APEX

Duration Of The Fellowship

The total duration of each fellowship is two years, commencing October 2018 (Call 1) and October 2019 (Call 2).

Eligibility Criteria

To be considered eligible, applicants must fulfill the following criteria:

• Applicants may be of any nationality
• Applicants must be fluent in English (written and spoken)
• Applicants must be Experienced Researchers
  • An experienced researcher must at the application deadline be in possession of a doctoral degree or have at least four years of full-time equivalent research experience in academia or industry. Full-Time Equivalent Research Experience is measured from the date when a researcher obtained the degree entitling him or her to embark on a doctorate, either in the country in which the degree was obtained or in the country in which the researcher is recruited, even if a doctorate was never started or envisaged.

• Mobility Requirements: International mobility is a core element of the APEX programme.
  • Applicants must be incoming fellows to Ireland and fulfill the mobility requirements:
    • Applicants may not have resided or carried out their main activity (work, study) in the Republic of Ireland for more than 12 months in the 3 years prior to the Call deadline.
    • For Career Restart and Reintegration: Applicants may not have resided or carried out their main activity in the Republic of Ireland for more than 3 years in the 5 years immediately prior to the call deadline.

• Secondment Eligibility
  • Eligible secondment hosts are research performing non-academic organisations located anywhere in the world.
  • Secondments must be 3 to 6 months in duration and can be a single period or split into short stays.
  • Secondments must be relevant to the fellow’s project and career development.

Project Eligibility

Proposals must describe a research project to be implemented during a 2-year period

Adhere to the ethical standards as stated in the programme documentation

Include a secondment in the non-academic sector

The topic must fall within the broad APC research themes

• Microbes to Molecules
• Diet and Microbes at the Extremes of Life
• Brain-Gut-Microbiota Axis
• Host-Microbe Dialogue

Industry Secondment

• Secondments must be 3 to 6 months in duration and can be a single period or split into short stays
• Eligible secondment hosts are research performing non-academic organisations located anywhere in the world
• The proposed academic supervisor will assist applicants to secure a high-quality secondment host
• Secondments must be relevant to the fellow’s project and career development
• A mandatory letter of commitment from the secondment host and capacity of secondment organisation table must be obtained within 6 months of starting their fellowship

Application Process Steps

Applicants are encouraged to start the process of preparing their application as early as possible

• Step 1: Read the APEX Application Guidelines carefully.
• Step 2: Check your eligibility
  • Ensure that you have the necessary research experience and that you do comply with the programme’s mobility requirements.
• Step 3: Expression of Interest
  • Complete the APEx Expression of Interest Form and send to the APEX Programme Manager APEX@ucc.ie.
• Step 4: Identify a potential host supervisor from the academic supervisors listed on this website.
  • Identify a potential host supervisor from the academic supervisors listed on this website.You should work with the supervisor of your choosing to develop your project proposal. Following submission, a letter of support from the host supervisor is required in order for your proposal to progress to peer-review. Applications without such support will not be considered.
• Step 4: Prepare your research project proposal
  • Ensure that your proposal complies with the necessary requirements. Use the Application Templates provided in the APEX Application Guidelines.
• Step 5: Submit your application
  • Submit all required documentation by email to APEX@ucc.ie before the call deadline.

Queries will be accepted up to 17 April 2019

Post Application Stage

All applications will go through an evaluation and selection process prior to final funding decision.

• Eligibility check
• International peer review
• Interview process

Guidelines

• Call 2 APEX Application Guidelines 
• Call 2 APEX Terms and Conditions
• Call 2 APEX Code of Conduct and Declaration of Conflict of Interest

Templates

APEX Application Form Template (Parts A-D)

The Application Templates consists of:

Part A

• 1. General Information: Administrative information on the project, academic supervisor and host institution.
• 2. Abstract. Applicants must indicate: a project thematic area, up to 5 keywords, and provide a 2000 character proposal summary.
• 3. Evidence of eligibility to the APEX programme (details on qualifications and evidence of compliance with the programme’s mobility requirements).
• 4. Ethics issues table.

Part B

• Project proposal (maximum 10 pages)

Part C

• Applicant’s Curriculum Vitae (maximum 5 pages)

Part D

• Ethics Self-Assessment

Applicants, who in “Part A – Ethics Issues Table” indicate that ethical issues are associated with their research, are required to provide additional information. Applicants must complete and  submit an “ Ethics Self-Assessment” document.

Please refer to the Horizon 2020 Guidance on Ethics Self-Assessment H2020 ethics-self-assessment

Other documents required

• Letter of commitment from the academic supervisors.
• Letter of commitment from secondment host. A mandatory letter of commitment from the secondment host must be obtained within 6 months of starting his/her fellowship.

Proposals must respect the following minimum standards

• A minimum font size of 11 points, except for the Gantt chart and tables where the minimum font size is 8 points · single line spacing · A4 page size · margins (top, bottom, left, right) of at least 15 mm (not including any footers or headers) · a clearly readable font (e.g. Arial or Times New Roman). Literature references should be placed as footnotes at the bottom of the page in which they are mentioned, in font 8 or 9. They also count toward the page limit.

Submitting your Application

• Applications must be submitted in ‘pdf format’, to the APEX email address APEX@ucc.ie
• Please use subject heading: Call 2
• Fully completed applications must be received on or before the call deadline (23 April 2019)
• The application system will close at 1pm (Irish time) on the submission date. Applications cannot be accepted after this date
• Applicants will receive acknowledgement of receipt of the submitted proposal
• All applications must be complete and in English
• All applications must have confirmed support of the proposed academic supervisor
• One application per call may be submitted
• The application document templates must be used
• Researchers at risk, who might not be able to submit an application in the aforementioned manner, should contact the APEX programme manager APEX@ucc.ie to discuss an alternative submission arrangement

UCC encourage the submission of applications well in advance of the closing date for the competition.

Microbes To Molecules

Pharmabiotics are any biological entity ‘mined’ from the gastrointestinal microbiota, including probiotics, bacteriocins, bacteriophages and bioactive molecules, and these are at the heart of the “Microbes to Molecules” theme. We believe that pharmabiotics will make significant impacts in the pharmaceutical, medical food and functional food sectors. For example, the current threat posed by multi-drug resistant bacteria is a major challenge. The APC Microbiome Institute has discovered, patented and licenced a narrow spectrum antimicrobial highly active against Clostridium difficile, while bacteriophages active against Pseudomonas aeruginosahave also been patented. We have also patented antimicrobial technologies for the animal husbandry sector against Salmonella and mastitis.

The APC has discovered, patented and licenced a narrow spectrum antimicrobial highly active against Clostridium difficile, while bacteriophages active against Pseudomonas aeruginosa have also been patented. Outputs from this theme will include new anti-inflammatory and anti-infective therapeutics. We will also develop functional ingredients for the food sector and will assist food companies to provide sufficient scientific and clinical validation to address health claim requirements of EFSA and other regulatory bodies.

Research Supervisors

• Professor Colin Hill
• Professor Paul Ross
• Professor Douwe VanSinderen

Diet & Microbes At The Extremes Of Life

The interaction between diet, the microbiota and health at the extremes of life – infants and older people – is the main topic of this research theme, with a unifying emphasis on nutrition, cognition and inflammatory disease. In infants and older people, the gut microbiota is in a state of flux, so these are particularly relevant life-stages in which to modulate the microbiota in a health-promoting direction.

Outputs will include new food ingredients for infant formula and for the elderly in addition to dietary advice for infants and elderly to address issues and conditions that are typically associated with these extremes of life. We will also develop biomarkers of microbiota alteration and metabolite depletion, both of which point to consequent risk for a reduced health status which can profoundly influence how individuals are medically treated and managed.

Research Supervisors

• Dr Paul Cotter
• Dr Jens Walter
• Professor Paul O’Toole
• Professor Catherine Stanton

Brain-Gut-Microbe Axis

This APC theme addresses the communication between the brain and gut and how it can be influenced by the gastrointestinal microbiota. This is an area of significance in infancy, where important links between diet, microbes and cognition are established. The influence of the microbiota on obesity and metabolic syndrome are also increasingly recognised. The APC Microbiome Institute has made significant contributions in this area, which represents a real opportunity for foods designed for cognition, infant brain development, functional gastrointestinal disorders and for healthy ageing, which are significant growth areas for healthcare and food companies. Microorganisms, or microbial components, have a role in either causing or preventing these conditions. A better understanding of the role of this axis in the stress response, and its links with other debilitating conditions, such as anxiety, stress, depression, autism spectrum disorders, obesity and IBS will provide new treatment and management strategies. These will represent opportunities for both the food ingredients business and the pharmaceutical industry.

Outputs from this theme will include new food ingredients or biotherapeutics which are designed to influence the microbiota in order to improve various aspects of mental health

Research Supervisors

• Dr Gerard Clarke
• Professor John Cryan
• Dr Cian McCafferty

Host–Microbe Dialogue

The APC’s Host-Microbe Dialogue theme explores the network of signalling interactions among the microbiota, host immune-inflammatory responses and metabolism and the impact of diet on each component of this triad. The gut microbiota influences human health and susceptibility to most common diseases, including immune-allergic, colon cancer and various metabolic diseases, such as obesity-related disorders, diabetes and cardiovascular disease. Each of these chronic disorders has an immune or inflammatory component, and indeed, the aging process itself, is associated with increases in low-grade inflammation (inflammageing). This low-grade inflammation, and the diseases associated with it, is a significant healthcare burden in developed countries, and represents a multi-billion € opportunity for companies in the food, pharmaceutical and diagnostic sectors.

The APC has built a global reputation in inflammatory diseases, particularly in functional gastrointestinal conditions, inflammatory bowel disease (IBD) and in inflammation of the aged. The challenge now is to develop outputs, such as new robust microbial and other biomarkers of disease risk and to manipulate disease risk by targeting the microbiota using designer foods and/or pharmabiotics. This is a strategically important area both in the context of the ageing population and evolving economic and public health policies.

Research Supervisors

• Dr Sinéad Corr
• Professor Noel Caplice
• Dr Marcus Claesson
• Dr David Clarke
• Professor Cormac Gahan
• Dr Liam Fanning
• Professor Liam O’Mahony
• Dr Susan Joyce
• Dr John MacSharry
• Dr Ken Nally
• Professor Mark Tangney

Eileen Ryan

• eileen.ryan@ucc.ie 

Research Title

IBD-ome: Unravelling the metabolic etiology of Inflammatory Bowel Disease (IBD) via lipidome, metabolome and microbiome multivariate analyses.

Project Background

Inflammatory bowel disease (IBD) is characterised by chronic intestinal inflammation that leads to diminished quality of life and sometimes to severe disability. Despite considerable suffering the exact cause of IBD is unknown. Besides genetic factors, IBD is associated with reduced gut microbial diversity and metabolic extremes indicating a role for diet, life style, host and microbial metabolism. Biological samples from male and female IBD sufferers and healthy controls have been bio-banked for analysis across the metabolic spectra (BMI ranges). Microbial and other biochemical analysis have been performed.

Project Aims

IBD-ome aims to examine the metabolic etiology of IBD, through a series of state-of-the-art lipidomic and metabolomic analysis. Using predetermined microbiome data, bioinformatics multivariate analysis will interrogate these data. The outcome from IBD-ome will be metabolic and microbial discrimination of the various forms and stages of IBD from the same patient cohort across the BMI ranges.

Mariana Perez Ibarreche

• mariana.perezibarreche@ucc.ie

Research Title

Inhibition of Pathogens Nisin resistant by nisin derivatives obtained by Bioengineering.

Project Summary

Antimicrobial resistance poses one of the biggest threats to global health today. According to the World Health Organization antibiotic resistance in the European Union alone, is estimated to cause 25,000 deaths and cost more than USD 1.5 billion every year in healthcare expenses and productivity losses. Without effective antibiotics for the prevention and treatment of infections, many of the achievements of modern medicine such as organ transplantations, chemotherapy and surgeries such as caesarean sections become much more dangerous. An alternative to this method would be to use antimicrobial compounds with a different mechanism of action than antibiotics to avoid the resistance developed by microorganisms. An alternative of that is the use of bacteriocins. Nisin is the most prominent member of bacteriocins and demonstrates significant potential as a clinical and food antimicrobial. However, some bacterial strains have been reported to be congenitally resistant to it. The last reported cases of nisin resistance were the identification of two-component systems (TCS) forming by two membrane associated proteases: nisin-resistant protein (NSR) and NsrFP (BceAB-type ABC transporter). NSR cleaves the last six amino acids of nisin resulting in nisin1-28, which has a 32-fold lower activity. This product of NSR (nisin1-28), is still recognized by NsrFP. The main objective of this work is to evaluate the inhibitory capacity of nisin derivatives on pathogens harboring NSR-like protein. Also, considering biofilm as the predominant form of growth of pathogens, the activity of nisin derived alone and in combination with other antimicrobial agents will be evaluated.

Carina Carbia Sinde

• carina.carbiasinde@ucc.ie

Research Title

Binge & Bugs. Gut Microbiota, Neuropsychology and young Binge Drinkers (MicroB&B)

Project Summary

Binge drinking (BD) is a prevalent pattern of alcohol consumption among young people, which has been associated with neuroanatomical impairments and neuropsychological deficits, as well as increased risk of developing psychopathology and addiction. BD alters immune and stress responses, which appears to contribute to the neurocognitive difficulties and the neurobiology of drinking escalation. This inflammatory cascade could be compatible with alterations in the gut-brain axis. MicroB&B is aimed at determining new biomarkers of dysfunction and their neurocognitive correlates in young BDs. Following a psychoneuroimmunology perspective, we will investigate the association between alterations in gut microbiota and neuropsychological functioning in BDs. This interdisciplinary approach has a clear impact as early perturbations in the gut-brain axis could contribute to the development of future alcohol addiction or other psychiatric disorders later in life. MicroB&B will be developed at the APC Microbiome Ireland under the supervision of Prof. Ted Dinan and Prof. John Cryan and will enable the continuation of previous studies on animal models of alcohol use and microbiota-alterations completed at the APC.

Martin Codagnone

• martin.codagnone@ucc.ie  

Research Title

PREG-CARE “Prebiotic-induced microbiota modulation during pregnancy: impact on offspring neurodevelopment”

Project Summary

Although it is well known that early life is a vulnerable period for brain development, the role of the maternal microbiota in neurodevelopment hasn’t been established yet. The general aims of PREG-CARE are to identify critical periods for microbiota modulation during pregnancy and lactation and develop maternal microbiota interventions that can protect offspring neurodevelopment. PREG-CARE takes an innovative approach to the study of early brain development and is expected to impact on the scientific, food industry and health communities

Jorge Nuno Pinheiro

• jorge.pinheiro@ucc.ie  

Research Title

ENLIST – Ethanolamine in gut Listeria monocytogenes infection and inflammation

Project Summary

Gut pathogens must adapt to the gastrointestinal environment and compete with the microbiota in order to cause infection. However relatively little is known about how the important foodborne pathogen Listeria monocytogenes adapts to the gut environment prior to causing invasive disease. This project aims to determine how L. monocytogenes utilizes ethanolamine during gut infection in the context of a westernized, pro-inflammatory diet. We propose to investigate the hypothesis that L. monocytogenes can exploit the high levels of ethanolamine produced locally in the inflamed gut in order to increase virulence and promote systemic infection.

Shakhinur Mondal

• shakhinur.mondal@ucc.ie 

Research Title

Effect of phage-derived endolysins on gut microbial populations: pathway to developing new therapies against multidrug resistant enteric pathogens.

Project Summary

Bacteriophage endolysins or lysins are highly evolved specific peptidoglycan hydrolases that digest the bacterial cell wall for phage progeny release. In recent years endolysins and their derivatives have emerged as a novel class of antibacterials. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora and the low or no chance of bacterial resistance to endolysins. Endolysins have been used successfully in various infectious models to control pathogenic antibiotic resistant bacteria. This project will focus on the effect of phage-derived endolysins on gut microbial populations in order to develop new therapies against multidrug resistant bacterial pathogen.

Sara Arbulu

• sara.arbulu@ucc.ie 

Research Title

Bacteriocins for a healthy oral cavity (SALIBACs)

Project Summary

Cavities are the most prevalent infectious disease in humans. They are a major public health concern in terms of pain, and impact on general health and life quality, as well as a significant economic burden in EU countries. From a scientific perspective, dental caries is a multifactorial complex disease in which the oral microbiota plays a key role. In this context, bacteriocins are antimicrobial peptides assumed to be produced by almost all bacteria that establish long-term commensal relationships. Metagenomic analysis has revealed a high density of putative bacteriocin genes in the oral cavity, but relatively few studies provide evidence for their ecological relevance.

This project aims at identifying bacteriocin transcripts that are likely to be translated into different functional bacteriocins from healthy mouth saliva, overexpress the most promising candidate genes in heterologous hosts, and ascertain their ability to control cariogenic bacteria on high prevalence cavity saliva.

In order to address these objectives, this project will take an interdisciplinary approach that involves screening of lead bacteriocins by state of the art next generation sequencing RNASeq techniques and quantitative real time PCR, functional expression and heterologous production of the best bacteriocin matches and evaluation of the impact of recombinant bacteriocins on the microbial diversity of saliva. Data from this study has the potential for commercialisation and findings of this project will target the research community, oral health related industries as well as the general public.

Fabiana A. Hoffmann Sarda

•  fabiana.hoffmannsarda@ucc.ie 

Research Title

Sugar replacers effects on microbiome modulation and glucose homeostasis

Project Summary

Sugar replacers have been used as a dietary strategy, but although data is available about sweeteners consumption and their general health effects, their specific effect on the gut microbiome and its health implications are still very scarce. New non-artificial sweeteners have been proposed as healthier alternatives. We aim to investigate the relationships existing among the consumption of sugar replacers (artificial and new natural sources) and the intestinal microbiome, the glycemic control and brain-gut aspects.

Data from this study can support larger cohorts and contribute for dietary and food/health regulatory recommendations.

Miguel Fernandez De Ullivarri

• miguel.fernandezdeullivarri@ucc.ie

Research Title

Expression of the antimicrobial killer peptide KP in Lactococcus lactis: its therapeutics properties in models of vulvovaginal candidiasis and its effect on the vaginal microbiome.

Project Summary

This project proposes to develop a model of a less-expensive alternative for the application of the antimicrobial peptide, KP, as a therapeutic agent for vaginal use, compared to the direct administration of the synthetic peptide. The proposal involves the expression of KP in a GRAS microorganism (Lactococcus lactis) and the evaluation of its antifungal properties through an in vivo model of vaginal infection with a pathogenic strain of Candida albicans. Finally, to study its modulatory effects, through next generation sequencing techniques, on the murine vaginal microbiota considering that KP is a potent and broad-spectrum antimicrobial agent.

Valentina Caputi

• valentina.caputi@ucc.ie 

Research Title

ELEVATE: ‘Early-Life PrEdiction Of Stress-Induced ViscerAl SensiTivity E’

Project Summary

Early-life represents a critical neuro-developmental window during which an organism is particularly vulnerable to stressful insults that can have deleterious effects on both psychological well-being and gastrointestinal (GI) function. The main aim of the ELEVATE project is to identify a microbiome-gut-brain axis signature of visceral pain to predict in early life the susceptibility to the development of stress-induced GI and mental disorders later in adulthood. ELEVATE represents a strategic approach to study the modulation of the gut microbiome-host interactions and opens a new scenario for innovative therapeutic strategies and personalized medicine with a positive impact on industry and society through improvement of body and mind healthcare along the lifespan

Henry Darch

• henry.darch@ucc.ie 

Research Title

Microbiome influences on neural activity: Investigating the electrophysiological impact of the microbiome

Project Background

Microorganisms within our gut are able to influence our behaviors. A strong link between a changed microbiome and increases in anxious behaviors has been found in both humans and animal models. Anxiety and mood disorders constitute a significant global burden with lifetime prevalence of around 1/5, and cost EU states up to 4% of GDP. Microbiome changes have also been linked with changes in brain anatomy, and molecular and genetic markers of neural activity in areas linked with mood and cognition. This implies that neuronal activity underpinning behaviors is influenced by the microbiome. However, studies to-date have lacked the temporal resolution to reveal neuronal activity during behavior, and how this is affected by microbiome perturbations. This project will be the first to directly address the question of how behaviorally relevant neuronal network activity is impacted by microbiome perturbations.

A rodent model of early life adversity (the maternal separation model) will be studied as it has been shown to exhibit alterations in the microbiome along with increased anxiety-like behaviors, compared to controls. Additionally, a probiotic diet has been shown to ameliorate the behavioral symptoms, suggesting a causal role for the microbiome in determining these behaviors.

The project will use state-of-the-art electrophysiological recordings of neuronal activity within two brain regions involved in anxiety (prelimbic cortex and amygdala). Recordings of neural activity at single cell resolution will be made in both anaesthetized and awake behaving animals across control, maternal stress, and maternal stress with probiotic diet groups. Analysis of the activity within, and functional connectivity between the two regions will provide a unique view into how changes in the microbiome alters brain activity driving anxiety-like behaviors, and may identify potential targets for therapeutic intervention in anxiety and mood disorders at the microbiome and neuronal network levels.

Ian O’Neill

• ian.oneill@ucc.ie 

Ian received his PhD from University College Cork, Ireland, and also holds a MSc in Computational biology from University of Manchester, UK. He held a postdoc position in Quadram Institute Bioscience, Norwich, UK in Dr Lindsay Hall’s lab researching Bifidobacterium-host interactions. Prior to receiving his APEX fellowship, he worked as a postdoc with work with Prof Douwe van Sinderen focusing on genomics of bifidobacteria.

Research Title

Exploring the role of bifidobacterial human milk oligosaccharide metabolism in shaping the early life microbiota.

Project Summary

The infant gut microbiota plays an important role in immune development and health throughout life, and diet is a key driver of infant gut microbiota composition. Breast-fed infants have a less diverse microbiota composition, dominated by certain members of the genus Bifidobacterium, compared to formula fed-infants who have a more diverse and adult-like composition. Metabolism of human milk oligosaccharides (HMOs) present in breast milk by Bifidobacterium account (at least partially) for high abundance of this genus in infants. HMO metabolism by bifidobacteria is both strain- and species-specific, but only a small number of strains have been tested for each species. Furthermore, there is essentially no information on HMO metabolism by other microbiota members.

Project Aims

1. Isolate bifidobacteria from faeces of mother-infant pairs.
2. Characterise general HMO metabolism in human-associated Bifidobacterium species/strains, and
3. investigate HMO metabolism in a complex microbial environment to identify other HMO metabolising bacteria.

Nayyer Taheri

• nayyer.taheri@ucc.ie 

Research Title

Effect of bacterial membrane vesicles (BMVs) released by human gut microbiota on cancer.

Project Summary

The gut microbiota has a strong impact on human health, and its disruption is increasingly being discovered to relate to multiple diseases, including cancer. Mechanisms involved in the microbiota’s influence on cancer are poorly understood. Bacteria constitutively release membrane vesicles (BMVs), which contain proteins, lipids, and nucleic acids. They can interact with host cells and modulate the immune system. The nanosize and non-replicative form of BMVs together with their resistance to low pH, enzyme degradation, and the ability to interact with the host, make them potential candidates for delivering biomolecules to host cells, with potentially positive or negative impacts. This project aims to understand the effect of BMVs release by gut microbiota on cancer. Although it has been shown that BMVs released by gut microbiota have immunomodulatory effects, what they carry and where their final destination is, is unclear.

Project Aims

This project aims to answer two main questions in a cancer context: i) What do BMVs released by gut microbiota naturally do? and ii) Could BMVs be exploited in tumour therapy? To address these questions, different in vitro and in vivo approaches will be applied. This project will generate much needed knowledge on the contribution of BMV to microbiota activity, in the context of cancer and beyond.

Andrius Buivydas

• andrius.buivydas@ucc.ie 

Research Title

IPA-LAB: Improved Production Of Anti-Fungal Compounds By Lactic Acid Bacteria

Project Summary

Fungal spoilage remains one of the major concerns for the food and feed industry and poses an enormous economic and safety issue throughout the world. It is estimated that 5-10% of all produced food is spoiled and eventually lost due to fungal contaminations. Importantly, certain fungal strains involved in food spoilage may produce mycotoxins which cause severe health issues, such as allergies or toxic responses, while such mycotoxins may also be neurotoxic or act as a carcinogen. Since processed and chemical preservative-containing foods are being progressively refused by ever more discerning consumers, the discovery of novel and natural antifungal compounds and associated development of antifungal preservation approaches is an urgent necessity. Novel LAB strains with potent antifungal properties will be isolated and analysed in detail during IPA-LAB project. The identify and biosynthetic pathway of LAB-produced natural antifungal compounds will be determined, and their activity and potency to diminish fungal spoilage in foods will be evaluated. The most efficacious strains obtained during IPA-LAB project will be employed in industrially relevant practices to provide safer foods to the consumer.

Project Aims

1. Isolation of novel LAB strains with potent antifungal properties and characterization and identification of compounds produced by selected antifungal LAB strains.
2. To employ novel characterized strains for industrially relevant food-manufacturing processes that ultimately will benefit the consumer.

Rubén García Cabrerizo

• ruben.garciacabrerizo@ucc.ie 

Research Title

Role of microbiota as a regulator of reward pathways

Project Background

Social interactions are fundamental to the mental health and well-being of an individual. A lack of social support during adolescence, due to parents neglected, bullying, or social exclusion, can induce the probability to develop psychiatric illnesses containing an important stress component such as depression or anxiety. These negative experiences during adolescence (i.e., a period of transition between childhood and adult life, which is critical for neurodevelopment) increase the likelihood of substance use and addiction in adulthood and such effects are sex dependent. There is accumulating evidence that microbiota could play a pivotal role affecting central neurochemistry and the development of psychiatric disorders.

However, to the date, there are a paucity of studies examining the link between the microbiota and rewarding properties of drug of abuse. Thus, this project’s overall objective is to determine the influence of social isolation during adolescence on the motivation for cocaine and the role of gut microbiota. Moreover, differential effects between sexes will be examined. Male and female mice will be exposed to an early-life stress (i.e., social isolation) during adolescence and will be conditioned with cocaine in adulthood to assess the reward response. Furthermore, the effects of a pre- or probiotic treatment on ameliorating the social isolation effects on drug reward will be evaluated.

Finally, we will take advantage using TRAP (Targeted Recombination in Active Populations), DREADDS (Designer Receptors Exclusively Activated by Designer Drugs) and optogenetics to delineate the specific signaling pathways between gut and brain involved in drug reward. This proposal will be key to understand how changes in microbiota interact with the brain to alter reward related responses.

Miguel Villoria Recio

• miguel.recio@ucc.ie 

Research Title

The effect of gut microbiota on the pathogenesis of Listeria monocytogenes.

Objective

The objective of this project is to determine how microbiota-derived metabolites may improve gut barrier function and influence resistance against infection of the Gram-positive foodborne pathogen Listeria monocytogenes.

Project Summary

My research focuses on further elucidating the mechanisms related to gut-barrier function which underpin colonization resistance against the foodborne pathogen Listeria monocytogenes by using a systems-biology approach. A more complete understanding of the molecular mechanisms behind the host-microbiota dialogue will be key to inform future strategies in manipulating microbiota as a barrier to infection to potentially reduce the use of antibiotics in the control of foodborne infectious diseases. We have previously identified key microbial taxa which are predicted to play a role in resistance to L. monocytogenes infection. However, the molecular mediators of colonization resistance against the pathogen remain to be fully established. This project will study the interplay between diet and gut microbiota in the context of L. monocytogenes infection through analysis of specific commensal taxa and metabolites as potential molecular mediators of host colonization resistance.

Maria Eugenia Jimenez

• maria.jimenez@ucc.ie 

Research Title

Lactic fermentation as a tool to improve the antioxidant characteristics of amaranth (Amaranthus caudatus) and faba beans (Vicia faba).

Project Background

There is an ever-increasing demand for healthy foods, including foods that are rich in bioactive peptides. Bioactive peptides are released from their precursor proteins by enzymatic hydrolysis or by microbial fermentation and can have a wide range of health-promoting activities, including antioxidant activity. Biologically active peptides with potential antioxidant activity can be derived from a variety of animal and plant protein sources. Indeed, recently, antioxidant peptides were isolated from various cereal flours fermented with sourdoughs. In particular, a pool of lactic acid bacteria (LAB), selected based on their proteolytic activities, showed the capacity to release antioxidant peptides during sourdough fermentation of whole wheat, spelt, rye, and kamut doughs.

The aim of this project is to evaluate the effect of fermentation, using LAB isolated from the raw materials, on the functional and nutritional properties of dough prepared with flours of faba beans grown in Ireland, and compare them with amaranth from Northwest Argentina.

To achieve this aim, the lactic bacteria of amaranth and faba beans will be isolated, identified and selected according to their proteolytic activity. The action of the selected bacteria on the proteins and the formation of antioxidant peptides will be studied. These peptides will be purified and identified, and their antioxidant activity will undergo initial testing in vitro and through cell culture assays. These assays will allow the identification of the ferments with the greatest health promoting potential and these will in turn be used for in vivo, murine, testing to evaluate the effect of the consumption of fermented amaranth and faba beans, enriched with antioxidant peptides, on health. The results obtained will allow the ultimate development of a functional food, rich in antioxidant peptides and LAB, which will beneficially impact on the health of consumers.

Shriram Patel

• Shriram.Patel@ucc.ie 

Research Title

Predicting histological and clinical outcome in coeliac disease by combining genetics and longitudinal microbiota profiling.

Project Summary

Coeliac disease (CD) is an important health problem because of its high prevalence, silent or atypical symptoms, associated specific and non-specific morbidity, and long-term complications. While there is no cure for CD, following a strict lifelong gluten-free diet (GFD) alleviates symptoms in two-thirds of patients. Unlike cancer and heart disease, we currently lack the tools to non-invasively diagnose CD and the medications to effectively treat it. CD occurs from an interaction between genes, eating foods containing gluten and other environmental factors, but the precise cause is not known. Some gene variants increase the risk of developing the disease but having those gene variants does not guarantee you will get CD, which suggests that additional factors must be involved. While preliminary research has already raised intriguing possibility of association of microbiota in CD, disease specific microbial signature is still not defined.

Project Aims

The study aims to investigate whether gastrointestinal microbiota combined with associated host molecular and clinical metadata can (a) classify symptoms and/or histology at diagnosis (baseline), and (b) predict symptoms and/or histology after 1 year of GFD.

Namrata Iyer

• IYERN@tcd.ie  

Namrata did her Masters degree in Biotechnology followed by a PhD from the Indian Institute of Science, Bangalore, India in 2014. Her work focused on virulence mechanisms employed by the pathogen Salmonella typhimurium. She further did her postdoctoral training with Dr. Shipra Vaishnava at Brown University on the influence of vitamin A on host-microbiome interactions. Namrata is a Postdoc in the Microbiome & Mucosal Immunity Lab, led by Dr Sinéad Corr, at Trinity College Dublin.

• https://scholar.google.co.in/citations?user=LxG1x74AAAAJ&hl=en
• https://www.researchgate.net/profile/Namrata-Iyer 

Research Title

Immunomodulatory potential of Free Microbial metabolites: Leveraging metabolomics to identify bioactive compounds that promote immune homeostasis in the gut. 

Project Background

The microbiome is the prominent force shaping the immune landscape in the gut. Changes in composition of the gut microbiota are associated with a myriad of autoimmune and metabolic disorders such as inflammatory bowel disease and obesity. Despite extensive research efforts, the molecular mechanism underlying these associations is lacking. Within the gut, microbial metabolites can cross the epithelial barrier and alter the metabolism or transcriptional programming in the host cell. As such, this study postulates that free microbial metabolites (FMMs) can exert immunomodulatory effects which can be harnessed for therapeutic potential. Using an unbiased approach, this study aims to parse out the impact of free microbial metabolites on key immune parameters such as gut permeability and immune makeup.

Friederike Uhlig

• friederike.uhlig@ucc.ie 

Research Title

TRANSMIT – enTeRic Afferent seNsing to aScribe MIcrobial activity.

Project Background

The term microbiota-gut-brain axis is widely used in presentations targeting the research and general public community but to date, it remains unclear what mechanisms underlie microbiota-related changes in brain function. Neurons constitute an important part of this gut-brain axis. The intestine comprises enteric neurons which form an interconnected network throughout the entire length of the intestine and regulate intestinal motility and secretion independent from the brain, and nerve fibers from neurons with direct input in the brain.
My project investigates the ability of individual microbes to produce soluble mediators that directly target intestinal neurons. I will determine the neuromodulatory capacity of microbial metabolites in assays for intestinal function which rely on enteric neuron activation and afferent nerve recordings which report the activity of nerve fibers that transmit information to the brain. I will also test the hypothesis that the response of intestinal neurons to bacterial metabolites is dependent on the microbiota.

Project Aims

This research will lead to a better understanding of bacteria-host interaction and evaluate the potential of microbes to modulate intestinal neuron activity as a mean to ultimately affect brain function.