Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens.
Little data exists on physiological outcomes associated with bacterial changes that occur after fructan feeding in healthy adults. To this end, we studied potential relationships between changes in gut bacteria composition and host physiological parameters after feeding 3 × 5 g/d of β2‐1 fructan (BF) or maltodextrin to a group of 13 male and 17 female healthy adults in a placebo‐controlled, double‐blinded, randomised crossover‐study consisting of two 28‐d exposures separated by a 14‐d washout. Fasting blood and 1‐d faecal collections were obtained on d0 and d28 of each phase. Well‐being and general health, as well as gastrointestinal symptoms, were determined by questionnaire. Serum lipopolysaccharides (LPS), faecal SCFA, faecal bifidobacteria and indigestion were higher during the BF‐supplemented phase. Numbers of circulating lymphocytes and macrophages were unchanged but BF supplementation decreased serum IL‐10 and increased serum IL‐4. In addition, circulating percentages of CD282 + /TLR2 + myeloid dendritic cells increased as did ex vivo responses to a TLR2 agonist. Culture‐based analysis of feces showed that 87 bacterial species encompassing 30 genera and four phyla were able to use BF as the sole carbon source. Fecal 16S rRNA analysis (26 subjects) showed BF reduced community richness. Two response patterns were observed: in 17/26 subjects, the relative abundance of Bacteroides was reduced and phylotypes within the Bifidobacterium , Faecalibacterium and the family Lachnospiraceae increased during the BF phase. In the remaining subjects, phylotypes aligning within the genera Bacteroides, Prevotella and to a lesser extent Bifidobacterium increased in abundance while abundance of phylotypes within the Faecalibacterium and the family Lachnospiraceae decreased during the BF phase. Few relationships between the faecal community composition and measured parameters were noted: (a) increases in Bacteroidetes relative abundance correlated with increased faecal propionate; (b) subjects in whom Bacteroidetes increased during the BF phase excreted more caproic acid (during both phases); and (c) subjects in whom Bacteroidetes decreased during the BF phase had higher LPS and LPS binding protein (during both phases). The most likely explanation for the observed patterns of faecal community change associated with the BF phase is a distal gut fermentation driven by differences in peptidyl nitrogen. We found no links between bacterial community changes and physiological changes nor was there evidence of physiological changes that would indicate a health benefit in these healthy subjects. Support or Funding Information This trial was undertaken with financial support from Agriculture and Agri‐Food Canada (RPBI# 1501, MK, GDI, LJY), Health Canada (SB), General Mills (MK), Alberta Innovates Bio Solutions (GDI), the Advanced Food and Materials Network (MK), and the National Science and Engineering Research Council (JMJG).
Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of biotechnological importance. Here, we report a 5.7-Mbp draft genome sequence of B. megaterium ATCC 14581, which is the type strain of the species.
Additional file 3: Table S3. Average nucleotide identity (ANI) values between Citrobacter strains falsely identified as Salmonella and reference genomes.
Furan is a naturally forming compound found in heat-processed foods such as coffee, canned meats, and jarred baby food. It is concurrently found with analogues including 2-methylfuran (2-MF) and 3-methylfuran (3-MF), and toxicity studies demonstrate all are potent liver toxins. Toxicity studies found 3-MF is more toxic than either furan, or 2-MF. The present analysis assesses the transcriptional response in liver samples taken from male Fischer (F344) rats exposed to furan or 3-MF from 0 to 2.0 and 0-1.0 mg/kg bw/day, respectively, for 90 days. Transcriptional analyses found decreased liver function and fatty acid metabolism are common responses to both furan and 3-MF exposure. Furan liver injury promotes a ductular reaction through Hippo and TGFB signalling, which combined with increased immune response results in ameliorating perturbed bile acid homeostasis in treated rats. Failure to activate these pathways in 3-MF exposed rats and decreased p53 activity leads to cholestasis, and increased toxicity. Finally, BMD analysis indicate many of the most sensitive pathways affected by furan and 3-MF exposure relate to metabolism - malate dehydrogenase and glucose metabolism with BMDLs of 0.03 and 0.01 mg/kg bw/day for furan and 3-MF exposure, respectively, which agrees with BMDLs previously reported for apical and microarray data.
Vitamin D status was assessed in 19-79 year old whites (8351 participants of European ancestry) and non-whites (1840 participants encompassing all other ancestries) from cycles 1 to 3 (years 2007-2013) of the Canadian Health Measures Survey. Status was assessed using the U.S. Institute of Medicine (IOM) 25-hydroxyvitamin D [25(OH)D] cut point values of 30 and 40 nmol/L. Overall, median 25(OH)D concentrations were significantly higher in whites [58.9 (28.6, 100.1) nmol/L; 5th and 95th percentile] compared with non-whites [43.5 (19.0, 83.2); P < 0.001]. Values were higher in females [58.5 (27.5, 101.3) nmol/L] when compared with males [53.5 (24.2, 92.7) nmol/L] and increased with age. Non-whites were more likely to have 25(OH)D values below IOM established cut points for optimum bone health with 20.1 (16.0, 24.2) and 42.2% (36.8, 47.7) of non-whites having serum 25(OH)D concentrations <30 and <40 nmol/L, respectively. The corresponding values for whites were 5.9 (4.6, 7.2) and 16.1% (14.0, 18.3). Values were lower during the first quarter when compared with the third quarter. Supplement intake was an important factor in determining 25(OH)D levels, but it did not alone account for the difference in status. Equivalent increases in 25(OH)D levels were observed in whites and non-whites during the summer months, suggesting there was no functional difference in sun exposure response. It is apparent that a complex interaction of factors affect 25(OH)D values in free-living Canadians.
