Biomarkers for monitoring intestinal health in poultry : present status and future perspectives

Intestinal health is determined by host (immunity, mucosal barrier), nutritional, microbial and environmental factors. Deficiencies in intestinal health are associated with shifts in the composition of the intestinal microbiome (dysbiosis), leakage of the mucosal barrier and/or inflammation. Since the ban on growth promoting antimicrobials in animal feed, these dysbiosis-related problems have become a major issue, especially in intensive animal farming. The economical and animal welfare consequences are considerable. Consequently, there is a need for continuous monitoring of the intestinal health status, particularly in intensively reared animals, where the intestinal function is often pushed to the limit. In the current review, the recent advances in the field of intestinal health biomarkers, both in human and veterinary medicine are discussed, trying to identify present and future markers of intestinal health in poultry. The most promising new biomarkers will be stable molecules ending up in the feces and litter that can be quantified, preferably using rapid and simple pen-side tests. It is unlikely, however, that a single biomarker will be sufficient to follow up all aspects of intestinal health. Combinations of multiple biomarkers and/or metabarcoding, metagenomic, metatranscriptomic, metaproteomic and metabolomic approaches will be the way to go in the future. Candidate biomarkers currently are being investigated by many research groups, but the validation will be a major challenge, due to the complexity of intestinal health in the field

The quorum sensing inhibitor hamamelitannin increases antibiotic susceptibility of Staphylococcus aureus biofilms by affecting peptidoglycan biosynthesis and eDNA release

Treatment of Staphylococcus aureus infections has become increasingly challenging due to the rapid emergence and dissemination of methicillin-resistant strains. In addition, S. aureus reside within biofilms at the site of infection. Few novel antibacterial agents have been developed in recent years and their bacteriostatic or bactericidal activity results in selective pressure, inevitably inducing antimicrobial resistance. Consequently, innovative antimicrobials with other modes of action are urgently needed. One alternative approach is targeting the bacterial quorum sensing (QS) system. Hamamelitannin (2′,5-di-O-galloyl-d-hamamelose; HAM) was previously suggested to block QS through the TraP QS system and was shown to increase S. aureus biofilm susceptibility towards vancomycin (VAN) although mechanistic insights are still lacking. In the present study we provide evidence that HAM specifically affects S. aureus biofilm susceptibility through the TraP receptor by affecting cell wall synthesis and extracellular DNA release of S. aureus. We further provide evidence that HAM can increase the susceptibility of S. aureus biofilms towards different classes of antibiotics in vitro. Finally, we show that HAM increases the susceptibility of S. aureus to antibiotic treatment in in vivo Caenorhabditis elegans and mouse mammary gland infection models

Host intestinal biomarker identification in a gut leakage model in broilers

International audienceAbstractIntestinal health problems are a major issue in the poultry industry. Quantifiable easy-to-measure biomarkers for intestinal health would be of great value to monitor subclinical intestinal entities that cause performance problems and to evaluate control methods for intestinal health. The aim of the study was to identify host protein biomarkers for intestinal inflammation and intestinal barrier damage. Proteomic analysis was conducted on ileal and colonic content samples of broilers under an experimental gut damage and inflammation model. Effects of the challenge treatment resulted in a worse gut condition based on macroscopic gut appearance (p < 0.0001). Also microscopic changes such as shortening of the villi and increased crypt depth (p < 0.0001) as well as higher infiltration of T-lymphocytes (p < 0.0001) were seen in the duodenal tissue of challenged animals. Several candidate proteins associated with inflammation, serum leakage and/or tissue damage were identified with an increased abundance in intestinal content of challenged animals (p < 0.05). Conversely, brush border enzymes were less abundant in intestinal content of challenged animals (p < 0.05). These candidate biomarkers have potential to be used in the field for detection of gut barrier failure in broilers

Applied research note : biomonitoring of mycotoxins in blood serum and feed to assess exposure of broiler chickens

Because European maximum guidance values of mycotoxins are only available for feed, mycotoxin exposure in animals is mainly monitored by feed analysis. However, proper sample collection is needed to ensure reliable results because of uneven distributions and disproportional spread of mycotoxins in feed which can hamper the evaluation of mycotoxin exposure in animals. A cross-sectional study was performed on 40 randomly selected broiler farms in Belgium. During a farm visit at the animal's age of 28 d, a pooled feed sample at the beginning and the end of the feed line was collected. Feed samples were analyzed by a validated multimycotoxin LC-MS/MS method. Moreover, serum samples were collected from 10 randomly selected chickens per farm. Serum concentrations of mycotoxins and major in vivo phase I metabolites were analyzed quantitatively, whereas the presence of phase II metabolites was determined in a qualitative approach by an UPLC-HRMS method. Deoxynivalenol (DON) was the most frequently occurring mycotoxin, being present in 74% of the feed samples, with an average concentration of 270 +/- 171 mu g/kg and a maximum concentration of 751 mu g/kg in positive samples. Also the acetylated forms 3and 15-acetyldeoxynivalenol (3 and 15ADON) were present in half of the samples, however, at lower concentrations (8 +/- 3 mu g 3ADON and 10 +/- 7 mu g 15ADON/kg). Only in 17.5% of the farms, DON was detected in serum samples at a mean serum concentration and standard deviation (SD) of 11 +/- 19 ng/mL. The maximum serum concentration of 49 ng DON/ mL was detected in broilers which were fed a diet that was contaminated with 191 mu g DON/kg, whereas the maximum concentration of DON in feed was 751 mu g/kg. Besides, 3 and 15ADON were only detected in 10% of the serum samples (max. 1.3 ng/mL). Sulfate conjugates of DON were only detected in a few serum samples. Qualitative screening for phase II metabolites of other mycotoxins showed similar results. Overall, correlations between feed and serum concentrations of all mycotoxins were lacking (R-2 = 0.18 for DON)

Surface alignment, anchoring transitions, optical properties, and topological defects in the thermotropic nematic phase of organo-siloxane tetrapodes

We address the status of oxadiazole mesogens, C7 and C12, reported to show the biaxial nematic phase, by exploring material aspects (chemical stability, surface anchoring, optical and dielectric properties, topological defects) linked to the type of nematic order. We demonstrate that the isogyres splitting in conoscopic patterns of homeotropic state depends on sample thickness and is associated with variations of molecular tilt along the normal to substrates. We observe isolated topological point defects (boojums and hedgehogs), as well as nonsingular “escaped” disclinations pertinent only to the uniaxial nematic order. Our conclusion is that C7 and C12 feature only a uniaxial nematic phase and the apparent biaxiality is caused by surface effects

Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome.

PURPOSE: Currently, it is unclear to what extent sampling procedures affect the epigenome. Here, this phenomenon was evaluated by studying the impact of artery ligation on DNA methylation in clear cell renal cancer. METHODS: DNA methylation profiles between vascularised tumour biopsy samples and devascularised nephrectomy samples from two individuals were compared. The relevance of significantly altered methylation profiles was validated in an independent clinical trial cohort. RESULTS: We found that six genes were differentially methylated in the test samples, of which four were linked to ischaemia or hypoxia (REXO1L1, TLR4, hsa-mir-1299, ANKRD2). Three of these genes were also found to be significantly differentially methylated in the validation cohort, indicating that the observed effects are genuine. CONCLUSION: Tissue ischaemia during normal surgical removal of tumour can cause epigenetic changes. Based on these results, we conclude that the impact of sampling procedures in clinical epigenetic studies should be considered and discussed, particularly after inducing hypoxia/ischaemia, which occurs in most oncological surgery procedures through which tissues are collected for translational research.This work was supported by the Chief Scientist Office, Scotland (ETM37; GDS, DJH), Cancer Research UK (Experimental Cancer Medicine Centre; TP, London, DJH, Edinburgh), Medical Research Council (AL, DJH), Royal College of Surgeons of Edinburgh Robertson Trust (AL), Melville Trust AL), Renal Cancer Research Fund (GDS), Kidney Cancer Scotland (GDS) and an educational grant from Pfizer (TP). CVN and TDM were funded by Ghent University Multidisciplinary Research Partnership 'Bioinformatics: from nucleotides to networks'

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

BACKGROUND : Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. RESULTS AND DISCUSSION : Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions. CONCLUSIONS : A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.Additional file 1. Assembly characteristics of all assembled crustacean genomes. Characteristics listed are: species, whether the species genome is annotated yes or no, N50 of the fragments with the highest assembly hierarchy, number of fragments with the highest assembly hierarchy in the assembly, haploid genome size, assembly size, completeness of the assembly (=haploid GS/assembly size), taxonomic lineage (NCBI taxonomy), reference for the genome paper.Additional file 2. Evolution of Artemia assembly quality metrics throughout the assembly steps. Evolution of the scaffold N50, the number of fragments and the genome completeness (assembly size/ genome size) in the subsequent Artemia assembly stagesAdditional file 3 BUSCO analysis results for the A. franciscana genome assembly and annotation.Additional file 4. BLAST results for mitochondrial genes in the Artemia genome. Listed: Query accession and gene name, presence of a (significant) BLAST hit in the Artemia proteome with the highest bit score, E-value and bit score of the hit, scaffold length of the scaffold on which the hit lies, percentage of mitochondrial genes on this scaffold.Additional file 5. Taxonomic groups of alien genomes identified in the Artemia genome.Additional file 6 Expanded or contracted Artemia orthogroups compared to other Branchiopoda. Listed: Orthogroup ID, number of genes in this orthogroup in A. franciscana, D. pulex, L. arcticus, and E. texana, expanded or contracted status of the orthogroup in Artemia compared to D. pulex, L. arcticus and E. texana, conservation in Branchiopoda (whether this orthogroup contains genes for each branchiopod), comma-separated IPR description of Artemia genes in this orthogroup, Artemia genes in this orthogroup.Additional file 7 GO enrichment of Artemia compared to other Branchiopoda. Listed: GO ID, name and category, false discovery rate (FDR) and P value of the Fisher’s exact test enrichment analysis in Blast2GO, number of Artemia genes from expanded/contracted orthogroups in this GO ID, number of whole Artemia genome genes in this GO category, number of Artemia genes from expanded/contracted orthogroups in this GO ID without GO annotation. The Fisher’s Exact Test is sensitive in the direction of the test: the genes that are present in the test-set and also in the reference genome set will be deleted from the reference, but not from the test set, resulting in zero sequences in the reference set and values above zero in the test set. Significantly enriched GOs (FDR ≤ 0.05, biological process) of Artemia genes in expanded or contracted orthogroups compared to Branchiopoda are given.Additional file 8 Expanded or contracted Artemia and H. dujardini orthogroups compared to other Arthropoda. Listed: Orthogroup ID, number of genes in this orthogroup in A. franciscana and in the other arthropod species, expanded or contracted status of the orthogroup in Artemia compared to the other arthropod species, comma-separated IPR description of Artemia genes in this orthogroup, H. dujardini genes in this orthogroup, Artemia genes in this orthogroup.Additional file 9. STAR mapping statistics for differential expression analysis in Artemia. Listed: sample name, total number of reads for this sample, percentage of uniquely mapped reads, absolute number of uniquely mapped reads, percentage of multi mapped reads, absolute number of multi mapped reads.Additional file 10. Summarization statistics for differential expression analysis in Artemia. Listed: sample name, total counts, percentage of counts assigned to a gene annotation, absolute counts assigned to a gene annotation. * notice that this amount can be more than the sum of uniquely mapped + multi-mapped in the mapping statistics since multimapped reads are considered.Additional file 11 Differentially expressed genes under high salinity (p < 0.05). Listed: functional annotation of the differentially expressed gene, gene ID in the genome annotation and on the ORCAE platform, p value, average log fold change of gene expression under high salinity, gene regulation of the differentially expressed gene (up or down), InterPro description of the gene family to which the gene belongs.Additional file 12 Differentially expressed genes under anoxia (p < 0.05). Listed: functional annotation of the differentially expressed gene, gene ID in the genome annotation and on the ORCAE platform, p value, log fold change of gene expression under anoxia, gene regulation of the differentially expressed gene (up or down), InterPro description of the gene family to which the gene belongs.Additional file 13 GO enrichment in Artemia under high salinity. Significantly Enriched GOs (FDR ≤ 0.05) of Artemia genes differentially expressed under high salinity. Listed: GO ID, name and category, false discovery rate (FDR) and P value of the Fisher’s exact test enrichment analysis in Blast2GO, number of DEG under high salinity in this GO category, number of whole Artemia genome genes in this GO category, number of DEG under high salinity without GO annotation. The Fisher’s Exact Test is sensitive in the direction of the test: the genes that are present in the test-set and also in the reference genome set will be deleted from the reference, but not from the test set, resulting in zero sequences in the reference set and values above zero in the test set.Additional file 14 Pathway enrichment in Artemia under high salinity. Significantly enriched (Fisher’s exact test corrected for multiple testing, FDR ≤ 0.05) pathways of Artemia genes differentially expressed under high salinity. Listed in first worksheet (STRING annotation): gene number, ORCAE gene ID, STRING Daphnia pulex gene ID, BLAST identity and bit score, gene name and gene annotation. Listed in second worksheet (STRING pathway enrichment): KEGG Daphnia pulex pathway name, pathway description, number of DEG under high salinity in this pathway, number of genes in the D. pulex genome that belong to this pathway, enrichment FDR, matching D. pulex gene IDs, matching gene names in pathways shown in figures and additional files, matching D. pulex gene ID labels.Additional file 15. Consolidation of DEG analysis, GO enrichment and pathway enrichment in Artemia under high salinity.Additional file 16. The enriched Carbon metabolism pathway in Artemia under high salinity. Up- and downregulated genes are indicated on the KEGG map dpx01200.Additional file 17. GO enrichment in Artemia under anoxia. Significantly enriched GOs (FDR ≤ 0.05) of Artemia genes differentially expressed under anoxia. Listed: GO ID, name and category, false discovery rate (FDR) and P value of the Fisher’s exact test enrichment analysis in Blast2GO, number of DEG under anoxia in this GO ID, number of whole Artemia genome genes in this GO ID, number of DEG under anoxia without GO annotation. The Fisher’s Exact Test is sensitive in the direction of the test: the genes that are present in the test set and also in the reference genome set will be deleted from the reference, but not from the test set, resulting in zero sequences in the reference set and values above zero in the test set.Additional file 18 Pathway enrichment in Artemia under anoxia. Significantly enriched (Fisher’s exact test corrected for multiple testing, FDR ≤ 0.05) pathways of Artemia genes differentially expressed under anoxia. Listed in first worksheet (STRING annotation): gene number, ORCAE gene ID, STRING Daphnia pulex gene ID, BLAST identity and bit score, gene name and gene annotation. Listed in second worksheet (STRING pathway enrichment): KEGG Daphnia pulex pathway name, pathway description, number of DEG under anoxia in this pathway, number of genes in the D. pulex genome that belong to this pathway, enrichment FDR, matching D. pulex gene IDs, matching gene names in pathways shown in figures and additional files, matching D. pulex gene ID labels.Additional file 19. Consolidation of DEG analysis, GO enrichment and pathway enrichment in Artemia under anoxia.Additional file 20. The enriched N-glycan biosynthesis pathway in Artemia under anoxia. Up- and downregulated genes are indicated on the KEGG map dpx00510.Additional file 21. The enriched Basal transcription factors pathway in Artemia under anoxia. Up- and downregulated genes are indicated on the KEGG map dpx03022.Additional file 22. Augustus custom training files for Artemia. Includes probabilities, parameters and weights used for Augustus training for annotation of the Artemia genome.Additional file 23. EuGene custom parameter file for Artemia. Includes parameters used for EuGene training for annotation of the Artemia genome.Additional file 24. Sequence GC-content profiles for all samples used for differential expression analysis.The Flemish Government Special Research Fund and the Laboratory of Aquaculture & Artemia Reference Center.http://www.biomedcentral.com/bmcgenomicsam2022BiochemistryGeneticsMicrobiology and Plant Patholog

Search for direct stau production in events with two hadronic tau-leptons in root s=13 TeV pp collisions with the ATLAS detector

A search for the direct production of the supersymmetric partners ofτ-leptons (staus) in final stateswith two hadronically decayingτ-leptons is presented. The analysis uses a dataset of pp collisions corresponding to an integrated luminosity of139fb−1, recorded with the ATLAS detector at the LargeHadron Collider at a center-of-mass energy of 13 TeV. No significant deviation from the expected StandardModel background is observed. Limits are derived in scenarios of direct production of stau pairs with eachstau decaying into the stable lightest neutralino and oneτ-lepton in simplified models where the two staumass eigenstates are degenerate. Stau masses from 120 GeV to 390 GeV are excluded at 95% confidencelevel for a massless lightest neutralino