Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform with shotgun metagenomic sequencing data

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Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis

Background: Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winterulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. Results: The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has an inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. Conclusions: From expression profiling of the transcriptomes, it is evident that the presence of A. wodanis is altering the global gene expression of M. viscosa. Co-cultivation studies showed that A. wodanis is impeding the growth of M. viscosa, and that the inhibitorial effect is not contact-dependen

Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida

Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84% identity to E. coli Spot 42. We generated a A. salmonicida spf deletion mutant. We then used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose, we found a surprisingly large number of ≥ 2X differentially expressed genes, and several major cellular processes were affected. A gene encoding a pirin-like protein showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, we discovered an sRNA named VSsrna24, which is encoded immediately downstream of spf. This new sRNA has an expression pattern opposite to that of Spot 42, and its expression is repressed by glucose. We hypothesize that Spot 42 plays a key role in the central metabolism, in part by regulating the pyruvat dehydrogenase enzyme complex via pirin

Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome

Irritable bowel syndrome (IBS) is a common disorder of the lower gastrointestinal tract. The pathophysiology is far from settled, but a gut microbial dysbiosis is hypothesized to be a contributing factor. We earlier published a randomized double-blind placebo-controlled clinical trial on fecal microbiota transplantation (FMT) for IBS – the REFIT trial. The present data set describes the engraftment and includes participants from the study who received active FMT; 14 participants with effect of FMT (Effect) and 8 without (No effect). Samples were collected at baseline, after 6 and 12 months. Samples from the transplants (Donor) served as a comparator. In total 66 recipient samples and 17 donor samples were subjected to deep metagenomic sequencing, and taxonomic and functional analyses were performed. Alpha diversity measures showed a significantly increased diversity and evenness in the IBS groups compared to the donors. Taxonomic profiles showed higher relative abundance of phylum Firmicutes, and lower relative abundance of phylum Bacteroidetes, compared to donors at baseline. This profile was shifted toward the donor profile following FMT. Imputed growth rates showed that the resulting growth pattern was a conglomerate of donor and recipient activity. Thirty-four functional subclasses showed distinct differences between baseline samples and donors, most of which were shifted toward a donor-like profile after FMT. All of these changes were less pronounced in the No effect group. We conclude that FMT induces long-term changes in gut microbiota, and these changes mirror the clinical effect of the treatment. The study was registered in ClinicalTrials.gov (NCT02154867)

Comunicazione italiana nel mondo: interviste a distanza. Prove d'Europa a Radio Colonia

L’Europa è di casa a Radio Colonia, l’emittente italiana del WDR, Westdeutscher Rundfunk, l’ente radiotelevisivo pubblico del Land Nord Reno-Westfalia, che il primo dicembre scorso ha celebrato il mezzo secolo di vita. Il suo direttore, Tommaso Pedicini, ricorda i motivi che portarono alla nascita della Radio, nel 1961, in un periodo in cui esplodeva il fenomeno dell’emigrazione italiana in Germania ed i Gastarbeiter (“lavoratori ospiti”) italiani avevano bisogno di una voce amica. Da allora molti sono stati i cambiamenti, ma Radio Colonia è rimasta la finestra italiana nel panorama radiofonico tedesco, impegnata in particolare, dopo l’avvio nel 1999 della Funkhaus Europa, a coltivare i temi del plurilinguismo e dell’integrazione degli immigrati

Haem-iron plays a key role in the regulation of the Ess/Type VII secretion system of <i>Staphylococcus aureus</i> RN6390

This study was supported by the Wellcome Trust (through Investigator Award 10183/Z/15/Z to T. P. and through Clinical PhD studentship support to C. P. H. through grant 104241/z/14/z), the Biotechnology and Biological Sciences Research Council and the Medical Research Council (through grants BB/H007571/1 and MR/M011224/1, respectively).The Staphylococcus aureus type VII protein secretion system (T7SS) plays important roles in virulence and intra-species competition. Here we show that the T7SS in strain RN6390 is activated by supplementing the growth medium with haemoglobin, and its cofactor haemin (haem B). Transcript analysis and secretion assays suggest that activation by haemin occurs at a transcriptional and a post-translational level. Loss of T7 secretion activity by deletion of essC results in upregulation of genes required for iron acquisition. Taken together these findings suggest that the T7SS plays a role in iron homeostasis in at least some S. aureus strains.Publisher PDFPeer reviewe

The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.

BACKGROUND: The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo. RESULTS: In total, 4 286 protein coding sequences were identified, and the 4.6 Mb genome of A. salmonicida has a six partite architecture with two chromosomes and four plasmids. Sequence analysis revealed a highly fragmented genome structure caused by the insertion of an extensive number of insertion sequence (IS) elements. The IS elements can be related to important evolutionary events such as gene acquisition, gene loss and chromosomal rearrangements. New A. salmonicida functional capabilities that may have been aquired through horizontal DNA transfer include genes involved in iron-acquisition, and protein secretion and play potential roles in pathogenicity. On the other hand, the degeneration of 370 genes and consequent loss of specific functions suggest that A. salmonicida has a reduced metabolic and physiological capacity in comparison to related Vibrionaceae species. CONCLUSION: Most prominent is the loss of several genes involved in the utilisation of the polysaccharide chitin. In particular, the disruption of three extracellular chitinases responsible for enzymatic breakdown of chitin makes A. salmonicida unable to grow on the polymer form of chitin. These, and other losses could restrict the variety of carrier organisms A. salmonicida can attach to, and associate with. Gene acquisition and gene loss may be related to the emergence of A. salmonicida as a fish pathogen

Moritella viscosa in lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar)

Post-print (lokagerð höfundar)Winter ulcer disease, caused by Moritella viscosa, is a significant problem in cold water salmonid farming, although the bacterium can infect and cause disease in a number of other fish species, such as lumpfish (Cyclopterus lumpus). Lumpfish are used as cleaner fish, to eat sea lice from Atlantic salmon (Salmo salar) in sea pens. It remains to be established whether M. viscosa can be transmitted between the fish species. In this study, we examined whether a salmon isolate of M. viscosa could infect and cause disease in lumpfish. We further examined whether a lumpfish isolate of M. viscosa could infect and cause disease in salmon. Finally, we examined whether vaccination of salmon with a salmon isolate of M. viscosa conferred protection against a lumpfish isolate. The data indicate that while lumpfish appeared to be resistant to a salmon isolate of M. viscosa, the salmon could be infected with a lumpfish isolate of M. viscosa. Vaccination protected the salmon against the salmon isolate of M. viscosa but did not confer sufficient protection to prevent infection with the lumpfish isolate.This work was supported by the AVS R&D Fund of Ministry of Fisheries and Agriculture in Iceland [grant number S 001‐17].Peer Reviewe