Draft genome sequence of MCPA-degrading <i>Sphingomonas </i>sp. strain ERG5, isolated from a groundwater aquifer in Denmark

Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function in bioaugmented sand filters. Genes associated with MCPA degradation are situated on a putative conjugative plasmid

Eco-Forecasting for Domestic Electricity Use

Over the past decade we have seen an increased awareness about domestic energy consumption and a growing focus on eco-feedback displays. In this paper we explore the concept of providing forecasts in such displays as a supplement to information about past usage. Our prototype, eForecast, extends the display of past electricity usage with forecasts about expected usage, electricity price, availability of wind power, and expected demand drops and peaks. Building on previous eco-feedback display research, our approach specifically enables people to use electricity at more opportune times – when it is cheap, green, or when there is an abundance of capacity. We evaluated eForecast in real world use in three domestic households for 22 weeks, where we explored potentials and limitations of forecasting for shifting electricity consumption. In this way, families were able to act in a more sustainable way – without necessarily reducing the amount of electricity consumed. Author Keywords Sustainability; forecasting; energy consumption; domesti

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults:a systematic review of randomized controlled trials

BACKGROUND: The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the potential evidence for an effect of probiotic supplementation on the composition of human fecal microbiota as assessed by high-throughput molecular approaches in randomized controlled trials (RCTs) of healthy adults. METHODS: The survey of peer-reviewed papers was performed on 17 August 2015 by a literature search through PubMed, SCOPUS, and ISI Web of Science. Additional papers were identified by checking references of relevant papers. Search terms included healthy adult, probiotic, bifidobacterium, lactobacillus, gut microbiota, fecal microbiota, intestinal microbiota, intervention, and (clinical) trial. RCTs of solely probiotic supplementation and placebo in healthy adults that examined alteration in composition of overall fecal microbiota structure assessed by shotgun metagenomic sequencing, 16S ribosomal RNA sequencing, or phylogenetic microarray methods were included. Independent collection and quality assessment of studies were performed by two authors using predefined criteria including methodological quality assessment of reports of the clinical trials based on revised tools from PRISMA/Cochrane and by the Jadad score. RESULTS: Seven RCTs investigating the effect of probiotic supplementation on fecal microbiota in healthy adults were identified and included in the present systematic review. The quality of the studies was assessed as medium to high. Still, no effects were observed on the fecal microbiota composition in terms of α-diversity, richness, or evenness in any of the included studies when compared to placebo. Only one study found that probiotic supplementation significantly modified the overall structure of the fecal bacterial community in terms of β-diversity when compared to placebo. CONCLUSIONS: This systematic review of the pertinent literature demonstrates a lack of evidence for an impact of probiotics on fecal microbiota composition in healthy adults. Future studies would benefit from pre-specifying the primary outcome and transparently reporting the results including effect sizes, confidence intervals, and P values as well as providing a clear distinction of between-group and within-group comparisons

Growth Factors Do Not Improve Muscle Function in Young or Adult mdx Mice

Hepatocyte growth factor; Leukemia inhibitory factor; Muscular regenerationFactor de crecimiento de los hepatocitos; Factor inhibidor de la leucemia; Regeneración muscularFactor de creixement dels hepatòcits; Factor inhibidor de la leucèmia; Regeneració muscularMuscular dystrophies constitute a broad group of genetic disorders leading to muscle wasting. We have previously demonstrated that treating a muscular atrophy mouse model with growth factors resulted in increased muscle mass. In the present study, we treated the Duchenne mouse model mdx for 12 weeks with myogenic growth factors peri- and post-onset of muscular degeneration to explore the effects in the oxidative muscle soleus and the glycolytic muscle extensor digitorum longus (EDL). We found no overall beneficial effect in the peri-onset group at the conclusion of the study. In the post-onset group, the functional improvement by means of electrophysiological examinations ex vivo was mostly confined to the soleus. EDL benefitted from the treatment on a molecular level but did not improve functionally. Histopathology revealed signs of inflammation at the end of treatment. In conclusion, the growth factor cocktail failed to improve the mdx on a functional level.This work was supported by grants from the Lundbeck Foundation (Grant No. R140-2013-13370 to J.V. and T.O.K.), Novo Nordisk Foundation (Grant No. 8091 to J.V. and T.O.K.), AP Møller Foundations (Grant No. 13-222 to T.O.K.), Instituto de Salud Carlos III y Fondos FEDER (FIS Project PI19/01313 to T.P.), and Augustinus Foundation (Grant No. 13-4153 to T.O.K.). None of the funding sources had any involvement in the study, data evaluation, or authoring of the manuscript

The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages

Abstract This study describes the first molecular characterization of a bacteriophage infecting a member of the environmentally important Sphingomonadaceae family. Both bacteriophage Lacusarx and its host Sphingobium sp. IP1 were isolated from activated sludge from a wastewater treatment plant. Genome sequencing revealed that the phage genes display little similarity to other known phages, despite a remarkable conservation of the synteny in which the functional genes occur among distantly related phages. Phylogenetic analyses confirmed that Lacusarx represents a hitherto undescribed genus of phages. A classical lysis cassette could not be identified in Lacusarx, suggesting that the genes encoding endolysin, holin, and spanin are host-specific and not found in phages infecting other bacteria. The virus harbors 24 tRNA genes corresponding to 18 different amino acids and furthermore has a significantly different codon usage than its host. Proteomic analysis of Lacusarx revealed the protein components of the phage particle. A lysogeny test indicated that Lacusarx is not a temperate phage

The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi. Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available

Impact of a vegan diet on the human salivary microbiota

Abstract Little is known about the effect of long-term diet patterns on the composition and functional potential of the human salivary microbiota. In the present study, we sought to contribute to the ongoing elucidation of dietary effects on the oral microbial community by examining the diversity, composition and functional potential of the salivary microbiota in 160 healthy vegans and omnivores using 16S rRNA gene amplicon sequencing. We further sought to identify bacterial taxa in saliva associated with host inflammatory markers. We show that compositional differences in the salivary microbiota of vegans and omnivores is present at all taxonomic levels below phylum level and includes upper respiratory tract commensals (e.g. Neisseria subflava, Haemophilus parainfluenzae, and Rothia mucilaginosa) and species associated with periodontal disease (e.g. Campylobacter rectus and Porphyromonas endodontalis). Dietary intake of medium chain fatty acids, piscine mono- and polyunsaturated fatty acids, and dietary fibre was associated with bacterial diversity, community structure, as well as relative abundance of several species-level operational taxonomic units. Analysis of imputed genomic potential revealed several metabolic pathways differentially abundant in vegans and omnivores indicating possible effects of macro- and micro-nutrient intake. We also show that certain oral bacteria are associated with the systemic inflammatory state of the host