The need for an integrated multi-OMICs approach in microbiome science in the food system

Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.

Postinfective bowel dysfunction following Campylobacter enteritis is characterised by reduced microbiota diversity and impaired microbiota recovery

OBJECTIVES

Persistent bowel dysfunction following gastroenteritis (postinfectious (PI)-BD) is well recognised, but the associated changes in microbiota remain unclear. Our aim was to define these changes after gastroenteritis caused by a single organism, Campylobacter jejuni, examining the dynamic changes in the microbiota and the impact of antibiotics.

DESIGN

A single-centre cohort study of 155 patients infected with Campylobacter jejuni. Features of the initial illness as well as current bowel symptoms and the intestinal microbiota composition were recorded soon after infection (visit 1, <40 days) as well as 40-60 days and >80 days later (visits 2 and 3). Microbiota were assessed using 16S rRNA sequencing.

RESULTS

PI-BD was found in 22 of the 99 patients who completed the trial. The cases reported significantly looser stools, with more somatic and gastrointestinal symptoms. Microbiota were assessed in 22 cases who had significantly lower diversity and altered microbiota composition compared with the 44 age-matched and sex-matched controls. Moreover 60 days after infection, cases showed a significantly lower abundance of 23 taxa including phylum Firmicutes, particularly in the order Clostridiales and the family Ruminoccocaceae, increased Proteobacteria abundance and increased levels of Fusobacteria and Gammaproteobacteria. The microbiota changes were linked with diet; higher fibre consumption being associated with lower levels of Gammaproteobacteria.

CONCLUSION

The microbiota of PI-BD patients appeared more disturbed by the initial infection compared with the microbiota of those who recovered. The prebiotic effect of high fibre diets may inhibit some of the disturbances seen in PI-BD.

TRIAL REGISTRATION NUMBER

NCT02040922.

Microbiome ethics, guiding principles for microbiome research, use and knowledge management

The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don't Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops.

Prediction and Assessment of Potential Microbial Substrate Utilisation Among More Recently Identified Health-Associated Gut Taxa

The contribution of the gut microbiota to health and disease is becoming ever more apparent in the last number of years, due to developments in DNA sequencing technology and more well-defined cultivation techniques. This has resulted in the identification of health-promoting bacteria. Until recently, prebiotics, non-digestible food substrates which are selectively utilised by beneficial bacteria, were employed with a view to increasing the growth of well-established health promoting bacteria, namely Lactobacillus and Bifidobacterium. However, other beneficial bacteria recently revealed may also be targeted to enhance their growth as they establish themselves as the next generation of health-promoting microbes. These include anaerobes such as Akkermansia muciniphila, Faecalibacterium prausnitziiand Eubacterium rectale. Identification of growth substrates/bioactives through the analysis of genome sequence data can aid in elucidating which substrates may best enhance the growth of these microbes which are often difficult to grow.

The phenotypic microbial trait analyser, Traitar, can predict 67 phenotypes based on the genome sequence inputted. Some of these traits include substrates that could potentially be utilised by the bacteria. Another tool, CarveMe, which has been created with the aim of making metabolic modelling more user-friendly, was also used with the same genomes. A select number of substrates identified in both tools have been chosen to be evaluated in vitroin order to establish the accuracy of these predictive tools as well as giving an indication as to how these beneficial microbes can be modulated through dietary components.

Angiotensin-Converting Enzyme Inhibitor-Induced Oropharyngeal edema with Subsequent Stress-Cardiomyopathy

Intramuscular adrenaline is a standard treatment approach for the symptomatic patient presenting with distress and oropharyngeal edema, requiring subsequent doses if oedema persists. This case demonstrates a delayed side-effect of stress-induced cardiomyopathy after adrenaline administration. A 62-year-old suffered acute oropharyngeal angioedema secondary to angiotensin-converting-enzyme inhibitor use. Two standard doses of intramuscular adrenaline 2 hours apart were administered, and she was monitored for 2 days. On day three post discharge, she represented with acute hypervolaemia. Transthoracic echocardiogram showed a globally dilated, poorly functioning left ventricle. Cardiac magnetic resonance imaging described takotsubo cardiomyopathy. One month later, left ventricular function had normalised with optimal medical treatment. Cardiomyopathy with a temporal relationship to a hypersensitivity reaction is thought to occur due to one of three mechanisms: Stress (takotsubo) cardiomyopathy, allergic acute coronary (Kounis) Syndrome, and hypersensitive myocarditis. If a clinical presentation of hypersensitivity is such that it requires treatment with epinephrine, it is particularly challenging to determine the exact cause of cardiomyopathy.

193 ARE OLDER PATIENTS IN IRELAND BEING ADEQUATELY SCREENED FOR DELIRIUM? RESULTS FROM AN IRISH PERIPHERAL HOSPITAL

Background

Delirium is associated with increased morbidity and mortality in the older person and still remains poorly detected. The Health Service Executive (HSE) has clear algorithms and guidelines which suggest that any person over the age of 65, especially so for patients with pre-existing dementia, presenting to the Emergency Department (ED) or Acute Medical Assessment Unit (AMAU) should be screened for delirium using the 4AT test. An earlier retrospective audit carried out by the authors in the same hospital showed that only 9% of patients with diagnosed delirium had a 4AT test at any point during inpatient stay and 0% had one on admission. We designed a prospective audit to assess what proportion of patients over 65 coming through the Acute Medical Assessment Unit (AMAU) had a delirium screening test performed on admission.

Methods

We reviewed the admission notes of all patients over 65 admitted through the AMAU over a continuous 14 day period from 10/11/20 to 24/11/2020. The admission notes were reviewed within 24 hours of admission. Exclusion criteria included patients presenting delirium tremens and patients presenting with a stroke.

Results

119 patients were identified. The mean age was 78.1 years. 20 (16.8%) had previously diagnosed dementia. 0 patients had a delirium screening test conducted by AMAU/ED staff on admission. 2 (1.7%) had 4AT tests done by members of the Geriatric Emergency Medical Services (GEMS) team within 24 hours. The GEMS team only sees patients who fulfill certain criteria on admission. 10 (8.4%) had ‘delirium’ listed on their differential diagnoses.

Conclusion

Our results show that the older patient being admitted through the AMAU in this hospital in Ireland is not being adequately screened for delirium. Additionally, even when delirium was suspected, delirium screening tools were not being implemented for further assessment. More needs to be done to ensure patients over 65 are assessed as per guidelines.

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

BACKGROUND

The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.

RESULTS

We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.

CONCLUSIONS

The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

Outbreak of acute larval cyathostominosis - A "perfect storm" of inflammation and dysbiosis

Background

Cyathostomins are prevalent and pathogenic intestinal helminths of horses, causing acute and chronic disease, including acute larval cyathostominosis, which has a mortality rate of 50%. Factors determining individual susceptibility to acute larval cyathostominosis are unknown. Investigation of these factors could lead to novel treatment and prevention strategies.

Objectives

To investigate clinicopathological and faecal microbiota changes associated with disease in individual horses in an acute larval cyathostominosis outbreak.

Study design

Case series.

Methods

The study population was a herd of 23 mixed breed horses in Ireland. The outbreak occurred in November 2018. Fourteen horses were clinically affected. Clinical status was monitored and recorded. Blood and faecal sampling allowed clinicopathological, faecal 16s rRNA gene sequencing and faecal egg count analyses.

Results

Two horses were euthanised, whilst 12 recovered. Common clinical signs included loose faecal consistency, weight loss and pyrexia. Consistent clinicopathological findings were borderline anaemia, leucocytosis, thrombocytosis, hyperfibrinogenaemia, hyperglobulinaemia and a reverse A: G ratio. Decreased alpha‐diversity of the faecal microbiota and greater relative abundance of the genus Streptococcus, class Bacilli, order Lactobacillales and family Streptococcaceae, and family Prevotelleceae was found in clinically affected horses compared to their clinically normal cohorts. An increase in obligate fibrolytic bacteria was seen in the clinically normal group compared to the clinical group. Histopathological findings of the colon and caecum revealed a severe necrotising typhlocolitis associated with cyathostomin larvae and bacterial overgrowth in the mucosa of the large intestine.

Main limitations

The study population in this outbreak is small. There are several confounding factors limiting this to a descriptive case series. Faecal microbiota has been shown to reflect the large intestinal microbiota but do not represent changes directly.

Conclusions

These findings suggest that acute larval cyathostominosis is associated with dysbiosis of the gut microbiota as well as the inflammatory stimulus of numerous emerging larvae leading to structural and functional pathology of the large intestine.

Association of Habitual Dietary Fiber Intake and Fecal Microbiome Gene Abundance with Gastrointestinal Symptoms in an Irritable Bowel Syndrome Cohort

Objectives

Dietary fibre supplementation is recognised as important for functional gastrointestinal disorders (FGID). The exact role of the microbiome in this relationship remains unclear. We explored differences in dietary fibre intake, GI symptoms and the fecal microbiome in those with FGID.

Methods

The COMFORT cohort is an observational case control study examining FGID, particularly irritable bowel syndrome (IBS) aetiology (Ethics 16/NTA/21). Participants prospectively completed a food and GI symptoms diary over 3 days. Severity of GI symptoms and mood disorders were assessed using clinical questionnaires; SAGIS and PROMIS for GI symptoms and HADS for anxiety and depression. Fecal samples were analysed by shotgun sequencing; 95 healthy controls (HC), 22 constipation IBS (IBS-C) and 50 diarrhea IBS (IBS-D). Taxonomic classifications were assigned by aligning sequences against the NCBI non-redundant database using DIAMOND.

Results

Diet diaries were completed by 292 participants (176 cases, 71.2% female). Average daily fibre intake was higher in HC compared to FGID (23.99g, 95% CI = –2.06-0.55; 20.28g, 95% CI = -1.96-0.45; P &lt; 0.05). Low fibre daily intake (&lt; 15g) was associated with higher depression scores (P &lt; 0.05) and increased anxiety in those with functional diarrhea (r2 = -0.554, P = 0.03). A negative association between fibre consumption and increased bloating in IBS (r2 = -0.19, P = 0.04) was also found. The GI microbiome in IBS was characterised by differences in Firmicutes belonging to the Lachnospiraceae family (e.g., Blautia and Ruminococcus, P &lt; 0.05). Other differentiating taxa included Bilophila (higher in IBS-D) and Methanobrevibacter (lower in IBS-D) (P &lt; 0.05). At the phylum level, bloating and constipation were correlated with Firmicutes relative abundance, and negatively correlated with Bacteroides (canonical r &gt; |0.5|). At the genus level, Blautia were correlated with diarrhea and faecal incontinence (canonical r &gt; 0.5).

Conclusions

Higher fibre consumption was associated with decreased bloating, anxiety and depression in different FGID subgroups. IBS was also associated with altered fecal microbiome composition including some taxa linked to carbohydrate and hydrogen metabolism.

Funding Sources

Funded by the Ministry of Business, Innovation and Employment through the High-Value Nutrition National Science Challenge.

A rapid viability and drug-susceptibility assay utilizing mycobacteriophage as an indicator of drug susceptibilities of Anti-TB drugs against Mycobacterium smegmatis mc2 155

Background

A rapid in-house TM4 mycobacteriophage-based assay, to identify multidrug resistance against various anti-tuberculosis drugs, using the fast-growing Mycobacterium smegmatis mc² 155 in a microtiter plate format was evaluated, based on phage viability assays.

Methods

A variety of parameters were optimized before the study including the minimum incubation time for the drugs, phage and M. smegmatis mc² 155 to be in contact. An increase in phage numbers over 2 h was indicative that M. smegmatis mc² 155 is resistant to the drugs under investigation, however when phage numbers remained static, M. smegmatis mc² 155 found to be sensitive to the drug.

Results

The study confirmed that the data are statistically significant and that M. smegmatis mc² 155 is, in fact, sensitive to isonazid, iifampicin, pyranzaimide, and ethambutol as phage numbers doubled over 2 h (P = 0.015, 0.018, 0.014, and 0.020). The study also confirmed that M. smegmatis mc² 155 is resistant to the drugs ampicillin, erythromycin, amoxicillin streptomycin as phage numbers remain static over the same 2 h period (P = 0.028, 0.052, 0.049, and 0.04). This drug-susceptibility profiling of eight different drugs against M. smegmatis mc² 155 was detected in as little as 1½ days with a cost of ~ one euro and fifteen cent to test four drugs.

Conclusion

This test is rapid to perform and will have widespread applications in drug-susceptibility testing of other members of the mycobacterial genus. In addition, the platform could also be used as a tool for high-throughput screening of novel antimycobacterial drugs. The main assets of this assay include its relatively cheap cost, versatility, and quick turnaround time.

306 The Changing Face of Stroke in the DOAC Era

Background

Patients prescribed oral anticoagulants (OAC) for atrial fibrillation (AF) can still present with stroke. The mechanism for stroke in these patients can be due to multiple factors including subtherapeutic dosing and non-compliance. With the increasing use of direct-acting OACs (DOACs) in favour of warfarin, it is unclear if the incidence of stroke in those already taking OAC has reduced.

Methods

Data was extracted from our unit’s stroke registry, a prospectively maintained database, for patients who presented with stroke while receiving OAC for AF from 2013 to 2017. Type of OAC, type of stroke, OAC dosing at time of event including non-compliance, stroke management and outcome were recorded.

Results

67 patients were included for analysis, with 55 ischaemic and 12 haemorrhagic strokes. 52 patients were receiving warfarin at the time of their stroke vs. 15 receiving DOACs. 33/55 (60%) of ischaemic strokes occurred in patients taking warfarin with a sub-therapeutic INR. In 3/55 (5%) of ischaemic strokes, the OAC was held for a procedure while in 6/55 cases (11%) the OAC had been stopped for another reasons e.g. bleeding. 5/55 (7%) were due to non-compliance. 1 ischaemic stroke was due to under-dosing of a DOAC (dabigatran). 16 strokes were recorded in 2013 for patients prescribed OAC vs. 3 in 2017. Overall the number of ischaemic strokes due to subtherapeutic OAC decreased from 14 in 2013 to 1 in 2017 (p value 0.06).

Conclusion

The majority of strokes occurring in anticoagulated patients are related to warfarin use. We observed an almost significant reduction in the proportion of ischaemic strokes due to under-dosing of OAC over the study period. Warfarin continues to be recommended as the first line anticoagulant for stroke prevention in atrial fibrillation by the HSE Medicines Management Programme, a decision which we would argue warrants review.

The Microbiome in Functional Gastrointestinal Disorders Is Characterized by Bacteria and Genes Involved in Carbohydrate and Bile Acid Metabolism (OR23-01-19)

Objectives

Irritable Bowel Syndrome (IBS) is a functional gastrointestinal (GI) disorder featuring chronic or recurrent abdominal discomfort, usually with changes in GI habit. To improve our understanding of links between the microbiome and IBS, and how these links can be manipulated through diet, we undertook shotgun metagenomic sequencing of fecal samples from a case-control study.

Methods

Fecal samples from 172 individuals were analyzed by shotgun sequencing using the Illumina NextSeq platform. Of these, 77 were classified as controls, 16 were constipation-predominant IBS (IBS-C), 39 were diarrhea-predominant IBS (IBS-D), 29 were diagnosed with functional constipation (FC), and 11 had functional diarrhea (FD). Taxonomic classifications were determined using Metaxa2 and the SILVA 128 database. Gene functions were assigned by alignment of sequences against a protein reference database using DIAMOND. Mean relative abundance of bacterial taxa and functional genes were compared using permutation ANOVA. Ethical approval was obtained from the University of Otago Human Ethics Committee (Health) (Reference H16/094).

Results

Bacterial genera that discriminated case-controls (P < 0.05) from those with constipation (IBS-C + FC) and diarrhea (IBS-D + FD) included Megasphaera (increased in those with constipation), Blautia (increased in those with diarrhea), and Bilophila (increased in both constipation and diarrhea groups). Megasphaera and Blautia include bacteria that are bile-resistant and produce butyrate, possessing a wide range of Carbohydrate-Active enzymes. Bilophila are sulfite-reducing bacteria that are able to utilize bile-acids. Associated with these taxonomic differences, a wide range of genes involved in carbohydrate, energy, and amino acid metabolism differed significantly (P < 0.05), including some involved in taurine and glycine metabolism. Bile acids are conjugated with taurine or glycine in the liver, and these amino acids are removed by the action of members of the GI microbiota.

Conclusions

Results from our study suggest carbohydrate and bile acid metabolism by the GI microbiome may be important distinguishing characteristics in functional GI disorders.

Funding Sources

Funded by the New Zealand National Science Challenge High-Value Nutrition program.

Four men in a boat: Ultra-endurance exercise alters the gut microbiome

OBJECTIVES

Compositional and functional adaptions occur in the gut microbiome in response to habitual physical activity. The response of the gut microbiome to sustained, intense exercise in previously active individuals, however, is unknown. This study aimed to prospectively explore the gut microbiome response of four well-trained male athletes to prolonged, high intensity trans-oceanic rowing, describing changes in microbial diversity, abundance and metabolic capacity.

DESIGN

A prospective, repeated-measures, within-subject report.

METHODS

Serial stool samples were obtained from four male athletes for metagenomic whole-genome shotgun sequencing to record microbial community structure and relevant functional gene profiles before, during and after a continuous, unsupported 33-day, 5000 km transoceanic rowing race. Calorific intake and macronutrient composition were recorded by validated food frequency questionnaire and anthropometry was determined by body composition analysis and cardiorespiratory testing.

RESULTS

Microbial diversity increased throughout the ultra-endurance event. Variations in taxonomic composition included increased abundance of butyrate producing species and species associated with improved metabolic health, including improved insulin sensitivity. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Many of the adaptions in microbial community structure and metaproteomics persisted at three months follow up.

CONCLUSIONS

These findings demonstrate that prolonged, intense exercise positively influences gut microbial diversity, increases the relative abundance of some bacterial species and up-regulates the metabolic potential of specific pathways expressing microbial gene products. These adaptions may play a compensatory role in controlling the physiological stress associated with sustained exertion as well as negating the deleterious consequences accompanying endurance exercise.

Removal of adult cyathostomins alters faecal microbiota and promotes an inflammatory phenotype in horses

The interactions between parasitic helminths and gut microbiota are considered to be an important, although as yet incompletely understood, factor in the regulation of immunity, inflammation and a range of diseases. Infection with intestinal helminths is ubiquitous in grazing horses, with cyathostomins (about 50 species of which are recorded) predominating. Consequences of infection include both chronic effects, and an acute inflammatory syndrome, acute larval cyathostominosis, which sometimes follows removal of adult helminths by administration of anthelmintic drugs. The presence of cyathostomins as a resident helminth population of the equine gut (the "helminthome") provides an opportunity to investigate the effect helminth infection, and its perturbation, has on both the immune system and bacterial microbiome of the gut, as well as to determine the specific mechanisms of pathophysiology involved in equine acute larval cyathostominosis. We studied changes in the faecal microbiota of two groups of horses following treatment with anthelmintics (fenbendazole or moxidectin). We found decreases in both alpha diversity and beta diversity of the faecal microbiota at Day 7 post-treatment, which were reversed by Day 14. These changes were accompanied by increases in inflammatory biomarkers. The general pattern of faecal microbiota detected was similar to that seen in the relatively few equine gut microbiome studies reported to date. We conclude that interplay between resident cyathostomin populations and the bacterial microbiota of the equine large intestine is important in maintaining homeostasis and that disturbance of this ecology can lead to gut dysbiosis and play a role in the aetiology of inflammatory conditions in the horse, including acute larval cyathostominosis.

The Research, Advising, and Mentoring Professional: A Unique Approach to Supporting Underrepresented Students in Biomedical Research

As a pilot intervention strategy to support undergraduate students, especially rural and Alaska Native students who are pursuing biomedical science research and career trajectories, we have developed a unique, mid-level Research, Advising, and Mentoring Professional (RAMP) position. In this article we outline the reasons for creating this position, RAMP qualifications, training, duties, and differences between RAMP and other positions typically found in higher education. Additionally, we discuss the evolution of the position and why it may be of interest to other institutions as they address similar issues involving students from underrepresented groups. Preliminary survey and focus group data from students mentored directly by RAMPs indicated that the holistic advising approach of RAMPs has had a positive impact on student experiences by supporting persistence in degree programs and providing psychosocial support of both personal and professional development.

A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid

The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.

Abstract P1-09-18: A clinically validated DNA microarray for high-resolution HER2 testing defines a new genomic subtype in high-risk breast cancer with equivocal results by IHC and FISH

Background: In all stages of breast cancer, the HER2 status of a patient's tumor is critically important as both a prognostic indicator, and for predicting response to targeted anti-HER2 therapies. CAP/ASCO 2013 guidelines recommend that newly diagnosed, recurrent, and metastatic breast tumors be evaluated for HER2 positivity by protein-based immunohistochemistry (IHC) and/or chromosome-based fluorescence in situ hybridization (FISH). In the majority of cases, these testing modalities provide a clearly actionable “positive” or “negative” answer. However, in an estimated 10- to 20% of breast cancers, both tests are reported as “equivocal” leaving the clinician with a treatment decision dilemma and no definitive alternative testing method. Here we report validation of an IHC-targeted DNA microarray comparative genomic hybridization (array CGH) assay for HER2 equivocal breast cancer, and definition of a new genomic subtype of HER2 status in high-risk breast cancer with equivocal IHC and FISH results.

Methods: IHC-targeted HER2 receptor “hot spot” DNA samples extracted from 25 formalin fixed paraffin embedded (FFPE) breast tumor tissue samples previously characterized by IHC and FISH, were analyzed by array CGH. Eight tumors were known to be highly HER2 positive, seven tumors had IHC scores of 0 with negative FISH, and ten tumors had HER2 receptor staining by IHC (1-2+) and equivocal results by FISH (4-6 HER2 gene copies.) Tumor DNA (test) and human genomic DNA (reference) were fluorescently labeled, and competitively hybridized to a custom-designed genomic DNA microarray with high-density probe coverage of the HER2 amplicon on chromosome 17 (Agilent Technologies, Santa Clara CA). The array design includes over 4,600 chromosome 17 probes representing the p arm, q arm, telomeric and centromeric regions with 66 tiling probes over the HER2 (ERBB2) gene. Following hybridization, average HER2 gene copy number was calculated for each tumor sample by converting mean log2 signal intensity ratio value into genomic region copy number adjusted for % clonal fraction and experimentally established log2 ratio compression of the assay.

Results: 25/25 (100%) of samples yielded adequate DNA for analysis and all highly HER2 positive and HER2 negative results were confirmed by array CGH. In 10/10 IHC equivocal cases with HER2 gene copy number 4-6 by FISH, CGH results confirmed HER2-Low gene copy number.

Results for 25 Validation SamplesNumber of CasesIHC ScoreFISHCGH Copy NumberResult83+Positive&gt; 6HER2-Positive101-2+Equivocal4-6HER2-Low70Negative&lt; 6HER2-Negative

Conclusions: High-resolution HER2 testing by IHC-targeted DNA microarray analysis accurately classifies HER2 status in breast cancer and better defines the HER2-Low genomic subtype most often called “equivocal” by standard IHC and FISH testing. This subcategory is characterized at the protein level by IHC evidence of anti-HER2 therapy target receptor expression on the surface of the cells, and at the genomic level by HER2 gene copy number &lt; 6. Results of the NSABP-B47 clinical trial and further studies with larger numbers of HER2-Low patients are needed to determine if these patients benefit from anti-HER2 therapy.

Citation Format: Gunn S, Yaziji H, Sims C, Govender S, Moore M, Cotter P, Jones S. A clinically validated DNA microarray for high-resolution HER2 testing defines a new genomic subtype in high-risk breast cancer with equivocal results by IHC and FISH [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-09-18.

Dietary threonine response of Pekin ducks from hatch to 14 d of age based on performance, serology, and intestinal mucin secretion

Two experiments were conducted to determine the dietary threonine (Thr) requirement of Pekin ducks from hatch to 14 d of age. In experiment 1, practical corn-soybean meal diets were formulated to contain 0.78, 0.84, 0.90, 0.96, and 1.02% Thr (0.74, 0.83, 0.88, 0.92, and 1.00% Thr on an analyzed basis). In experiment 2, corn-soybean meal diets supplemented with 11 crystalline amino acids were formulated to contain 0.60, 0.70, 0.80, 0.90, 1.00, and 1.10% Thr (0.60, 0.75, 0.89, 0.95, 1.01, and 1.09% Thr on an analyzed basis). In both experiments, diets were fed to 8 replicate cages with 6 male ducks per cage. Body weight and feed intake from each cage were recorded weekly. At 14 d of age, breast meat, ileal digesta, and serum were collected to determine breast meat yield, mucin secretion, and serology parameters. In both studies, the estimated Thr requirement (expressed as % dietary Thr basis) for 14 d BW and BW gain (BWG) by quadratic broken-line (QBL) regression were similar, which were 0.87 and 0.86%, respectively. Additional measures in both experiments resulted in Thr requirements via QBL regression in rank order of crude mucin secretion < breast meat yield < serum immune activity. Summing up the estimates from both studies, the Thr requirement ranged from a low of 0.81% to maximize feed intake (FI) to a high of 1.00% to maximize serum Rb L100 by QBL regression. Correspondingly, the Thr requirement varied between a low of 0.90% to maximize crude mucin secretion on a dry matter intake (DMI) basis and a high of 0.98% to maximize feed-to-gain when using quadratic regression.

N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota

Background

Early life stress is a risk factor for many psychiatric disorders ranging from depression to anxiety. Stress, especially during early life, can induce dysbiosis in the gut microbiota, the key modulators of the bidirectional signalling pathways in the gut-brain axis that underline several neurodevelopmental and psychiatric disorders. Despite their critical role in the development and function of the central nervous system, the effect of n-3 polyunsaturated fatty acids (n-3 PUFAs) on the regulation of gut-microbiota in early-life stress has not been explored.

Methods and Results

Here, we show that long-term supplementation of eicosapentaenoic acid (EPA)/docosahexaenoic acid (DHA) (80% EPA, 20% DHA) n-3 PUFAs mixture could restore the disturbed gut-microbiota composition of maternally separated (MS) female rats. Sprague-Dawley female rats were subjected to an early-life stress, maternal separation procedure from postnatal days 2 to 12. Non-separated (NS) and MS rats were administered saline, EPA/DHA 0.4 g/kg/day or EPA/DHA 1 g/kg/day, respectively. Analysis of the gut microbiota in adult rats revealed that EPA/DHA changes composition in the MS, and to a lesser extent the NS rats, and was associated with attenuation of the corticosterone response to acute stress.

Conclusions

In conclusion, EPA/DHA intervention alters the gut microbiota composition of both neurodevelopmentally normal and early-life stressed animals. This study offers insights into the interaction between n-3 PUFAs and gut microbes, which may play an important role in advancing our understanding of disorders of mood and cognitive functioning, such as anxiety and depression.

Victimisation and psychosocial difficulties associated with sexual orientation concerns: a school-based study of adolescents

This study examined victimisation, substance misuse, relationships, sexual activity, mental health difficulties and suicidal behaviour among adolescents with sexual orientation concerns in comparison to those without such concerns. 1112 Irish students (mean age 14 yrs) in 17 mixed-gender secondary schools completed a self-report questionnaire with standardised scales and measures of psychosocial difficulties. 58 students (5%) reported having concerns regarding their sexual orientation. Compared with their peers, they had higher levels of mental health difficulties and a markedly-increased prevalence of attempted suicide (29% vs. 2%), physical assault (40% vs. 8%), sexual assault (16%vs. 1%) and substance misuse. Almost all those (90%) with sexual orientation concerns reported having had sex compared to just 4% of their peers. These results highlight the significant difficulties associated with sexual orientation concerns in adolescents in Ireland. Early and targeted interventions are essential to address their needs.

Mechanisms of donor-specific tolerance in recipients of haploidentical combined bone marrow/kidney transplantation

We recently reported long-term organ allograft survival without ongoing immunosuppression in four of five patients receiving combined kidney and bone marrow transplantation from haploidentical donors following nonmyeloablative conditioning. In vitro assays up to 18 months revealed donor-specific unresponsiveness. We now demonstrate that T cell recovery is gradual and is characterized by memory-type cell predominance and an increased proportion of CD4⁺ CD25⁺ CD127⁻ FOXP3⁺ Treg during the lymphopenic period. Complete donor-specific unresponsiveness in proliferative and cytotoxic assays, and in limiting dilution analyses of IL-2-producing and cytotoxic cells, developed and persisted for the 3-year follow-up in all patients, and extended to donor renal tubular epithelial cells. Assays in two of four patients were consistent with a role for a suppressive tolerance mechanism at 6 months to 1 year, but later (≥ 18 months) studies on all four patients provided no evidence for a suppressive mechanism. Our studies demonstrate, for the first time, long-term, systemic donor-specific unresponsiveness in patients with HLA-mismatched allograft tolerance. While regulatory cells may play an early role, long-term tolerance appears to be maintained by a deletion or anergy mechanism.

ARHGEF9 disruption in a female patient is associated with X linked mental retardation and sensory hyperarousal

We identified a female patient with mental retardation and sensory hyperarousal. She has a de novo paracentric inversion of one X chromosome with completely skewed inactivation of the normal X chromosome. We aimed to identify whether a single gene or gene region caused her cognitive and behavioural impairment and that of others. Fluorescent in situ hybridisation (FISH) showed that the centromeric breakpoint disrupts a single gene: ARHGEF9 (CDC42 guanine nucleotide exchange factor (GEF) 9). We also found that the levels of the ARHGEF9 transcript from the patient are 10-fold less than those found in control samples. ARHGEF9 encodes a RhoGEF family protein: collybistin (hPEM), which is highly expressed in the brain. Collybistin can regulate actin cytoskeletal dynamics and may also modulate GABAergic and glycinergic neurotransmission through binding of a scaffolding protein, gephyrin, at the synapse. This potential dual role may explain both the mental retardation and hyperarousal observed in our patient.

ARHGEF9 disruption in a female patient is associated with X linked mental retardation and sensory hyperarousal

INTRODUCTION

We identified a female patient with mental retardation and sensory hyperarousal. She has a de novo paracentric inversion of one X chromosome with completely skewed inactivation of the normal X chromosome.

OBJECTIVE

We aimed to identify whether a single gene or gene region caused her cognitive and behavioural impairment and that of others.

RESULTS

Fluorescent in situ hybridisation (FISH) showed that the centromeric breakpoint disrupts a single gene: ARHGEF9 (CDC42 guanine nucleotide exchange factor (GEF) 9). The telomeric break lies in a gene poor region. We also found that the levels of the ARHGEF9 transcript from the patient are 10-fold less than those found in control samples. Consequently, we sequenced the coding exons and intron/exon borders of the ARHGEF9 gene in 99 probands from families with X linked mental retardation (XLMR) and 477 mentally retarded males in whom a diagnosis of Fragile X syndrome had been excluded. We did not identify any pathogenic changes; however, we did identify intronic nucleotide changes that might alter splicing.

CONCLUSION

ARHGEF9 encodes a RhoGEF family protein: collybistin (hPEM), which is highly expressed in the developing and adult brain. Collybistin can regulate actin cytoskeletal dynamics and may also modulate GABAergic and glycinergic neurotransmission through binding of a scaffolding protein, gephyrin, at the synapse. This potential dual role may explain both the mental retardation and hyperarousal observed in our patient. While ARHGEF9 appears to be an uncommon cause of mental retardation in males, it should be considered in patients with mental retardation and sensory hyperarousal.

Causes of the acute abdomen: add thrombophilia to your list

A47-year-old male was admitted with a 2-week history of periumbilical discomfort. For 48 hours before admission, the patient suffered from associated vomiting and anorexia. Upon admission the abdominal pain had become more severe and began to radiate to both flanks.

His past medical history included a deep vein thrombosis 18 months previously. He was taking Tegretol for epilepsy (seizure free for many years) and regular inhalers for asthma. He had no recent episode of prolonged immobility. He was a non-smoker and did not drink alcohol.

On examination, he was obese (96 kg). He had a low grade pyrexia with a sinus tachycardia (120 beats per minute). He was normotensive. Abdominal examination revealed tenderness over the umbilical and epigastric areas. At this stage, there was no evidence of guarding or rigidity and bowel sounds were present.

Investigations including serum bioprofile, amylase, coagulation screen, chest X-ray, plain film of abdomen and ultrasound of abdomen were all reported as normal. Full blood count revealed a moderate leucocytosis (13.2 × 109/litre).

At this stage he was managed conservatively with intravenous fluids and antibiotics. However, over the next 12 hours, the patient's condition deteriorated and he developed diffuse peritonism with guarding and rebound tenderness. He was prepared for theatre. Laparoscopy demonstrated haemosanguinous fluid and gangrenous loops of small bowel. Laparotomy confirmed the presence of a 24” gangrenous segment of distal jejenum and proximal ileum. Perioperatively, this segment was noted to have good arterial pulsation with obvious clot in the venous arcades. Formal resection with end to end anastomosis was completed. Postoperative recovery was uneventful. After surgery he was anticoagulated with unfractionated heparin.

Histology confirmed mesenteric venous infarction. In view of the past history of deep vein thrombosis, a thrombophilia screen was performed. Our patient was heterozygous positive for the factor V leiden mutation. He was anticoagulated and discharged on warfarin indefinitely (under ongoing review).

Effects of nicotine and amphetamine on latent inhibition in human subjects

Latent inhibition (LI) is a phenomenon in which repeated non-reinforced exposure to a stimulus retards subsequent conditioning to that stimulus; it reflects a process whereby irrelevant stimuli become ignored, and has been the subject of study concerning attentional abnormalities in schizophrenia. Low doses of the indirect dopamine (DA) agonists, amphetamine and nicotine, disrupt LI in the rat. These drugs are believed to disrupt LI via DA release in the nucleus accumbens; LI in amphetamine- and nicotine-treated rats is reinstated by administration of the DA antagonist haloperidol. In human subjects, low doses of amphetamine abolish LI, and more recently haloperidol has been shown to potentiate LI. The present study investigated the effects of nicotine on LI in human subjects, and also attempted to replicate the abolition of LI by amphetamine. Nicotine failed to affect LI when administered either subcutaneously or by cigarette smoking. LI was, however, abolished in a group of subjects given 5 mg amphetamine 90 min before testing. Supplementary analyses of the data pooled from all three experiments showed that, in contrast to an earlier report, LI was no weaker in smokers than in nonsmokers.

Effect of clonidine on the human acoustic startle reflex

The present study investigated in healthy human volunteers whether clonidine reduced the amplitude of the acoustic startle reflex and whether this effect, if found, was due to an accelerated rate of habituation. Subjects were presented with startle-eliciting noise-bursts after intravenous (iv) infusion of clonidine (1.5 microgram/kg) and saline on separate days. Clonidine significantly reduced the amplitude of the acoustic startle reflex (as indexed by the eyeblink component) relative to the saline treated condition. This effect was neither due to an accelerated rate of habituation of the startle reflex nor to the sedative effect of clonidine. These findings complement an earlier report (Morgan et al. 1993) that yohimbine augments the amplitude of the startle reflex in man. Taken together, the two reports indicate a new model for the clinical investigation of central alpha2 adrenoceptor function in humans.

Effect of cell growth rate on expression of the anaerobic respiratory pathway operons frdABCD, dmsABC, and narGHJI of Escherichia coli

The fumarate reductase (frdABCD), dimethyl sulfoxide (DMSO)-trimethylamine-N-oxide (TMAO) reductase (dmsABC), and nitrate reductase (narGHJI) operons in Escherichia coli encode enzymes involved in anaerobic respiration to the electron acceptors fumarate, DMSO or TMAO, and nitrate, respectively. They are regulated in response to anaerobiosis and nitrate availability. To determine how each operon is regulated in response to changes in cell growth rate and in oxygen availability, expression of frdA-lacZ, dmsA-lacZ, and narG-lacZ fusion genes was examined during continuous culture. After a change in the cell growth rate, each anaerobic electron transport pathway operon fusion responded somewhat differently. Whereas frdA-lacZ expression increased by fivefold as the growth rate decreased from 0.60 to 0.12/hour during aerobic growth, little change was seen under anaerobic conditions. In contrast, growth rate-dependent expression of narG-lacZ expression occurred under anaerobic conditions but not under aerobic conditions. Finally, dmsA-lacZ expression did not vary greatly for any of the growth rates tested. When cells were shifted from aerobic to anaerobic growth conditions, expression of each fusion increased at a moderate rate and peaked or "overshot" before reaching a new equilibrium value. This "overshoot" phenomenon was independent of the fnr gene product, which functions as a transcriptional activator of each respiratory operon during anaerobic conditions. In contrast to the moderate rate of anaerobic induction seen for narG-lacZ expression, the addition of nitrate caused a rapid induction response. The cell appears to have many ways to adjust cell respiration in response to changes in cell growth conditions.

Attempted homicide in hospital

Strychnine poisoning is reported in a patient who was the victim of attempted homicide in his home and in a General hospital. The diagnosis proved to be an elusive one over five months. The question of a primary psychiatric diagnosis, raised by the patient's wife proved to be an attempt by her to cover her crime. Medico-legal issues relating to the management of attempted homicide in hospital are discussed.