Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets

The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture

Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

<p>Abstract</p> <p>Background</p> <p><it>Helicobacter pylori </it>is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global <it>H. pylori </it>population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent <it>H. pylori </it>migration and admixture.</p> <p>Results</p> <p>Seventy eight <it>H. pylori </it>isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified <it>H. pylori </it>ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the <it>H. pylori </it>populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates.</p> <p>Conclusion</p> <p>The majority of the Malay and Indian <it>H. pylori </it>isolates share the same origin while the Malaysian Chinese <it>H. pylori </it>is distinctive. The Malay population, known to have a low infection rate of <it>H. pylori</it>, was likely to be initially <it>H. pylori </it>free and gained the pathogen only recently from cross infection from other populations.</p

Gastric Helicobacter pylori infection perturbs human oral microbiota

Background We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota. Methods Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status. Results Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples. Discussion Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals

Evaluation of appendicitis risk prediction models in adults with suspected appendicitis

Background Appendicitis is the most common general surgical emergency worldwide, but its diagnosis remains challenging. The aim of this study was to determine whether existing risk prediction models can reliably identify patients presenting to hospital in the UK with acute right iliac fossa (RIF) pain who are at low risk of appendicitis. Methods A systematic search was completed to identify all existing appendicitis risk prediction models. Models were validated using UK data from an international prospective cohort study that captured consecutive patients aged 16–45 years presenting to hospital with acute RIF in March to June 2017. The main outcome was best achievable model specificity (proportion of patients who did not have appendicitis correctly classified as low risk) whilst maintaining a failure rate below 5 per cent (proportion of patients identified as low risk who actually had appendicitis). Results Some 5345 patients across 154 UK hospitals were identified, of which two‐thirds (3613 of 5345, 67·6 per cent) were women. Women were more than twice as likely to undergo surgery with removal of a histologically normal appendix (272 of 964, 28·2 per cent) than men (120 of 993, 12·1 per cent) (relative risk 2·33, 95 per cent c.i. 1·92 to 2·84; P < 0·001). Of 15 validated risk prediction models, the Adult Appendicitis Score performed best (cut‐off score 8 or less, specificity 63·1 per cent, failure rate 3·7 per cent). The Appendicitis Inflammatory Response Score performed best for men (cut‐off score 2 or less, specificity 24·7 per cent, failure rate 2·4 per cent). Conclusion Women in the UK had a disproportionate risk of admission without surgical intervention and had high rates of normal appendicectomy. Risk prediction models to support shared decision‐making by identifying adults in the UK at low risk of appendicitis were identified

Population structure and genomic analysis of Helicobacter pylori

This study tested the Suppressive Subtractive Hybridisation (SSH) method by extracting the strain specific genes from H. pylori strain, 10700. Nine clones were identified as 10700-specific clones; 16 clones as the pHPS1-specific sequences; and 137 clones homologous to sequences in 26695 and J99 genomes. The high recovery of divergent genes suggested that SSH is not suitable for divergent strains. Seventy eight H. pylori Malaysia isolates in three ethnic backgrounds were analysed by Multilocus Sequence Typing (MLST). STRUCTURE analysis assigned the Malaysian isolates to hpEastAsia, hpAsia2 and hpEurope and revealed a new subpopulation, hspIndia, within hpAsia2. The majority of Malay isolates were found to be grouped together with Indian isolates. Therefore, the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. DNA microarrays were employed to analyse 10 Malaysian isolates, comprising three Chinese, three Indian and four Malay isolates. However, 217 oligonucleotides were identified with non-specific bindings and were excluded from subsequent analysis. The remaining oligonucleotides were classified as common gene oligonucleotides, Strain Specific Genes (SSGs), and common but non-homologous oligonucleotides (CNHOs). Microarray analysis has also revealed 99.6% of common genes, 73.5% of SSGs and 89.9% of CNHOs universally present in the 10 Malaysian isolates. However, higher number of genes was detected among the Malaysian isolates than the global isolates. This may due to the different microarrays used between microarray studies. In addition, 268 genes variably present among hspIndia and hspLadakh; 259 genes were shown to be variably present among the three Malaysian and six global isolates. Then again, the 10 Malaysian isolates were not clustered together according to the population structure established by MLST studies. Therefore, Microarrays data does not reflect the evolutionary history of H. pylori but can be used to provide information on gene acquisition and loss between populations established by MLST

Choosing a Benchtop Sequencing Machine to Characterise <i>Helicobacter pylori</i> Genomes

<div><p>The fully annotated genome sequence of the European strain, 26695 was first published in 1997 and, in 1999, it was directly compared to the USA isolate J99, promoting two standard laboratory isolates for <i>Helicobacter pylori</i> (<i>H. pylori</i>) research. With the genomic scaffolds available from these important genomes and the advent of benchtop high-throughput sequencing technology, a bacterial genome can now be sequenced within a few days. We sequenced and analysed strains J99 and 26695 using the benchtop-sequencing machines Ion Torrent PGM and the Illumina MiSeq Nextera and Nextera XT methodologies. Using publically available algorithms, we analysed the raw data and interrogated both genomes by mapping the data and by <i>de novo</i> assembly. We compared the accuracy of the coding sequence assemblies to the originally published sequences. With the Ion Torrent PGM, we found an inherently high-error rate in the raw sequence data. Using the Illumina MiSeq, we found significantly more non-covered nucleotides when using the less expensive Illumina Nextera XT compared with the Illumina Nextera library creation method. We found the most accurate <i>de novo</i> assemblies using the Nextera technology, however, extracting an accurate multi-locus sequence type was inconsistent compared to the Ion Torrent PGM. We found the <i>cag</i>PAI failed to assemble onto a single contig in all technologies but was more accurate using the Nextera. Our results indicate the Illumina MiSeq Nextera method is the most accurate for <i>de novo</i> whole genome sequencing of <i>H. pylori.</i></p></div