lowermost placed on an impervious surface. Low‐temperature gasification straw‐biochar (at 0, 0.50, 1.0, 2.0, and 4.0 wt%) and slow pyrolysis hardwood‐biochar (at 2 wt%) were investigated. One wt% can be scaled up to 10² Mg/ha of char. After full irrigation and drainage, the in‐situ moisture content at 30‐80 cm depth increased linearly (R² = 0.99) with straw‐biochar content at a rate corresponding to 0.029 m³/m³/%. The lab determined wilting point also increased linearly with char content (R² = 0.99) but at a much lower rate (0.003 m³/m³/%). Biochar at concentrations up to 2% significantly increased the density of roots in the 40–80 cm depth interval. Addition of 1% straw‐biochar had the most positive effect on root penetration resulting in the highest average root density (54% coverage compared to 33% without biochar). This treatment also resulted in the greatest spring barley grain yield increase (22%). Improving the quality of sandy subsoils has global potentials, and incorporation of the right amount of correctly treated residues from bioenergy technologies such as straw‐biochar is a promising option.
Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering ...the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas ( https://gutsyatlas.serve.scilifelab.se/ ). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition.
Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the ...choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.
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