Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study.

INTRODUCTION: Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota. METHODS: The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD. ETHICS AND DISSEMINATION: Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER: ACTRN12619000911190

Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlight novel therapeutic targets

Background and Aim: The earliest macroscopic lesion in Crohn’s disease(CD) is the aphthous ulcer, which overlies Peyer’s patches and lymphoidfollicles. Our aim was to characterize differences in gene expression andthe virome of aphthous ulcers and Peyer’s patches.Methods: Biopsies (n = 24) were obtained from the terminal ileum of 12patients (six with CD and six healthy controls). Aphthous ulcers and adja-cent unaffected mucosa were obtained from patients with CD, and Peyer’spatches and adjacent mucosa from the controls. All patients, except one,were medication free. RNA was extracted using Qiagen kits. NextSeq500 libraries were constructed using NextSeq 500/550 High output kits(Illumina) in a 150 bp paired-end format. Whole genome transcripts wereassessed for quality using FASTQC, trimmed using Trimmomatic, andaligned to the human reference genome using subread mapper. Fragmentcounts were obtained using featureCount, and expression values normal-ized using the trimmed mean of M-values normalization method (TMM).Differential gene expression analyses were performed using generalizedlinear models in edgeR. Cell-specific gene expression was determinedusing ImSig. Reads that did not map to the human genome were used tomine for virus sequences using the VirusSeeker pipeline.Results: We obtained 36 million tags per sample, 87% were retained fordownstream processing, and 93% of these mapped to the human genome.A total of 920 genes were significantly differentially expressed betweenaphthous ulcers and Peyer’s patches (P = <0.001); all were upregulatedin aphthous ulcers. Differential gene expression analysis revealed 34 path-ways that were upregulated in aphthous ulcers relative to Peyer’s patches.Pathways that were over-expressed included those involved in respondingto bacteria, leukocyte chemotaxis, inflammatory response, and creation ofC2 and C4 activators. Receptors for the constant region of IgG were repre-sented in 13 pathways. The cytokine OSM and its receptor (OSMR) werealso over-expressed in aphthous ulcers. ImSig, which is capable of usingtranscriptome data to indicate cell types and their activation state, revealedthat core marker genes for plasma cells were overrepresented in aphthousulcers relative to Peyer’s patches and unaffected or normal mucosa. Therewas no virus common to all aphthous ulcers. We detected human herpesvirus 4 in one aphthous ulcer, human herpes virus 1 in mucosa from apatient with CD, and a novel Totivirus in mucosa of one control patient.Conclusions: A number of gene clusters and immune pathways are over-expressed in aphthous ulcers compared with Peyer’s patches. These bio-logically relevant gene lists highlight a number of new therapeutic targetsand potential biomarkers for early stage disease. Viruses are an unlikelyinitiator of C

Active Whey Protein Edible Films and Coatings Incorporating Lactobacillus buchneri for Penicillium nordicum Control in Cheese

Fungal contamination of food is responsible for health issues and food waste. In this work, the incorporation of a lactic acid bacteria (LAB) with antifungal properties (Lactobacillus buchneri UTAD104) into whey protein-based films and coatings was tested for the control of an ochratoxigenic fungi (Penicillium nordicum) in a cheese matrix. The incorporation of L. buchneri cells resulted in thicker films with less luminosity than control films and colour alteration. Nevertheless, cells inclusion did not alter moisture content, water vapour permeability, mechanical properties, hydrophobicity and chemical structure of the films. Whey protein films were able to maintain the viability of L. buchneri UTAD104 cells in 105 CFU/mL after 30 days of storage at 25 \textdegreeC. When applied in cheese, films and coatings containing L. buchneri cells prevented fungal contamination for at least 30 days, while control cheeses with films and coatings either without LAB or with Lactobacillus casei UM3 (a strain without antifungal ability) showed fungal contamination during that period. Ochratoxin A was not found in cheeses treated with films and coatings containing L. buchneri UTAD104. Results showed that the inclusion of a LAB with antifungal properties in edible films and coatings can help to reduce or eliminate P. nordicum contamination in cheeses.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. Ana Guimarães received support through grant SFRH/BD/103245/2014 from the Portuguese FCT.info:eu-repo/semantics/publishedVersio

Ustekinumab as Induction and Maintenance Therapy for Crohn’s Disease

BACKGROUND Ustekinumab, a monoclonal antibody to the p40 subunit of interleukin-12 and inter-leukin-23, was evaluated as an intravenous induction therapy in two populations with moderately to severely active Crohn’s disease. Ustekinumab was also evaluated as subcutaneous maintenance therapy. METHODS We randomly assigned patients to receive a single intravenous dose of ustekinumab (either 130 mg or approximately 6 mg per kilogram of body weight) or placebo in two induction trials. The UNITI-1 trial included 741 patients who met the criteria for primary or secondary nonresponse to tumor necrosis factor (TNF) antagonists or had unacceptable side effects. The UNITI-2 trial included 628 patients in whom conventional therapy failed or unacceptable side effects occurred. Patients who completed these induction trials then participated in IM-UNITI, in which the 397 patients who had a response to ustekinumab were randomly assigned to receive subcutaneous maintenance injections of 90 mg of ustekinumab (either every 8 weeks or every 12 weeks) or placebo. The primary end point for the induction trials was a clinical response at week 6 (defined as a decrease from baseline in the Crohn’s Disease Activity Index [CDAI] score of ≥100 points or a CDAI score <150). The primary end point for the maintenance trial was remission at week 44 (CDAI score <150). RESULTS The rates of response at week 6 among patients receiving intravenous ustekinumab at a dose of either 130 mg or approximately 6 mg per kilogram were significantly higher than the rates among patients receiving placebo (in UNITI-1, 34.3%, 33.7%, and 21.5%, respectively, with P≤0.003 for both comparisons with placebo; in UNITI-2, 51.7%, 55.5%, and 28.7%, respectively, with P<0.001 for both doses). In the groups receiving maintenance doses of ustekinumab every 8 weeks or every 12 weeks, 53.1% and 48.8%, respectively, were in remission at week 44, as compared with 35.9% of those receiving placebo (P = 0.005 and P = 0.04, respectively). Within each trial, adverse-event rates were similar among treatment groups. CONCLUSIONS Among patients with moderately to severely active Crohn’s disease, those receiving intravenous ustekinumab had a significantly higher rate of response than did those receiving placebo. Subcutaneous ustekinumab maintained remission in patients who had a clinical response to induction therapy. (Funded by Janssen Research and Development; ClinicalTrials.gov numbers, NCT01369329, NCT01369342, and NCT01369355.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Achievements and prospects in breeding for rhizomania resistance in sugar beet

Economic viability of a sugar beet crop largely depends on its successful protection against rhizomania, a most devastating disease that causes severe losses in root yield, sucrose content and quality. Rhizomania disease is caused by Beet necrotic yellow vein virus (BNYVV), a virus present in most sugar beet growing regions being vectored by the widely spread soil borne protoctist Polymyxa betae Keskin. The only prac- tical means to control the disease is the use of genetically resistant varieties and, to date, such resistance is mainly based on a dominant gene (Rz1) that when present confers a sufficiently high level of protec- tion against BNYVV. However, the emergence of virus strains capable of compromising the resistance employed in commercial varieties as well as a possible spread of more pathogenic isolates threatens crop’s protection efficiency in the future. All these point to the necessity for exploiting new and more effective genetic sources of rhizomania resistance, both by classical and molecular breeding approaches, a practice that is being pursued by the relevant breeding firms. This article critically reviews the various issues related to the disease and its management and particularly to the ones pertaining to pathogen genetic diversity, types of genetic resistance currently employed, as well as to novel biotechnological approaches aiming at the development of better resisting cultivars